Gene loci information

Transcript annotation

  • This transcript has been annotated as Paired amphipathic helix protein Sin3a.

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 g3724 g3724.t1 isoform g3724.t1 27659526 27666799
chr_3 g3724 g3724.t1 exon g3724.t1.exon1 27659526 27659978
chr_3 g3724 g3724.t1 cds g3724.t1.CDS1 27659526 27659978
chr_3 g3724 g3724.t1 exon g3724.t1.exon2 27660057 27660782
chr_3 g3724 g3724.t1 cds g3724.t1.CDS2 27660057 27660782
chr_3 g3724 g3724.t1 exon g3724.t1.exon3 27660853 27662385
chr_3 g3724 g3724.t1 cds g3724.t1.CDS3 27660853 27662385
chr_3 g3724 g3724.t1 exon g3724.t1.exon4 27662453 27662681
chr_3 g3724 g3724.t1 cds g3724.t1.CDS4 27662453 27662681
chr_3 g3724 g3724.t1 exon g3724.t1.exon5 27663205 27663575
chr_3 g3724 g3724.t1 cds g3724.t1.CDS5 27663205 27663575
chr_3 g3724 g3724.t1 exon g3724.t1.exon6 27664078 27664407
chr_3 g3724 g3724.t1 cds g3724.t1.CDS6 27664078 27664407
chr_3 g3724 g3724.t1 exon g3724.t1.exon7 27664478 27664684
chr_3 g3724 g3724.t1 cds g3724.t1.CDS7 27664478 27664684
chr_3 g3724 g3724.t1 exon g3724.t1.exon8 27664748 27664969
chr_3 g3724 g3724.t1 cds g3724.t1.CDS8 27664748 27664969
chr_3 g3724 g3724.t1 exon g3724.t1.exon9 27666023 27666493
chr_3 g3724 g3724.t1 cds g3724.t1.CDS9 27666023 27666493
chr_3 g3724 g3724.t1 exon g3724.t1.exon10 27666554 27666799
chr_3 g3724 g3724.t1 cds g3724.t1.CDS10 27666554 27666799
chr_3 g3724 g3724.t1 TTS g3724.t1 27667125 27667125
chr_3 g3724 g3724.t1 TSS g3724.t1 NA NA

Sequences

>g3724.t1 Gene=g3724 Length=4788
ATGAAGAAAAGAGTGGATGAAATTCAAACTTTTCACAGTACAGCACGTGTAACTGGAGGT
ACGGCTCGAATATTAACGCCACCGCAGCATAATAACAGTCCAAATGCCACGCAAAGTCAG
TTTCAAATTTTAAACGTTCTACGCGATTCAGCTCCAGCAGCACAAAGCGTCCAATATACA
TATACTCCAGCAATAACTACTACAAACATTCAAAGAAATAATGTAGCACAGCAGCAACAG
CAACAATCACAGAATCAACCAACAGTGCAGGTTGTCACTGCTTCAGCTATAGCAAATACT
GTTCGTCCAAAACCTCCAGTTACATCTGGAAGTATAACGCCAACGCCAGTTACTGTTACA
AGTCCAACTGGCAATTCGATTCCAGCTCAAAATGCTAGTAGCCAAAATTTTCCACGATTA
AAAGTAGAAGACGCTCTTAGTTATCTCGATCAGGTCAAATACAAATTTGGGAATCAACCA
CAAGTGTACAATGATTTTCTTGATATAATGAAAGAATTCAAATCTCAAAGCATCGATACA
CCAGGTGTCATTCAACGTGTATCAAATCTCTTCAAAGGGCATCCTGAATTGATTGTTGGA
TTTAATACTTTTCTACCGCCTGGATATAAAATTGAAGTTCAGGCCAATGATCAAGGTTTC
GCATATCAAGTGTCAGTCTCAGTCCCGTCACCATCAGGTAATCAAACTATCAGTACTCAG
CATTCGCCTCCGTCAAAGTTTATTCAGGGCACACACATCATTCAACCGCCCGTTAATCTC
ATAACGCATACTGGACATACCCAAACTTTGCACATTCAGCCACAATCAACACCACAAAAT
CAACAAGATCAACGATCAATTCAAAGTCACAACATAACCAATATCAACATTGCACAAAAT
TTTGCTCGTGATCGATCTTTGCCTGCAGTCTCAAATTCTGCAAGTGGAGTTAATAATGCT
TCTACCGGCAACAGTGGTACAAATGTACAATCAAATCAACAACAATCATCTGCAATTTCG
TCTCAACAGCAACAACAACAACAACATCACTCTCAACCAAATCAAATTCAATCTACAATT
AATGAATCTTCTGGCTTGCATAGAATGCAACCAATCTTTCAAAACGACAACCAACCAGTT
CAATTTAATCAAGCAATTGTCTACGTTAATAAAATCAAGTGTCGTTTCCAAGAACAACCA
GAGAAATATAAGCATTTCCTGAGAATCCTTCATAAATATCAAAATGAACAGAGACGAAAA
GATAATGCTGGAAAGGCAGGCTCACCTCTCACTGAGACAGAGGTTTTTAAACAAGTTGCG
CATTTATTTGATAATCAAGAAGATTTATTACGAGAATTTGGACAATTTTTACCCGATGCT
TCACCTGGAGCAACAAACATTCTCACTGGAAAAAGTGCATCTATGACTGGACTAAATGAA
TCTAATGACAAGTCTAACTCTTCAATCGGCAATCAAAATGCCAATTCTAAGCAGTTAGGC
AATAATATATCTCGAAATAGTATTATTAATCCAATGGATATTTTTCAAGCAAGCAATAAT
GAAAAAGAGTTTCATGTAACACCATACAGCACTATTAATCGTGAAAAAGATTCGAATAGA
AATCATATAAATTCAAATAATCAAAAATATGGAAGTATCGGAACGTCCTCACTCAAGCGT
TCGCCAGGAATGGCACTTAATCACGTTAATCGTGGTCATGATAGAAATGAGCCGCCACTT
AAACGTTATAAACCAGTATTTCGTGATGTTTCATATGCTGATGCCGCTCGTTCAGGCACA
TTACAAGATTATGCTTTCTTTGATAAAGTACGAGAAGCATTAAAGACATCAGATGTTTAT
GACAACTTTTTACGTTGTTTGACTCTGTATAATCAAGAGATTGTTAGTAAGTCAGAATTA
ATGACTTTAGTTGCACCTTTCCTCAATAAGGAACCTGAACTTTTGAAACGTTTTCAAGAA
TTTCTCAAATTTTCAACTGCACCTGAATCACTTCCACTTTCTGTTGCTCAACGACAAGAT
CATCGCGTACAAATTGATACTGCAACTGAAATTGATGTAACACAATGCAAACGACTTGGT
ACTAGTTACTGTGCAATTCCCAAATCAAGTGAGTTGAAAAAATGCAGTGGAAGAACGCCA
TTATGTAAAGAAGTGCTCAATGATACGTGGGTATCTTTTCCATCATGGTCTGAAGATTCG
ACTTTTAATACATCACGCAAGACTCAATATGAAGAGTTTATTTATCGATGCGAAGATGAA
CGCTTTGAACTTGATGTCGTTATTGAAACAAATAGTGCGACAATTCGTGTGCTTGAGGGT
GTTCAAAAGAAAATGTCGAAAATGGCAGCTGATGAACTAGCAAGATTCAAATTGGATGAT
TCACTTGGAGGTACATCACAAACAATTCATCAGCGTGCACTTAGACGCATTTATGGAGAT
AAAGCTCCTGACATTATTGAAGGATTAAAGAAAAATCCAAATGTAGCCGTGCCTGTTGTT
CTTCGAAGATTAAAAGCGAAAGAAGAAGAATGGAGAGAGGCGCAAAAAGGATTCAATCAA
CAATGGCGTGAGCAAAATGAGAAATATTATTTGAAATCACTTGATCATCAAGGCATTAAC
TTTAAACATGCCGATACAAAAGCATTAAGATCGAAAAGTTTAATGAATCAAATTGAATCC
GCTTATGAAGAGCGTAATGAAGGCAATAATGGAGAAGCAATTCCTGGGCCACATCTAATT
TTGCATTATAAAGATAAATCAATTCTTGAAGATGCTGCAAACTTACTCATTCATCATGTG
AAAAGACAAACTGGCATTCAAAAACTCGAGAAAGCAAGAATAAAACATATACTAAGACAG
TTTGTTCCGGAACTGTTCTTTGCTCCTCGACAACCTTTAAGTGATGATGAAAGGGAAGAC
GTGTTTCCTTTTTCAGTAGAAGACAAAGAATCAAATATTTCTGAGAGTGATGGAAAATCA
AAGTCAAACAAAACTCTATCCTCCTCCTCGAATGAAAATGTGCCTGCAAACAAATCGACA
AACTGCGAACAGTCGTCAAAAAATAATACAAGCACAACTGATGAACAAATACAACAAGCA
AGTACAAATAGTAGTTCGTCTGATAAGGCGTCGTCAGAAGATGTAAATGCTAAAGATAGT
GATATCAAAATGGAAATAAAGGCTGATCCAGATGGTGTTAAGTTAACAAACAGCAGTAAC
ACAATAACACAACCAGCTTTTGCACTTGGAAGCAATCTGCTACCTTCACATGCAACAAGT
GCAAAACATCAGGACGAAGCATATACCTTATTCTTTGCGAATAGTAACTGGTACTATTTC
TTACGACTCCATGCAATTTTATGTGAGCGATTAAGAACAATGTATGAGCGAACACAAATA
TTGGCTGCAGAAGAAGATAAATACAAAGTTAATAGAAGAGAAAGTGTTGCCATTGCGCTG
AGATTAAAGCCGCAGAACGAATTTGAGATTCCAGATTACTATCCAGCATTTTTGGATATG
CTCAAGAGTCTATTAGATGGCAATATGGATGCAACAACTTATGAAGATAAATTAAGAGAC
ATGTACGGAATTCATGCATACATTGCATTTACACTGGATAGAGTTGTCTCAAACGCAGTG
CGTCAACTTCAATTTTGTGTAACTGAACGCAATGCTCTAGAATGCTTTGAGCTATATCAA
CTTGAAAGTCGAAATCATGGAACTGGTGGATTATGTTCGACAGCCTATAAGCGAACTGCA
GCTGAGCTGGCTTATCAACGAAAAACTGAAACAAATCTCCAGGAAGAAATGTACTTCAAA
GTGATTATTTATAAAATTGACTGTCGTGTAACAATTGAAATGCTTGAGAATGATACAGAA
GACACATCGACAACAAACTTTGAGCAAATTCAATCTACAAGCAAATATATTGAACGTTAC
ACAAATCCATCTGTTTCAGGAGGCAATGGAAAGTCGAGTCGAAATAATTCTGTAAACGGT
GCTTCATTTAGCAACGTTGACATTAAAACTGAAAAATCTGAGGAAGAAATGACAAAAATC
CGCAAGCCATTGTTTCTACATAGAAACATTAGAAAATTCAATAGACGAATGTCAACAACT
GTGAAATATGAAAATGGTGAAAGTGTAGTAAACAATGCGACTTCTTCCGTATCAACTACA
ACCACTACAACAACATCTACGACGAGTTCTTCTACCGTTCAAATTACAAAAGGTGATGCA
TCAATATTTTCAACCATATCGACTGCAACAACTTCCTCATGTACCTTAACAACATCAACC
TCCTCGATTCCTCCACCATTAATTTTACCTGAACTAACTGCTGTTAGCAGTAAAAGTACA
CCAACAAGAATCGGTCAATCATCAAATTCATTTGGTGAATTTTTCGTTGATGATCAGGAA
CAAGTGAAATTTAATTTCCAAACGTACAAAACTGTATTTTGCAATACAACCAATAAAGGC
TATATCCTTTATCGATACAACTCATTAAAAAGAGCAAAAGAGACACATATGAAAGTGACG
AAACTAATGGACTTGCGATTTAATGAACATGTACAAAAATGGCTCCAAAAAAATGTTAGT
GACTTGCAAAGAATAACAATTAATGATTGGCTTCTAGGTCGAAATCAAAATGATTTTGCA
CCATGCAGGACAACAATTAAGAAAGATAATAATATTACAGAAACGCCATATTGCATCTAT
AATCGATATAAAGTTGAATACATTTCAGCAAATACCGATAAGTGTTAA

>g3724.t1 Gene=g3724 Length=1595
MKKRVDEIQTFHSTARVTGGTARILTPPQHNNSPNATQSQFQILNVLRDSAPAAQSVQYT
YTPAITTTNIQRNNVAQQQQQQSQNQPTVQVVTASAIANTVRPKPPVTSGSITPTPVTVT
SPTGNSIPAQNASSQNFPRLKVEDALSYLDQVKYKFGNQPQVYNDFLDIMKEFKSQSIDT
PGVIQRVSNLFKGHPELIVGFNTFLPPGYKIEVQANDQGFAYQVSVSVPSPSGNQTISTQ
HSPPSKFIQGTHIIQPPVNLITHTGHTQTLHIQPQSTPQNQQDQRSIQSHNITNINIAQN
FARDRSLPAVSNSASGVNNASTGNSGTNVQSNQQQSSAISSQQQQQQQHHSQPNQIQSTI
NESSGLHRMQPIFQNDNQPVQFNQAIVYVNKIKCRFQEQPEKYKHFLRILHKYQNEQRRK
DNAGKAGSPLTETEVFKQVAHLFDNQEDLLREFGQFLPDASPGATNILTGKSASMTGLNE
SNDKSNSSIGNQNANSKQLGNNISRNSIINPMDIFQASNNEKEFHVTPYSTINREKDSNR
NHINSNNQKYGSIGTSSLKRSPGMALNHVNRGHDRNEPPLKRYKPVFRDVSYADAARSGT
LQDYAFFDKVREALKTSDVYDNFLRCLTLYNQEIVSKSELMTLVAPFLNKEPELLKRFQE
FLKFSTAPESLPLSVAQRQDHRVQIDTATEIDVTQCKRLGTSYCAIPKSSELKKCSGRTP
LCKEVLNDTWVSFPSWSEDSTFNTSRKTQYEEFIYRCEDERFELDVVIETNSATIRVLEG
VQKKMSKMAADELARFKLDDSLGGTSQTIHQRALRRIYGDKAPDIIEGLKKNPNVAVPVV
LRRLKAKEEEWREAQKGFNQQWREQNEKYYLKSLDHQGINFKHADTKALRSKSLMNQIES
AYEERNEGNNGEAIPGPHLILHYKDKSILEDAANLLIHHVKRQTGIQKLEKARIKHILRQ
FVPELFFAPRQPLSDDEREDVFPFSVEDKESNISESDGKSKSNKTLSSSSNENVPANKST
NCEQSSKNNTSTTDEQIQQASTNSSSSDKASSEDVNAKDSDIKMEIKADPDGVKLTNSSN
TITQPAFALGSNLLPSHATSAKHQDEAYTLFFANSNWYYFLRLHAILCERLRTMYERTQI
LAAEEDKYKVNRRESVAIALRLKPQNEFEIPDYYPAFLDMLKSLLDGNMDATTYEDKLRD
MYGIHAYIAFTLDRVVSNAVRQLQFCVTERNALECFELYQLESRNHGTGGLCSTAYKRTA
AELAYQRKTETNLQEEMYFKVIIYKIDCRVTIEMLENDTEDTSTTNFEQIQSTSKYIERY
TNPSVSGGNGKSSRNNSVNGASFSNVDIKTEKSEEEMTKIRKPLFLHRNIRKFNRRMSTT
VKYENGESVVNNATSSVSTTTTTTTSTTSSSTVQITKGDASIFSTISTATTSSCTLTTST
SSIPPPLILPELTAVSSKSTPTRIGQSSNSFGEFFVDDQEQVKFNFQTYKTVFCNTTNKG
YILYRYNSLKRAKETHMKVTKLMDLRFNEHVQKWLQKNVSDLQRITINDWLLGRNQNDFA
PCRTTIKKDNNITETPYCIYNRYKVEYISANTDKC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
27 g3724.t1 Gene3D G3DSA:1.20.1160.11 PAH2 domain 144 206 9.7E-23
25 g3724.t1 Gene3D G3DSA:1.20.1160.11 PAH2 domain 373 460 2.8E-32
26 g3724.t1 Gene3D G3DSA:1.20.1160.11 PAH2 domain 593 666 5.1E-22
22 g3724.t1 MobiDBLite mobidb-lite consensus disorder prediction 309 356 -
23 g3724.t1 MobiDBLite mobidb-lite consensus disorder prediction 984 1070 -
20 g3724.t1 MobiDBLite mobidb-lite consensus disorder prediction 998 1051 -
21 g3724.t1 MobiDBLite mobidb-lite consensus disorder prediction 1052 1070 -
24 g3724.t1 MobiDBLite mobidb-lite consensus disorder prediction 1318 1338 -
7 g3724.t1 PANTHER PTHR12346 SIN3B-RELATED 70 246 0.0
12 g3724.t1 PANTHER PTHR12346:SF2 PAIRED AMPHIPATHIC HELIX PROTEIN SIN3A 70 246 0.0
6 g3724.t1 PANTHER PTHR12346 SIN3B-RELATED 325 484 0.0
11 g3724.t1 PANTHER PTHR12346:SF2 PAIRED AMPHIPATHIC HELIX PROTEIN SIN3A 325 484 0.0
9 g3724.t1 PANTHER PTHR12346 SIN3B-RELATED 576 1006 0.0
14 g3724.t1 PANTHER PTHR12346:SF2 PAIRED AMPHIPATHIC HELIX PROTEIN SIN3A 576 1006 0.0
10 g3724.t1 PANTHER PTHR12346 SIN3B-RELATED 1090 1331 0.0
15 g3724.t1 PANTHER PTHR12346:SF2 PAIRED AMPHIPATHIC HELIX PROTEIN SIN3A 1090 1331 0.0
8 g3724.t1 PANTHER PTHR12346 SIN3B-RELATED 1479 1568 0.0
13 g3724.t1 PANTHER PTHR12346:SF2 PAIRED AMPHIPATHIC HELIX PROTEIN SIN3A 1479 1568 0.0
4 g3724.t1 Pfam PF02671 Paired amphipathic helix repeat 161 205 2.1E-18
5 g3724.t1 Pfam PF02671 Paired amphipathic helix repeat 401 457 1.1E-15
3 g3724.t1 Pfam PF02671 Paired amphipathic helix repeat 618 662 7.9E-8
1 g3724.t1 Pfam PF08295 Sin3 family co-repressor 697 792 3.8E-39
2 g3724.t1 Pfam PF16879 C-terminal domain of Sin3a protein 1111 1408 1.8E-51
30 g3724.t1 ProSiteProfiles PS51477 PAH domain profile. 138 208 19.493
28 g3724.t1 ProSiteProfiles PS51477 PAH domain profile. 378 460 15.627
29 g3724.t1 ProSiteProfiles PS51477 PAH domain profile. 597 665 11.978
19 g3724.t1 SMART SM00761 hdac_interact2seq4b 695 795 1.8E-60
17 g3724.t1 SUPERFAMILY SSF47762 PAH2 domain 138 207 1.01E-23
16 g3724.t1 SUPERFAMILY SSF47762 PAH2 domain 377 459 4.97E-20
18 g3724.t1 SUPERFAMILY SSF47762 PAH2 domain 601 663 1.57E-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:0003714 transcription corepressor activity MF
GO:0006355 regulation of transcription, DNA-templated BP
GO:0016580 Sin3 complex CC

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