Hello, Thanks for UCSC genome browser. I would like to extract all geneID (same as NCBI geneID) from Human hg18 version. I downloaded the data and found refLink table has LocusLinkId which is same as NCBI geneID. Thats great! However, I found other species too present in the table which makes the extraction difficult as there is no species column.
FOr example: in refLink table, look for name = 'AR' It pulls out 10 entries with AR name: [image: Full Texts]<http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27&pos=0&session_max_rows=30&pos=0&disp_direction=horizontal&repeat_cells=100&goto=db_details.php&dontlimitchars=1> name <http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27+ORDER+BY+%60name%60+ASC> product <http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27+ORDER+BY+%60product%60+ASC> mrnaAcc <http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27+ORDER+BY+%60mrnaAcc%60+ASC> protAcc <http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27+ORDER+BY+%60protAcc%60+ASC> geneName <http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27+ORDER+BY+%60geneName%60+ASC> prodName <http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27+ORDER+BY+%60prodName%60+ASC> locusLinkId <http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27+ORDER+BY+%60locusLinkId%60+ASC> omimId <http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27+ORDER+BY+%60omimId%60+ASC> [image: Edit]<http://pulitzer.compbio.iupui.edu/phpmyadmin/tbl_change.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&primary_key=+%60mrnaAcc%60+%3D+%27NM_001032911%27&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27&goto=sql.php> [image: Delete]<http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=DELETE+FROM+%60refLink%60+WHERE+%60mrnaAcc%60+%3D+%27NM_001032911%27+LIMIT+1&zero_rows=The+row+has+been+deleted&goto=sql.php%3Flang%3Den-iso-8859-1%26server%3D1%26db%3Ducsc_human%26table%3DrefLink%26pos%3D0%26session_max_rows%3D30%26disp_direction%3Dhorizontal%26repeat_cells%3D100%26dontlimitchars%3D0%26sql_query%3DSELECT%2B%2B%252A%2B%250AFROM%2B%2B%2560refLink%2560%2B%250AWHERE%2B%2B%2560name%2560%2B%2B%253D%2B%2B%2527AR%2527%26zero_rows%3DThe%2Brow%2Bhas%2Bbeen%2Bdeleted%26goto%3Ddb_details.php> AR androgen receptor NM_001032911 NP_001028083 26021 45774 574293 0 [image: Edit]<http://pulitzer.compbio.iupui.edu/phpmyadmin/tbl_change.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&primary_key=+%60mrnaAcc%60+%3D+%27NM_001009012%27&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27&goto=sql.php> [image: Delete]<http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=DELETE+FROM+%60refLink%60+WHERE+%60mrnaAcc%60+%3D+%27NM_001009012%27+LIMIT+1&zero_rows=The+row+has+been+deleted&goto=sql.php%3Flang%3Den-iso-8859-1%26server%3D1%26db%3Ducsc_human%26table%3DrefLink%26pos%3D0%26session_max_rows%3D30%26disp_direction%3Dhorizontal%26repeat_cells%3D100%26dontlimitchars%3D0%26sql_query%3DSELECT%2B%2B%252A%2B%250AFROM%2B%2B%2560refLink%2560%2B%250AWHERE%2B%2B%2560name%2560%2B%2B%253D%2B%2B%2527AR%2527%26zero_rows%3DThe%2Brow%2Bhas%2Bbeen%2Bdeleted%26goto%3Ddb_details.php> AR androgen receptor NM_001009012 NP_001009012 26021 45774 449595 0 [image: Edit]<http://pulitzer.compbio.iupui.edu/phpmyadmin/tbl_change.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&primary_key=+%60mrnaAcc%60+%3D+%27NM_001003053%27&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27&goto=sql.php> [image: Delete]<http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=DELETE+FROM+%60refLink%60+WHERE+%60mrnaAcc%60+%3D+%27NM_001003053%27+LIMIT+1&zero_rows=The+row+has+been+deleted&goto=sql.php%3Flang%3Den-iso-8859-1%26server%3D1%26db%3Ducsc_human%26table%3DrefLink%26pos%3D0%26session_max_rows%3D30%26disp_direction%3Dhorizontal%26repeat_cells%3D100%26dontlimitchars%3D0%26sql_query%3DSELECT%2B%2B%252A%2B%250AFROM%2B%2B%2560refLink%2560%2B%250AWHERE%2B%2B%2560name%2560%2B%2B%253D%2B%2B%2527AR%2527%26zero_rows%3DThe%2Brow%2Bhas%2Bbeen%2Bdeleted%26goto%3Ddb_details.php> AR androgen receptor NM_001003053 NP_001003053 26021 45774 403588 0 [image: Edit]<http://pulitzer.compbio.iupui.edu/phpmyadmin/tbl_change.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&primary_key=+%60mrnaAcc%60+%3D+%27NM_214314%27&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27&goto=sql.php> [image: Delete]<http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=DELETE+FROM+%60refLink%60+WHERE+%60mrnaAcc%60+%3D+%27NM_214314%27+LIMIT+1&zero_rows=The+row+has+been+deleted&goto=sql.php%3Flang%3Den-iso-8859-1%26server%3D1%26db%3Ducsc_human%26table%3DrefLink%26pos%3D0%26session_max_rows%3D30%26disp_direction%3Dhorizontal%26repeat_cells%3D100%26dontlimitchars%3D0%26sql_query%3DSELECT%2B%2B%252A%2B%250AFROM%2B%2B%2560refLink%2560%2B%250AWHERE%2B%2B%2560name%2560%2B%2B%253D%2B%2B%2527AR%2527%26zero_rows%3DThe%2Brow%2Bhas%2Bbeen%2Bdeleted%26goto%3Ddb_details.php> AR androgen receptor AR NM_214314 NP_999479 26021 46433 397582 0 [image: Edit]<http://pulitzer.compbio.iupui.edu/phpmyadmin/tbl_change.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&primary_key=+%60mrnaAcc%60+%3D+%27NM_012502%27&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27&goto=sql.php> [image: Delete]<http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=DELETE+FROM+%60refLink%60+WHERE+%60mrnaAcc%60+%3D+%27NM_012502%27+LIMIT+1&zero_rows=The+row+has+been+deleted&goto=sql.php%3Flang%3Den-iso-8859-1%26server%3D1%26db%3Ducsc_human%26table%3DrefLink%26pos%3D0%26session_max_rows%3D30%26disp_direction%3Dhorizontal%26repeat_cells%3D100%26dontlimitchars%3D0%26sql_query%3DSELECT%2B%2B%252A%2B%250AFROM%2B%2B%2560refLink%2560%2B%250AWHERE%2B%2B%2560name%2560%2B%2B%253D%2B%2B%2527AR%2527%26zero_rows%3DThe%2Brow%2Bhas%2Bbeen%2Bdeleted%26goto%3Ddb_details.php> Ar androgen receptor NM_012502 NP_036634 212673 45774 24208 0 [image: Edit]<http://pulitzer.compbio.iupui.edu/phpmyadmin/tbl_change.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&primary_key=+%60mrnaAcc%60+%3D+%27NM_001011645%27&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27&goto=sql.php> [image: Delete]<http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=DELETE+FROM+%60refLink%60+WHERE+%60mrnaAcc%60+%3D+%27NM_001011645%27+LIMIT+1&zero_rows=The+row+has+been+deleted&goto=sql.php%3Flang%3Den-iso-8859-1%26server%3D1%26db%3Ducsc_human%26table%3DrefLink%26pos%3D0%26session_max_rows%3D30%26disp_direction%3Dhorizontal%26repeat_cells%3D100%26dontlimitchars%3D0%26sql_query%3DSELECT%2B%2B%252A%2B%250AFROM%2B%2B%2560refLink%2560%2B%250AWHERE%2B%2B%2560name%2560%2B%2B%253D%2B%2B%2527AR%2527%26zero_rows%3DThe%2Brow%2Bhas%2Bbeen%2Bdeleted%26goto%3Ddb_details.php> AR androgen receptor isoform 2 NM_001011645 NP_001011645 26021 285742 367 313700 [image: Edit]<http://pulitzer.compbio.iupui.edu/phpmyadmin/tbl_change.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&primary_key=+%60mrnaAcc%60+%3D+%27NM_000044%27&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27&goto=sql.php> [image: Delete]<http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=DELETE+FROM+%60refLink%60+WHERE+%60mrnaAcc%60+%3D+%27NM_000044%27+LIMIT+1&zero_rows=The+row+has+been+deleted&goto=sql.php%3Flang%3Den-iso-8859-1%26server%3D1%26db%3Ducsc_human%26table%3DrefLink%26pos%3D0%26session_max_rows%3D30%26disp_direction%3Dhorizontal%26repeat_cells%3D100%26dontlimitchars%3D0%26sql_query%3DSELECT%2B%2B%252A%2B%250AFROM%2B%2B%2560refLink%2560%2B%250AWHERE%2B%2B%2560name%2560%2B%2B%253D%2B%2B%2527AR%2527%26zero_rows%3DThe%2Brow%2Bhas%2Bbeen%2Bdeleted%26goto%3Ddb_details.php> AR androgen receptor isoform 1 NM_000044 NP_000035 26021 286049 367 313700 [image: Edit]<http://pulitzer.compbio.iupui.edu/phpmyadmin/tbl_change.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&primary_key=+%60mrnaAcc%60+%3D+%27NM_013476%27&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27&goto=sql.php> [image: Delete]<http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=DELETE+FROM+%60refLink%60+WHERE+%60mrnaAcc%60+%3D+%27NM_013476%27+LIMIT+1&zero_rows=The+row+has+been+deleted&goto=sql.php%3Flang%3Den-iso-8859-1%26server%3D1%26db%3Ducsc_human%26table%3DrefLink%26pos%3D0%26session_max_rows%3D30%26disp_direction%3Dhorizontal%26repeat_cells%3D100%26dontlimitchars%3D0%26sql_query%3DSELECT%2B%2B%252A%2B%250AFROM%2B%2B%2560refLink%2560%2B%250AWHERE%2B%2B%2560name%2560%2B%2B%253D%2B%2B%2527AR%2527%26zero_rows%3DThe%2Brow%2Bhas%2Bbeen%2Bdeleted%26goto%3Ddb_details.php> Ar androgen receptor NM_013476 NP_038504 212673 45774 11835 0 [image: Edit]<http://pulitzer.compbio.iupui.edu/phpmyadmin/tbl_change.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&primary_key=+%60mrnaAcc%60+%3D+%27NM_001040090%27&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27&goto=sql.php> [image: Delete]<http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=DELETE+FROM+%60refLink%60+WHERE+%60mrnaAcc%60+%3D+%27NM_001040090%27+LIMIT+1&zero_rows=The+row+has+been+deleted&goto=sql.php%3Flang%3Den-iso-8859-1%26server%3D1%26db%3Ducsc_human%26table%3DrefLink%26pos%3D0%26session_max_rows%3D30%26disp_direction%3Dhorizontal%26repeat_cells%3D100%26dontlimitchars%3D0%26sql_query%3DSELECT%2B%2B%252A%2B%250AFROM%2B%2B%2560refLink%2560%2B%250AWHERE%2B%2B%2560name%2560%2B%2B%253D%2B%2B%2527AR%2527%26zero_rows%3DThe%2Brow%2Bhas%2Bbeen%2Bdeleted%26goto%3Ddb_details.php> AR androgen receptor NM_001040090 NP_001035179 26021 45774 422165 0 [image: Edit]<http://pulitzer.compbio.iupui.edu/phpmyadmin/tbl_change.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&primary_key=+%60mrnaAcc%60+%3D+%27NM_001076688%27&sql_query=SELECT++%2A+%0AFROM++%60refLink%60+%0AWHERE++%60name%60++%3D++%27AR%27&goto=sql.php> [image: Delete]<http://pulitzer.compbio.iupui.edu/phpmyadmin/sql.php?lang=en-iso-8859-1&server=1&db=ucsc_human&table=refLink&pos=0&session_max_rows=30&disp_direction=horizontal&repeat_cells=100&dontlimitchars=0&sql_query=DELETE+FROM+%60refLink%60+WHERE+%60mrnaAcc%60+%3D+%27NM_001076688%27+LIMIT+1&zero_rows=The+row+has+been+deleted&goto=sql.php%3Flang%3Den-iso-8859-1%26server%3D1%26db%3Ducsc_human%26table%3DrefLink%26pos%3D0%26session_max_rows%3D30%26disp_direction%3Dhorizontal%26repeat_cells%3D100%26dontlimitchars%3D0%26sql_query%3DSELECT%2B%2B%252A%2B%250AFROM%2B%2B%2560refLink%2560%2B%250AWHERE%2B%2B%2560name%2560%2B%2B%253D%2B%2B%2527AR%2527%26zero_rows%3DThe%2Brow%2Bhas%2Bbeen%2Bdeleted%26goto%3Ddb_details.php> AR androgen receptor (dihydrotestosterone receptor; NM_001076688 NP_001070156 26021 322566 751774 0 If you look at locuslinkId = 574293 in NCBI. It is from Mullatta (monkey). So I wonder why do we have AR from other species in Human database. Is there a table that contains entries from human alone that can give me the locuslinkID? Thanks, -Vidhya _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
