Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA damage-binding protein 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 g1181 g1181.t1 TSS g1181.t1 8508335 8508335
chr_3 g1181 g1181.t1 isoform g1181.t1 8508409 8512285
chr_3 g1181 g1181.t1 exon g1181.t1.exon1 8508409 8508469
chr_3 g1181 g1181.t1 cds g1181.t1.CDS1 8508409 8508469
chr_3 g1181 g1181.t1 exon g1181.t1.exon2 8508626 8508774
chr_3 g1181 g1181.t1 cds g1181.t1.CDS2 8508626 8508774
chr_3 g1181 g1181.t1 exon g1181.t1.exon3 8508831 8511384
chr_3 g1181 g1181.t1 cds g1181.t1.CDS3 8508831 8511384
chr_3 g1181 g1181.t1 exon g1181.t1.exon4 8511442 8511631
chr_3 g1181 g1181.t1 cds g1181.t1.CDS4 8511442 8511631
chr_3 g1181 g1181.t1 exon g1181.t1.exon5 8511692 8512008
chr_3 g1181 g1181.t1 cds g1181.t1.CDS5 8511692 8512008
chr_3 g1181 g1181.t1 exon g1181.t1.exon6 8512066 8512145
chr_3 g1181 g1181.t1 cds g1181.t1.CDS6 8512066 8512145
chr_3 g1181 g1181.t1 exon g1181.t1.exon7 8512205 8512285
chr_3 g1181 g1181.t1 cds g1181.t1.CDS7 8512205 8512285
chr_3 g1181 g1181.t1 TTS g1181.t1 NA NA

Sequences

>g1181.t1 Gene=g1181 Length=3432
ATGGCTCACAATTACATTGTGACAGCTCAAAAGCCGACAGCAGTTAATGCTTGCGTCACA
GGAAATTTCACATCAGAGACAGATTTAAATTTAGTTATTGCAAAAAACTCGAGACTAGAG
ATTTTCTTAGTAACTCCTGAAGGTCTAAAGCCGATCAAAGAAGTTGGAATTTATGGAAAA
ATTGCCGTTCTTAAATTGTTTCGGCCTGCGGATGAGAAAAAAGATCTCATTTTCATACTT
ACGCAAGCCTATCAAGCTATGATTCTTGAATGTAAATACAACAAAGAGCGCGAAGATTTT
GAGATAATTACAAAAGCGTGCGGAAATGTTAGCGATAAAGTAGGAAAACCAGCAGAGACT
GGCATTTTAGCTGTTATAGATCCAAAGGCACGTGTTATAGGTATGAGACTATATGAAGGA
CTTTTTAAAATAATTCCTCTTGAAAAGGACAGTAATGAACTTAAAGCATATAGTCTGCGA
ATGGAAGATGTAAATGTGCAAGACGTTGAATTTCTTTATGGATGTGCATCACCAACACTG
ATAGTTATACATCAAGATTTAAATGGCCGTCATATAAAGTCTCATGAAATCAGTTTACGT
GAAAAAGAATTTGTTAAAATGAGCTGGAAACAAGAAAATGTAGAGACTGAAGCAACGATG
TTGATTCCTGTTCCCACACCTCTTGGCGGAGCGATTGTAATTGGACAAGAATCGATAGTT
TATCATGATGGCTCAAATTATGTAGCATCAGCTCCACCGATTATAAAACAAAGCACAATC
ACTTGTTATGCTCGTGTTGATAGGAAGGGCTATCGATATTTGCTTGGAAATATGTCTGGA
AATTTATTCATGCTCTTTCTGGAGGCTGACACAAATTCTCAAGGCAATTTATATGTTAAA
GATCTCAAAGTTGAACTTCTTGGTGAAATTTCAATACCTGAATGCATCACTTACCTTGAT
AATGGAGTTTTATTTATCGGATCACGTCATGGAGATTCGCAATTGGTGAGATTAAACACA
GTTCCAGATGAAAATGGAGCCTATGTTGTAGTGATGGATACTTATACTAACCTCGGACCG
ATTCTTGATATGTGTGTAGTTGATCTCGAAAGGCAAGGGCAAGGTCAAATAATTACATGT
AGTGGATCTTTTAAAGATGGCACATTAAGAATTATTAGAAATGGTATTGGGATACAAGAG
CATGCATGCATTGATTTACCTGGAATAAAAGGTATGTGGGCGTTACAAGTGGGCATAGAC
GATTCAAAATACGATAATACACTTGTTCTCTCATTCGTTGGTCATACAAGAATTCTTACA
TTGACGGGAGAGGAAGTTGAAGAAACTGAAATTGAAGGTTTTCTAAGTGATCAACAAACA
TTTTATTGTGCGAATGTCAATTATGGTCAAATTATACAAGTTACGCCATCAACCGCAAGA
GTTATTAAATGCGATAGTAAATCAATGGTTGCAGAATGGAGTCCACCAGAGGGAAGAAGA
ATTGGCGTTGTTGCATGCAATAATGAACAACTTGTTTGTGCATCAGGTACAGAAATTTAT
TATATTGAAATTCAAGATGGAAAATTAGAACAAAAATCTACCGTTCAACTGGAACATGAA
ATTGCATGTCTGGATATATCACCACTCGATGAAGGAGCTACTCGTTCTGATATTGTTGCA
GTTGGTTTATGGACAGACATCTCAGTGTGTCTTCTTAAATTACCATCACTGGAAAAATTC
TACACAGAAAAACTCGGTGGAGAAATAATACCGAGATCCATATTAGTAGCACAGTTTGAA
GGCATAAATTATCTACTATGTGCACTCGGTGATGGTTCAATGTTTTATTTTGTTTACGAT
AATGAATCTGGCGTTTTAACAGACCAAAAGAAAGTAACTTTAGGTACACAACCGACAATT
TTAAAAACCTTCAGTTCACTATCAACAAGAAATGTTTTTGCATGTAGTGATCGACCAACA
GTTATATATTCTTCAAATCACAAATTGGTTTTTAGTAATGTTAATTTGAAGGAAGTAAAT
CACATGTGCTCTTTAAATGCTGAAGCATATCCCGACAGTTTAGCGTTAGCAACGAAAAAT
TCTGTCATTTTGGGGACAATTGATGAAATACAAAAATTGCATATTAGAACAGTTCAGCTT
GGTGAGAGTCCAAGAAGAATTGCTCATCAAGAAGCATCAAATTCATTTGGTGTGATTTCT
GTCAGGACAGATGTTCAAAAAAGTGAAGGTTTGTTGCCAACAAGGCCATCGGCTTCAACT
CAAACCCAAAATATTACGACATCAAGTACTATTACAACATTAGCTCAGCGACCAGGTGTA
TGCACTCAAGTAGAATTTGGTCAAGAAGTGGAAGTTAACAATCTATTAATTATGGACCAA
AATACTTTTGAAGTACTTCATGCACATCAGTTTATGCAAACAGAATTTGCTATGTCACTC
ATGTCTGCAAAATTAGGTGATGATCCAAACACTTATTATATTGTTGGAACTGCAATTGTC
AATCCCGAAGAACCGGATCCAAAAACTGGCCGAATAATTGTTTTTCATTATGCAGATGGG
AAACTACATCAAATTTGTGAAAAGGAAATTAAAGGTGCATGTTATTCACTTGTAGAATTT
AATGGTAAAGTTCTTGCCAGTATCAATACTACTGTACGTTTATATGAATGGACTTCTGAA
AAAGACCTCAGATTAGAGTGCAGTCATTTTAATAATGTGCTGGCACTTTACTTAAAAACA
AAAGGTGATTTTATACTGGTTGGAGATTTAATGCGTTCAATAACATTGCTACAATACAAA
CAAATGGAAGGAAGTTTTGAAGAGATTGCAAGAGATTATGAACCAAATTGGATGACAGCC
ATTGAAATTCTTGATGATGACAACTTTTTAGGAGCTGAAAATTCTTGTAATTTGTTTGTT
GGACAAAAAGATAGTGCTGCAACAACCGATGAAGAAAGACAACAAATGCCAGAAGTTGCA
CAATTTCATCTTGGCGATATGATTAACGTTTTCCGACACGGTTCACTTGCAATGCAAAAT
GTTGGTGAACGAACAACACCAACGACTGGTTGTGTGCTTTATGGAACAGTCAGTGGAGCA
ATTGGATTAGTTACACAAATACCTCAAGATTTTTACGAATTTCTGAGCTTCCTTGAAAAG
CGTCTTAAAGAAACGATCAAGTCAGTTGGTAAAATTGATCATACGTCATGGAGAAGTTTT
AGAACAGATCAAAAAGTAGAACCATGCGAAGGATTTATTGATGGAGATCTCGTTGAAAGT
TTTTTAGATTTGAGTCGCGATAAAATGCGAGAATGTGTTGCCGGTTTGCAAATTGATGTT
AATGGTGTTAAAGAGGAGGCTACAGTAGATAATGTCATCAAAATCGTTGAAGATCTTACG
AGAATGCATTAA

>g1181.t1 Gene=g1181 Length=1143
MAHNYIVTAQKPTAVNACVTGNFTSETDLNLVIAKNSRLEIFLVTPEGLKPIKEVGIYGK
IAVLKLFRPADEKKDLIFILTQAYQAMILECKYNKEREDFEIITKACGNVSDKVGKPAET
GILAVIDPKARVIGMRLYEGLFKIIPLEKDSNELKAYSLRMEDVNVQDVEFLYGCASPTL
IVIHQDLNGRHIKSHEISLREKEFVKMSWKQENVETEATMLIPVPTPLGGAIVIGQESIV
YHDGSNYVASAPPIIKQSTITCYARVDRKGYRYLLGNMSGNLFMLFLEADTNSQGNLYVK
DLKVELLGEISIPECITYLDNGVLFIGSRHGDSQLVRLNTVPDENGAYVVVMDTYTNLGP
ILDMCVVDLERQGQGQIITCSGSFKDGTLRIIRNGIGIQEHACIDLPGIKGMWALQVGID
DSKYDNTLVLSFVGHTRILTLTGEEVEETEIEGFLSDQQTFYCANVNYGQIIQVTPSTAR
VIKCDSKSMVAEWSPPEGRRIGVVACNNEQLVCASGTEIYYIEIQDGKLEQKSTVQLEHE
IACLDISPLDEGATRSDIVAVGLWTDISVCLLKLPSLEKFYTEKLGGEIIPRSILVAQFE
GINYLLCALGDGSMFYFVYDNESGVLTDQKKVTLGTQPTILKTFSSLSTRNVFACSDRPT
VIYSSNHKLVFSNVNLKEVNHMCSLNAEAYPDSLALATKNSVILGTIDEIQKLHIRTVQL
GESPRRIAHQEASNSFGVISVRTDVQKSEGLLPTRPSASTQTQNITTSSTITTLAQRPGV
CTQVEFGQEVEVNNLLIMDQNTFEVLHAHQFMQTEFAMSLMSAKLGDDPNTYYIVGTAIV
NPEEPDPKTGRIIVFHYADGKLHQICEKEIKGACYSLVEFNGKVLASINTTVRLYEWTSE
KDLRLECSHFNNVLALYLKTKGDFILVGDLMRSITLLQYKQMEGSFEEIARDYEPNWMTA
IEILDDDNFLGAENSCNLFVGQKDSAATTDEERQQMPEVAQFHLGDMINVFRHGSLAMQN
VGERTTPTTGCVLYGTVSGAIGLVTQIPQDFYEFLSFLEKRLKETIKSVGKIDHTSWRSF
RTDQKVEPCEGFIDGDLVESFLDLSRDKMRECVAGLQIDVNGVKEEATVDNVIKIVEDLT
RMH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g1181.t1 Gene3D G3DSA:2.130.10.10 - 5 1019 0.0e+00
9 g1181.t1 Gene3D G3DSA:2.130.10.10 - 14 357 0.0e+00
11 g1181.t1 Gene3D G3DSA:2.130.10.10 - 396 712 0.0e+00
12 g1181.t1 Gene3D G3DSA:3.30.980.30 - 1048 1143 0.0e+00
3 g1181.t1 PANTHER PTHR10644:SF20 DNA DAMAGE-BINDING PROTEIN 1B 3 746 0.0e+00
5 g1181.t1 PANTHER PTHR10644 DNA REPAIR/RNA PROCESSING CPSF FAMILY 3 746 0.0e+00
4 g1181.t1 PANTHER PTHR10644:SF20 DNA DAMAGE-BINDING PROTEIN 1B 787 1139 0.0e+00
6 g1181.t1 PANTHER PTHR10644 DNA REPAIR/RNA PROCESSING CPSF FAMILY 787 1139 0.0e+00
1 g1181.t1 Pfam PF10433 Mono-functional DNA-alkylating methyl methanesulfonate N-term 75 546 0.0e+00
2 g1181.t1 Pfam PF03178 CPSF A subunit region 795 1103 0.0e+00
8 g1181.t1 SUPERFAMILY SSF50998 Quinoprotein alcohol dehydrogenase-like 291 937 3.0e-07
7 g1181.t1 SUPERFAMILY SSF69322 Tricorn protease domain 2 456 661 6.9e-06

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:0005634 nucleus CC
GO:0005515 protein binding MF
GO:0003676 nucleic acid 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