Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t2 TTS g2410.t2 17762482 17762482
chr_3 g2410 g2410.t2 isoform g2410.t2 17762558 17764176
chr_3 g2410 g2410.t2 exon g2410.t2.exon1 17762558 17763322
chr_3 g2410 g2410.t2 cds g2410.t2.CDS1 17762558 17763322
chr_3 g2410 g2410.t2 exon g2410.t2.exon2 17763664 17764176
chr_3 g2410 g2410.t2 cds g2410.t2.CDS2 17763664 17764164
chr_3 g2410 g2410.t2 TSS g2410.t2 NA NA

Sequences

>g2410.t2 Gene=g2410 Length=1278
GATCAATTAAAGATGGAGGCAAACGGTGGTGCAAACAGCATGGACATGCTCGGATTGACT
GAAGATTCAATGGATACTGATATTGGGTCAGCTGATGGTTTTGGTTTGAATACATCATCT
CCAATTCCGACTACTGCTCTTAGTACACCAGCATCATCAAACAAACGTCCTGCTGCATTT
ACTGGTGGCAAAAGTGGCAAGAAAGTCATAACAGGTTACATTCTTTATTCGAGTGAAGTT
CGAAAGGCAAAAGTTATTGAAAATCCTGATTGCAAGTTTGGTGACATTTCACGAATGATT
GGTGATGAATGGCGTGCGTTGCCACAAAATGAACGTCGTCAATGGGAAGATAGAGCTTCA
GCTATCAATGAACAAAATGCATCAAAATATGCTGAAGAAATGGCGATGAATGGAGGAAAA
GAATCAAGTAACAAAGAAAGTTCAAGCACAAGTTCATCAATGATCCTCACACCAAATCAA
CTTTCGATGCAGCACGAATTCATTCCCAATCAAGTTTTTGAGTGTGCTTGGGACAAATGT
GATTATCAGTTTGAAGACCCTGGAGATGCCTTAGAGCATGCTATAGCTGACAGTAATGGA
TGCGTGCAAAGACATTTTACACAAATGGCTTCACAAAATGAGCCAATCGTTTATCATTGC
TTGTGGCGTAATTGTATTCGTGCTAGACGTAATCAACCACCACTTCCAAATATTCAACGA
TTAGTGAAACATGTTAGGGAAGTTCATGTTATTAAAGCGCCTGGAAAAATTGTTCAACCA
CAAGATCGTGGTCGAAATTATGTTCCAAGTACAAGAAAGCATTTGCATCAAAACAATCAA
CAGCCACAACAGCATCATACACAAGTTATCTATCATCCACTTCAAGCTGCTCAAACAACA
CCAACAGCATCTGGAAGTCCACAAACTCAAATTATTGCCCATCATCAAGCACCAGTGCAA
CAAAATGTTATAAATTATGTGACTGCACCAGTTGAGCCTCTTTTTGTAACAGTTCCACCA
CGACCTCAACGCGTTTTACATTCAGAAGCTTACATCAAATATATTGAAGGATTGCAGAAC
AATAACTCTTATGTTGGTAATTGGGAGAAAACAATTAAAGCAACTCGTGAAACTGTTACA
CATGATACATCAAAATTGCCGCTTCATTGGTTAGGTCAACGTGGAAAAGAGAAACCGGAA
GAAGTTGTTGATGCATTGTGGAAATTGAGAAATTTTATGTGGCGTGATGCACTTTCGTTG
AGTCGCAGCAATTATTAA

>g2410.t2 Gene=g2410 Length=421
MEANGGANSMDMLGLTEDSMDTDIGSADGFGLNTSSPIPTTALSTPASSNKRPAAFTGGK
SGKKVITGYILYSSEVRKAKVIENPDCKFGDISRMIGDEWRALPQNERRQWEDRASAINE
QNASKYAEEMAMNGGKESSNKESSSTSSSMILTPNQLSMQHEFIPNQVFECAWDKCDYQF
EDPGDALEHAIADSNGCVQRHFTQMASQNEPIVYHCLWRNCIRARRNQPPLPNIQRLVKH
VREVHVIKAPGKIVQPQDRGRNYVPSTRKHLHQNNQQPQQHHTQVIYHPLQAAQTTPTAS
GSPQTQIIAHHQAPVQQNVINYVTAPVEPLFVTVPPRPQRVLHSEAYIKYIEGLQNNNSY
VGNWEKTIKATRETVTHDTSKLPLHWLGQRGKEKPEEVVDALWKLRNFMWRDALSLSRSN
Y

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g2410.t2 CDD cd00084 HMG-box 63 131 0.000
6 g2410.t2 Gene3D G3DSA:1.10.30.10 DNA Binding (I) 58 149 0.000
2 g2410.t2 PANTHER PTHR16062:SF19 POLYBROMO 17 406 0.000
3 g2410.t2 PANTHER PTHR16062 SWI/SNF-RELATED 17 406 0.000
1 g2410.t2 Pfam PF00505 HMG (high mobility group) box 66 125 0.000
7 g2410.t2 ProSiteProfiles PS50118 HMG boxes A and B DNA-binding domains profile. 62 130 13.218
5 g2410.t2 SMART SM00398 hmgende2 61 131 0.000
4 g2410.t2 SUPERFAMILY SSF47095 HMG-box 48 126 0.000

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

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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