Gene loci information

Transcript annotation

  • This transcript has been annotated as Retinoblastoma family protein.

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_2 g8044 g8044.t1 TSS g8044.t1 28201681 28201681
chr_2 g8044 g8044.t1 isoform g8044.t1 28201820 28204728
chr_2 g8044 g8044.t1 exon g8044.t1.exon1 28201820 28201936
chr_2 g8044 g8044.t1 cds g8044.t1.CDS1 28201820 28201936
chr_2 g8044 g8044.t1 exon g8044.t1.exon2 28202092 28202231
chr_2 g8044 g8044.t1 cds g8044.t1.CDS2 28202092 28202231
chr_2 g8044 g8044.t1 exon g8044.t1.exon3 28202304 28202516
chr_2 g8044 g8044.t1 cds g8044.t1.CDS3 28202304 28202516
chr_2 g8044 g8044.t1 exon g8044.t1.exon4 28202576 28203995
chr_2 g8044 g8044.t1 cds g8044.t1.CDS4 28202576 28203995
chr_2 g8044 g8044.t1 exon g8044.t1.exon5 28204063 28204509
chr_2 g8044 g8044.t1 cds g8044.t1.CDS5 28204063 28204509
chr_2 g8044 g8044.t1 exon g8044.t1.exon6 28204567 28204728
chr_2 g8044 g8044.t1 cds g8044.t1.CDS6 28204567 28204728
chr_2 g8044 g8044.t1 TTS g8044.t1 NA NA

Sequences

>g8044.t1 Gene=g8044 Length=2499
ATGATGGAGAAAGACCCGTTTTTTAATGAAATTTGTTCAAAATTGGCTATTGATTCAGCT
GTGAGAAAAAGTGCATATTTGCAATTTGCAGAAGTCTCCCGCAATACAATTCTTGATGGC
GATATGAGACATTGGATTTGCTGTGCTCTTTTTACCGCATGCATCAAACAAAAAATTCCA
ACAGTTGTTGTAAGTGACACTTTTGTACAAGGCAATGGCATCTCTTTGGTGAAACTCATA
AACGAATGCAATTTGAACATTTACACTTTCTTCGAAAAAATTGAAATTTGGTTCAAAGTT
TCATCTGTACCTAATGCTATTCAACAAAAAGTAGAAGTGCTCAAAAGGAATTTTCAGTTG
TCGCAGTTGATTTACAAAGATTTCATGAACATGTTTGCTAAACTATTCAAATGCAACGAT
GGTTCGACCAATGCTGATGAGCCAAAGACTAAAAGCAGAAAAAAAGCAAGTAATGTTCCA
ATTTCACCACAAAAACTTTTTGAAATGTGCTGGACACTTTTCGTATGCGTAAAAGGTTAC
TCCCCAAATGAAAAGCCAAGCGATTTGGTTGCTTCAATCAATCTTTTACTTTGCTGTATT
GATTTGATGTTTACAAATGTGATAAATATTAATCGCACTGATCTCATCAATACTTCTTTT
CCTGGATTACCAAAAAGCCTCTTCACTGCTTCATATGATGCAAAAAAAGAACCTGAAATT
AATATCATTGATAAACTATCAGATGATTCTATAATCAAAATGAAAAGTGCACATTGGGAG
TTAATTATTCGACGCTTTCTTACGGATAAAAACTTTCAAGGAGAATACAATAATATCTTA
TCTGTTGAAAATTTTGAGTCCAACTTTAAGAAACTTAATGATCTCTATGAGACTTTTATT
TTGAGCTGTGGACAGTTTGACGAACGTATTTTTCTTTATGCAAAACCTGCTATGCAGCAA
TCAATGAATTCTCAATTGATACCACAAACACCTCTAAGTCATCATCAAGATGTTTTACAT
CATACATCATCTTCCAGTAAATTATCTCCTATATCAAGCTACAAACAAAATGTTCAGAAA
TTGCAAGCTCTTTACAATCAGTGTCAACCATCAAACGCCCTCAAAGTTCTACTTTGTTCA
GGTTCTGATTCAATTTTAAATGATCTTGCAGAACGTTTAGAACGTATGAAAGAAACATTT
TGCACGAAAATGATGCCGAATGGACAAGACCGTTTTCAAATTGCTGAAGCATTATATTAT
CGATTGCTAGAAAATATCATCAATTCTGAGATGAAAACACACGGACGTTTTGACCTTTTT
ATCAATGATGATGTTTTTAATCAAACGCTCATTGTTCTATGCTTAGAAATTGTACTCTTT
GCTTTCTCGCTTCATAAAAAACTTACTACGTTACTTGAATGTTTTAATATGGAAGCTTTT
CATTTTTACAAACTGATTGAAGTTGTCATTAGAAATAATAAGGATTATTTTACAAATGAT
ATAATCAAACATTTGAAAGCCATTGAAGAGCAATGTTTAGATTCACTTGCTTGGGTATCA
GGTTCATTGCTGTGGCAAAAAATTGGAGAGATTAATGGTAAATTACCAACAAATCAAGAG
GTCAGTACATCACAACCTAGTAACAGTCAAAATAGCAGTCCAAGTCAAACACCGAAAAGC
ATTAAGCTTTTCTTTCGAAAATTTTATCAATTGGCTCACTTGAGATTGCAAGATTTACAC
AAAAACTTGCAATTTACAAATAATACAGATCTCTTGAGAAAGATCTGGACTCTCTTTGAG
TATGCAATTTTGGAGCATACCAGTTTAATGAAAGATCGTCATTTAGATCAAATTTTGATG
TGTTGTGTTTATGTCCTTTGTAAGATTAGGCCAAATGAAAATCGTCACACATTTGCAGAC
ATCATGAAGTTTTACAGAAATCAGCCACAATCTGACTCGCATATCTATCGTAGTGTCTTC
ATAGAATATGTTCAAACGGATAAAGCTAATGAGATGCAAGAACCGAAGGCAAGTGCTGCT
GAGCCAGAAGTCGTTAATGGTAGAAACACTATATATGGAACTGAAAGTCGAGGAGACATC
ATTTATTTTTACAACAAAATATTTGTTCCAAAAATGCAACAATTTGCGATGAGATTTTCA
ACTTCTTCACAAAATAATCTTCTTCTATCACCATTGCCACAGTCACGTCCTCTGATCTCA
CCTAGAAAAAAAATTTCACCTTATCATGATGTATATGTACAACCGTTGACAAAACAAAGC
ATTCTTTCACCTTCAGCACGTACTCTTACTTTTACAATTGAACAAAGCCCCTCAAAGGAT
CTCCAGAAAATAAATTCCATGATTAATCAGAATAAGAAGGCAAGCGTTGCAAAGCGTTTT
ATGATGGATACTGAAGATGATTTCCGTCCTGCAAAAGTTTCAAAGGACTCTTCTTTACAA
CTTCGACTTTTAATTGACCGTGAAGAGATTAGCAATTAG

>g8044.t1 Gene=g8044 Length=832
MMEKDPFFNEICSKLAIDSAVRKSAYLQFAEVSRNTILDGDMRHWICCALFTACIKQKIP
TVVVSDTFVQGNGISLVKLINECNLNIYTFFEKIEIWFKVSSVPNAIQQKVEVLKRNFQL
SQLIYKDFMNMFAKLFKCNDGSTNADEPKTKSRKKASNVPISPQKLFEMCWTLFVCVKGY
SPNEKPSDLVASINLLLCCIDLMFTNVININRTDLINTSFPGLPKSLFTASYDAKKEPEI
NIIDKLSDDSIIKMKSAHWELIIRRFLTDKNFQGEYNNILSVENFESNFKKLNDLYETFI
LSCGQFDERIFLYAKPAMQQSMNSQLIPQTPLSHHQDVLHHTSSSSKLSPISSYKQNVQK
LQALYNQCQPSNALKVLLCSGSDSILNDLAERLERMKETFCTKMMPNGQDRFQIAEALYY
RLLENIINSEMKTHGRFDLFINDDVFNQTLIVLCLEIVLFAFSLHKKLTTLLECFNMEAF
HFYKLIEVVIRNNKDYFTNDIIKHLKAIEEQCLDSLAWVSGSLLWQKIGEINGKLPTNQE
VSTSQPSNSQNSSPSQTPKSIKLFFRKFYQLAHLRLQDLHKNLQFTNNTDLLRKIWTLFE
YAILEHTSLMKDRHLDQILMCCVYVLCKIRPNENRHTFADIMKFYRNQPQSDSHIYRSVF
IEYVQTDKANEMQEPKASAAEPEVVNGRNTIYGTESRGDIIYFYNKIFVPKMQQFAMRFS
TSSQNNLLLSPLPQSRPLISPRKKISPYHDVYVQPLTKQSILSPSARTLTFTIEQSPSKD
LQKINSMINQNKKASVAKRFMMDTEDDFRPAKVSKDSSLQLRLLIDREEISN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g8044.t1 CDD cd00043 CYCLIN 569 652 0.0058386
9 g8044.t1 Gene3D G3DSA:1.10.472.140 - 2 320 0.0000000
11 g8044.t1 Gene3D G3DSA:1.10.472.10 - 353 518 0.0000000
10 g8044.t1 Gene3D G3DSA:1.10.472.10 - 520 737 0.0000000
4 g8044.t1 PANTHER PTHR13742 RETINOBLASTOMA-ASSOCIATED PROTEIN RB -RELATED 8 806 0.0000000
2 g8044.t1 Pfam PF11934 Domain of unknown function (DUF3452) 69 206 0.0000000
1 g8044.t1 Pfam PF01858 Retinoblastoma-associated protein A domain 349 528 0.0000000
3 g8044.t1 Pfam PF01857 Retinoblastoma-associated protein B domain 560 713 0.0000000
8 g8044.t1 SMART SM01367 DUF3452_2 57 206 0.0000000
7 g8044.t1 SMART SM01368 RB_A_2 349 528 0.0000000
6 g8044.t1 SUPERFAMILY SSF47954 Cyclin-like 359 530 0.0000000
5 g8044.t1 SUPERFAMILY SSF47954 Cyclin-like 560 734 0.0000000

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:0006357 regulation of transcription by RNA polymerase II BP
GO:0005634 nucleus CC
GO:0051726 regulation of cell cycle BP

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