Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein polybromo-1.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g2410 g2410.t1 TTS g2410.t1 17762482 17762482
chr_3 g2410 g2410.t1 isoform g2410.t1 17762558 17769463
chr_3 g2410 g2410.t1 exon g2410.t1.exon1 17762558 17763322
chr_3 g2410 g2410.t1 cds g2410.t1.CDS1 17762558 17763322
chr_3 g2410 g2410.t1 exon g2410.t1.exon2 17763664 17764176
chr_3 g2410 g2410.t1 cds g2410.t1.CDS2 17763664 17764176
chr_3 g2410 g2410.t1 exon g2410.t1.exon3 17764727 17764777
chr_3 g2410 g2410.t1 cds g2410.t1.CDS3 17764727 17764777
chr_3 g2410 g2410.t1 exon g2410.t1.exon4 17764910 17766691
chr_3 g2410 g2410.t1 cds g2410.t1.CDS4 17764910 17766691
chr_3 g2410 g2410.t1 exon g2410.t1.exon5 17767115 17767253
chr_3 g2410 g2410.t1 cds g2410.t1.CDS5 17767115 17767253
chr_3 g2410 g2410.t1 exon g2410.t1.exon6 17767306 17768116
chr_3 g2410 g2410.t1 cds g2410.t1.CDS6 17767306 17768116
chr_3 g2410 g2410.t1 exon g2410.t1.exon7 17768340 17769282
chr_3 g2410 g2410.t1 cds g2410.t1.CDS7 17768340 17769282
chr_3 g2410 g2410.t1 exon g2410.t1.exon8 17769353 17769463
chr_3 g2410 g2410.t1 cds g2410.t1.CDS8 17769353 17769463
chr_3 g2410 g2410.t1 TSS g2410.t1 17769706 17769706

Sequences

>g2410.t1 Gene=g2410 Length=5115
ATGAGTAAAAGAAGAAGAACATCATCTGATATTGAAACAGATGACTCAGACGATGATTCT
GAACAATTTCCAACCACTCCAGCTATTAGAAAAAAGAAAAAATTAGATCCGATGGAGCAA
TGTCAATCTCTTTATGAATCAATCAGAAATTTTAAGAAAGAAGATGGTACACAACTCTGT
GACAGCTTTATACGCGCACCAAAGCGTCGTCAAGAACCAAATTATTATGAAATTGTCACC
AACCCGATAGATTTATTGCGCGTACAACAAAAACTTAAAACTGATTCATATGAAGACATC
GATGATCTTACAAATGACATTGAGTTGCTAGTGAAAAATGCAAAAGCATTCTATAAACCA
GATAGTGTTGAGTATAAAGATGCATGCACATTATGGGATGTGTACAATTCTAATAAAGTG
AAACTCATTGAAAGTCTAAATGAAGAGTCAACTCCTGTTGCTTTTGATTCTTCAAAACCA
CGTCGAATTGGACGTCCAAGAAAATCAACTACAGTTGATGATGATCAAATTTCAGAAAAT
TCATCTGAAAATAATGACTTTGATGCATATGAAGAACTTTTTGCTTCAATAATGACAGCT
ACTGATCCACTTGATGATCGTGCTCTTCATACAATGTTTCAGCTTTTACCATCAAAGAGA
ACTTTTCCTAGTTATTATGAAGTCATCGATCATCCAATTGATCTCAAATTTATAGCCAAT
AAAATTCAAACAAACGCTTATACAAGTCTCAATGAGATGGAAAAAGATGTCCTGCAAATG
GTTAAAAATACACAAATTTTCAATGAACCTGGCAGTCAAATTTACAAAGATGCAAAAACT
ATCAAGAAAATTTTCTTGCAAAAGAAACTTGATATTGAAACTGGAAAATACAAGAAACCT
ATGAGAAGAGGCCGTCAAATTAGTTATAGCGCGGCATGTGCTGCACTTAAAGAGGAGCTT
GAATCATCTGAAGAAGAAATGGACATGGATGATGAGGAGCAAACTGGACCATTGTGGCAG
CTATTTGATTCTCTCTACCAACAACCAAATTCAGATGGATCTTTAGGGGGTAATTCACCT
TTAGGTGAGAGTTTGTGGAAACTACCGAATAAAAGATTTCATCCTGAGTATTACACGCTT
ATCAAAAAACCTCTCTCAATGTCGATGATTCAAAAGAAGTTGAAAAAGAATGAATATGCG
AATGTGACTGAGTTATCAGCTGATTTATATCTTATGATTGACAATGCTAAGAAAGCTAAT
TTACCATCATCGAAAATTTATAAAGATGCTGTAAAAATGCAAAAGATTCTTAATCAAAAG
CTTGTCGATGAAGGTGGTTTAGATGATGACGATACAGAAGACACAGATTCTTCACAACAT
GCCTTTCCACTTGGTGGTATGGAAAAAAAGAAAAAAGGACGTCCTCGCATTCACCCATTG
TCATCAACTTCACCGGCACCATCGACATCTATAACTCCAGCATCTTCAACGAAGAACTAT
AAATTTCCCAGCAACCCGATGCTTAAGAAAAAGTTACATGCTATTCACAAACACTTATTG
GAGTTTACATTCGATAATCGTCAACCTGCTGAGCCATTTTTAGAGAAACCTTCAAAAAAA
TTATATCCAGATTACTATTCGATTATAACACATCCAATTGATATGAATACTATTTATAAA
AACATTGAAAATGAACGGTATGCTACACTCGATGATATCGTTAGTGACTATAGATTAATG
TTCCAAAATTGTCGAAAATATAATGAAGAGAATTCAATGATTTATGATGATGCAAATATG
CTAGAAAGAGCATTGAATGAGAAATTAAAAGAAATTACTGGTGTTGATCGAAAACCAATG
AAAATGTTGAAAGCACATAATAAGAAAATGCAAGCGATTTTAGATGCAAAATTAAAACAG
CTCTATGAAACAATCAAAGAATATAAAGACCCAAAAACTAATCGACAAGTCGCAACAATA
TTTATGAAACTTCCAAGTAAAATGGAACATCCACTTTACTTTGAAATCATCAAATCTCCA
ATTGATTTAGAAAAAATCGGTATGAAATTACGAATGCAACAATATGATTCAGTCGATGAA
CTTTCAGCTGATTTAATGTTGATGTTTGAAAATGCATGCAAATATAACGAACCCGACAGT
CAAATCTATAAAGATGCTCTGATGTTGCAACAAGTATGCATTCAAACAAAACAAGAATTA
AGAATGGAAGATGAAAATGTGCCAGATGTTCCACAAGTTATTGTCGATTTACTGTTACAA
CTTTTTACAACAGTTTACAACTATCAAGATGAAGAAGGACGCTGCTATTCTGACTCGATG
GCTGAATTGCCTGACCATGATGAAATCGAAGGAGGACTTAAACAAAGAGTAATCTCATTA
GATCTTATAAAACGTAGACTCGACAAAGGAATTTATAAACGTCTCGATATTTTTCAAGAA
GATATGTTTGCATGCTTTGAACGTGCACGACGACTTTCACGCACTGATTCACAAGTATTT
GAGGATTCTATTGAATTGCAATCATTCTTTATAAGAAAACGTGATGAATTATGCAAAAAT
GGAGAAGTACTTTCATCGCCAGCACTATGTTATACAGCCATGCATTTGAGTGCAGCTGTT
GAGTCTGTTCGTCAAACAAAACTTTTGCAGGAAGAAGAGCCCGAGCCAGAAGCTACAATT
CCAGATGTCGTTGCTCCAGCACAAAGTGAAAGCATGACAATTGATAATGGAAAAGTATTT
ACACCCGGTGACTTTGTCTATTATTCACTTGCTGATGATACAACGCCTGGCATTATTTAC
ATTGAGCGACTTTATACAGATGCTGGCGGTGAAAAAATGTGCGAAGGCAATGTTTATTTG
CGACCATATCAAACTTATCATTTGACAACAAGGAAATTTCTTGAACAAGAAGTTTTCAAA
AGCGACCAACATCAAACTATTCCATTGCAAGATTTGCTACAAAAATGTTATGTTATGAGT
GTTAAAGACTACTTTAAACTCAAGCCTGAAAATTTTGCTGATAAAGATGTTTATGTTTGT
GAATTTCGATATAATTCACGTGCGAGATCTTTCAAGAAAATTAAAGCATGGCCTTTCCAA
ACACATAATACAAAGTTAGTTCTACGCGAAGAACCTCTTGAACCTAAACGAGTGCAGTCA
GTTTTCAAAGATCGACCAGTTGATCCATTAAAACTCGATATTCCAATTGATGAAGTTGAT
TTGGCACTAACTGAACGTGAGAAGCCAAATGTTGAAGTTGTCGTTCAAGGTAGTGATGAA
ATGAACACATATTATGAACAGTTTAACACTGTTTGCAGTGGTGTGGTCAAGACTGGTGAC
TATGTGTATGTTGCAACAGAATCTGGCAAACAAGCAATTGCGCAAATCAATTCAATTTGG
GAGACAAAAGATGGAAAATCTTTCTTCAGAGGTCCATGGCTTTTAACTCCAGCTGAATTA
CCTGCATCGATTCTTGCAAATAGACCTCAATATCGTCAAGAAGTTTTTTTGTCAACCGTT
CAAGAAACAACACCCACAATTGGAATAGTTGGCAAATGTTGTGTACTTGAAATTGAAGAA
TATACAACAAGAAGACCAACAGAAATACCAGAAACTGATGTTTATCTTTGTGAATCAATC
TATGATGAATTTAATAAGCAAATAAGAAAAATCATTGGACCAGACGGACTGAAAAAATTT
ACACATACAACTTCAGTCACTGCTGATGAAATTTATTTTTTCCGAAGACCAATTACTGTT
CAAAAGATGCTTGCAAATGAATTGGATTCAAAGACTGCAGCAATGTCTCTTGATATTGAT
CAATTAAAGATGGAGGCAAACGGTGGTGCAAACAGCATGGACATGCTCGGATTGACTGAA
GATTCAATGGATACTGATATTGGGTCAGCTGATGGTTTTGGTTTGAATACATCATCTCCA
ATTCCGACTACTGCTCTTAGTACACCAGCATCATCAAACAAACGTCCTGCTGCATTTACT
GGTGGCAAAAGTGGCAAGAAAGTCATAACAGGTTACATTCTTTATTCGAGTGAAGTTCGA
AAGGCAAAAGTTATTGAAAATCCTGATTGCAAGTTTGGTGACATTTCACGAATGATTGGT
GATGAATGGCGTGCGTTGCCACAAAATGAACGTCGTCAATGGGAAGATAGAGCTTCAGCT
ATCAATGAACAAAATGCATCAAAATATGCTGAAGAAATGGCGATGAATGGAGGAAAAGAA
TCAAGTAACAAAGAAAGTTCAAGCACAAGTTCATCAATGATCCTCACACCAAATCAACTT
TCGATGCAGCACGAATTCATTCCCAATCAAGTTTTTGAGTGTGCTTGGGACAAATGTGAT
TATCAGTTTGAAGACCCTGGAGATGCCTTAGAGCATGCTATAGCTGACAGTAATGGATGC
GTGCAAAGACATTTTACACAAATGGCTTCACAAAATGAGCCAATCGTTTATCATTGCTTG
TGGCGTAATTGTATTCGTGCTAGACGTAATCAACCACCACTTCCAAATATTCAACGATTA
GTGAAACATGTTAGGGAAGTTCATGTTATTAAAGCGCCTGGAAAAATTGTTCAACCACAA
GATCGTGGTCGAAATTATGTTCCAAGTACAAGAAAGCATTTGCATCAAAACAATCAACAG
CCACAACAGCATCATACACAAGTTATCTATCATCCACTTCAAGCTGCTCAAACAACACCA
ACAGCATCTGGAAGTCCACAAACTCAAATTATTGCCCATCATCAAGCACCAGTGCAACAA
AATGTTATAAATTATGTGACTGCACCAGTTGAGCCTCTTTTTGTAACAGTTCCACCACGA
CCTCAACGCGTTTTACATTCAGAAGCTTACATCAAATATATTGAAGGATTGCAGAACAAT
AACTCTTATGTTGGTAATTGGGAGAAAACAATTAAAGCAACTCGTGAAACTGTTACACAT
GATACATCAAAATTGCCGCTTCATTGGTTAGGTCAACGTGGAAAAGAGAAACCGGAAGAA
GTTGTTGATGCATTGTGGAAATTGAGAAATTTTATGTGGCGTGATGCACTTTCGTTGAGT
CGCAGCAATTATTAA

>g2410.t1 Gene=g2410 Length=1704
MSKRRRTSSDIETDDSDDDSEQFPTTPAIRKKKKLDPMEQCQSLYESIRNFKKEDGTQLC
DSFIRAPKRRQEPNYYEIVTNPIDLLRVQQKLKTDSYEDIDDLTNDIELLVKNAKAFYKP
DSVEYKDACTLWDVYNSNKVKLIESLNEESTPVAFDSSKPRRIGRPRKSTTVDDDQISEN
SSENNDFDAYEELFASIMTATDPLDDRALHTMFQLLPSKRTFPSYYEVIDHPIDLKFIAN
KIQTNAYTSLNEMEKDVLQMVKNTQIFNEPGSQIYKDAKTIKKIFLQKKLDIETGKYKKP
MRRGRQISYSAACAALKEELESSEEEMDMDDEEQTGPLWQLFDSLYQQPNSDGSLGGNSP
LGESLWKLPNKRFHPEYYTLIKKPLSMSMIQKKLKKNEYANVTELSADLYLMIDNAKKAN
LPSSKIYKDAVKMQKILNQKLVDEGGLDDDDTEDTDSSQHAFPLGGMEKKKKGRPRIHPL
SSTSPAPSTSITPASSTKNYKFPSNPMLKKKLHAIHKHLLEFTFDNRQPAEPFLEKPSKK
LYPDYYSIITHPIDMNTIYKNIENERYATLDDIVSDYRLMFQNCRKYNEENSMIYDDANM
LERALNEKLKEITGVDRKPMKMLKAHNKKMQAILDAKLKQLYETIKEYKDPKTNRQVATI
FMKLPSKMEHPLYFEIIKSPIDLEKIGMKLRMQQYDSVDELSADLMLMFENACKYNEPDS
QIYKDALMLQQVCIQTKQELRMEDENVPDVPQVIVDLLLQLFTTVYNYQDEEGRCYSDSM
AELPDHDEIEGGLKQRVISLDLIKRRLDKGIYKRLDIFQEDMFACFERARRLSRTDSQVF
EDSIELQSFFIRKRDELCKNGEVLSSPALCYTAMHLSAAVESVRQTKLLQEEEPEPEATI
PDVVAPAQSESMTIDNGKVFTPGDFVYYSLADDTTPGIIYIERLYTDAGGEKMCEGNVYL
RPYQTYHLTTRKFLEQEVFKSDQHQTIPLQDLLQKCYVMSVKDYFKLKPENFADKDVYVC
EFRYNSRARSFKKIKAWPFQTHNTKLVLREEPLEPKRVQSVFKDRPVDPLKLDIPIDEVD
LALTEREKPNVEVVVQGSDEMNTYYEQFNTVCSGVVKTGDYVYVATESGKQAIAQINSIW
ETKDGKSFFRGPWLLTPAELPASILANRPQYRQEVFLSTVQETTPTIGIVGKCCVLEIEE
YTTRRPTEIPETDVYLCESIYDEFNKQIRKIIGPDGLKKFTHTTSVTADEIYFFRRPITV
QKMLANELDSKTAAMSLDIDQLKMEANGGANSMDMLGLTEDSMDTDIGSADGFGLNTSSP
IPTTALSTPASSNKRPAAFTGGKSGKKVITGYILYSSEVRKAKVIENPDCKFGDISRMIG
DEWRALPQNERRQWEDRASAINEQNASKYAEEMAMNGGKESSNKESSSTSSSMILTPNQL
SMQHEFIPNQVFECAWDKCDYQFEDPGDALEHAIADSNGCVQRHFTQMASQNEPIVYHCL
WRNCIRARRNQPPLPNIQRLVKHVREVHVIKAPGKIVQPQDRGRNYVPSTRKHLHQNNQQ
PQQHHTQVIYHPLQAAQTTPTASGSPQTQIIAHHQAPVQQNVINYVTAPVEPLFVTVPPR
PQRVLHSEAYIKYIEGLQNNNSYVGNWEKTIKATRETVTHDTSKLPLHWLGQRGKEKPEE
VVDALWKLRNFMWRDALSLSRSNY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
36 g2410.t1 CDD cd05524 Bromo_polybromo_I 35 144 4.6416E-56
37 g2410.t1 CDD cd05517 Bromo_polybromo_II 188 289 3.22927E-42
34 g2410.t1 CDD cd05526 Bromo_polybromo_VI 757 860 1.82467E-50
35 g2410.t1 CDD cd04717 BAH_polybromo 917 1036 1.92658E-46
38 g2410.t1 CDD cd00084 HMG-box 1346 1414 4.84426E-14
33 g2410.t1 Coils Coil Coil 313 333 -
28 g2410.t1 Gene3D G3DSA:1.20.920.10 Histone Acetyltransferase; Chain A 32 146 7.0E-35
27 g2410.t1 Gene3D G3DSA:1.20.920.10 Histone Acetyltransferase; Chain A 179 297 1.1E-30
29 g2410.t1 Gene3D G3DSA:1.20.920.10 Histone Acetyltransferase; Chain A 332 471 4.9E-25
31 g2410.t1 Gene3D G3DSA:1.20.920.10 Histone Acetyltransferase; Chain A 504 630 2.8E-34
30 g2410.t1 Gene3D G3DSA:1.20.920.10 Histone Acetyltransferase; Chain A 631 745 1.2E-34
32 g2410.t1 Gene3D G3DSA:1.20.920.10 Histone Acetyltransferase; Chain A 747 895 1.9E-32
26 g2410.t1 Gene3D G3DSA:2.30.30.490 - 907 1099 8.0E-49
25 g2410.t1 Gene3D G3DSA:2.30.30.490 - 1100 1381 7.5E-45
53 g2410.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 35 -
49 g2410.t1 MobiDBLite mobidb-lite consensus disorder prediction 154 183 -
51 g2410.t1 MobiDBLite mobidb-lite consensus disorder prediction 160 174 -
50 g2410.t1 MobiDBLite mobidb-lite consensus disorder prediction 444 500 -
52 g2410.t1 MobiDBLite mobidb-lite consensus disorder prediction 481 500 -
10 g2410.t1 PANTHER PTHR16062:SF19 POLYBROMO 21 131 0.0
13 g2410.t1 PANTHER PTHR16062 SWI/SNF-RELATED 21 131 0.0
9 g2410.t1 PANTHER PTHR16062:SF19 POLYBROMO 67 610 0.0
12 g2410.t1 PANTHER PTHR16062 SWI/SNF-RELATED 67 610 0.0
11 g2410.t1 PANTHER PTHR16062:SF19 POLYBROMO 595 1689 0.0
14 g2410.t1 PANTHER PTHR16062 SWI/SNF-RELATED 595 1689 0.0
17 g2410.t1 PRINTS PR00503 Bromodomain signature 542 558 3.7E-14
15 g2410.t1 PRINTS PR00503 Bromodomain signature 558 576 3.7E-14
16 g2410.t1 PRINTS PR00503 Bromodomain signature 704 723 3.7E-14
5 g2410.t1 Pfam PF00439 Bromodomain 58 128 3.4E-17
2 g2410.t1 Pfam PF00439 Bromodomain 202 279 5.8E-19
1 g2410.t1 Pfam PF00439 Bromodomain 364 431 2.0E-17
4 g2410.t1 Pfam PF00439 Bromodomain 523 599 5.6E-23
3 g2410.t1 Pfam PF00439 Bromodomain 654 726 2.7E-18
7 g2410.t1 Pfam PF01426 BAH domain 920 1035 2.2E-22
8 g2410.t1 Pfam PF01426 BAH domain 1116 1228 1.8E-14
6 g2410.t1 Pfam PF00505 HMG (high mobility group) box 1349 1408 4.6E-11
48 g2410.t1 ProSitePatterns PS00633 Bromodomain signature. 530 587 -
57 g2410.t1 ProSiteProfiles PS50014 Bromodomain profile. 55 125 16.625
59 g2410.t1 ProSiteProfiles PS50014 Bromodomain profile. 205 275 17.384
61 g2410.t1 ProSiteProfiles PS50014 Bromodomain profile. 357 427 15.963
58 g2410.t1 ProSiteProfiles PS50014 Bromodomain profile. 525 595 21.013
60 g2410.t1 ProSiteProfiles PS50014 Bromodomain profile. 653 723 18.529
55 g2410.t1 ProSiteProfiles PS51038 BAH domain profile. 918 1035 20.262
56 g2410.t1 ProSiteProfiles PS51038 BAH domain profile. 1114 1232 20.604
54 g2410.t1 ProSiteProfiles PS50118 HMG boxes A and B DNA-binding domains profile. 1345 1413 13.218
41 g2410.t1 SMART SM00297 bromo_6 34 144 3.2E-28
46 g2410.t1 SMART SM00297 bromo_6 186 294 1.3E-23
45 g2410.t1 SMART SM00297 bromo_6 331 446 1.1E-26
44 g2410.t1 SMART SM00297 bromo_6 501 614 6.5E-35
43 g2410.t1 SMART SM00297 bromo_6 627 742 4.8E-35
42 g2410.t1 SMART SM00297 bromo_6 751 859 9.2E-7
39 g2410.t1 SMART SM00439 BAH_4 918 1035 7.7E-31
40 g2410.t1 SMART SM00439 BAH_4 1114 1232 6.7E-14
47 g2410.t1 SMART SM00398 hmgende2 1344 1414 9.6E-12
22 g2410.t1 SUPERFAMILY SSF47370 Bromodomain 28 144 5.63E-25
20 g2410.t1 SUPERFAMILY SSF47370 Bromodomain 183 289 5.1E-27
19 g2410.t1 SUPERFAMILY SSF47370 Bromodomain 340 443 1.7E-23
18 g2410.t1 SUPERFAMILY SSF47370 Bromodomain 492 614 3.01E-32
21 g2410.t1 SUPERFAMILY SSF47370 Bromodomain 619 740 2.22E-29
23 g2410.t1 SUPERFAMILY SSF47370 Bromodomain 798 861 4.84E-10
24 g2410.t1 SUPERFAMILY SSF47095 HMG-box 1332 1409 2.23E-13

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0016586 RSC-type complex CC
GO:0006338 chromatin remodeling BP
GO:0005515 protein binding MF
GO:0003682 chromatin binding MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values