Gene loci information

Transcript annotation

  • This transcript has been annotated as X-ray repair cross-complementing protein 5.

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_1 g9372 g9372.t1 TSS g9372.t1 2288982 2288982
chr_1 g9372 g9372.t1 isoform g9372.t1 2289145 2291380
chr_1 g9372 g9372.t1 exon g9372.t1.exon1 2289145 2289162
chr_1 g9372 g9372.t1 cds g9372.t1.CDS1 2289145 2289162
chr_1 g9372 g9372.t1 exon g9372.t1.exon2 2289223 2289572
chr_1 g9372 g9372.t1 cds g9372.t1.CDS2 2289223 2289572
chr_1 g9372 g9372.t1 exon g9372.t1.exon3 2289631 2291380
chr_1 g9372 g9372.t1 cds g9372.t1.CDS3 2289631 2291380
chr_1 g9372 g9372.t1 TTS g9372.t1 2291443 2291443

Sequences

>g9372.t1 Gene=g9372 Length=2118
ATGTCAAGAACACAAAGGGAAGCTCTTGTGATTATAATTGATGTTGGTGCAAATACAACA
GCTCTATCAGGAAAAAGCGGCAAGACATTCTTTGAAAGAGCAAAAGAATGCGCTAAGAAA
ATTATTTTAAGAAGAATTTTAACAAAACCTGAAGATGAAATTGGTGTAATTTTATTTGGC
ACTGGTGAGACAAAGAATGATTTAAATTCGTCTGATTTAGGCTTTGAGAATATTGTTGAA
ATGGATTTTCTTCAATGTGGCACATGGAAATTAGTCAAAGCACTTGATAATGTTAAACCG
GGAAATGCAACTTGTGATTGGATTGATGCTTTACTTGTTGGCATTAATTACATTAAAAAT
GAAACTGGAGCCAAAAACTTTTGCAAAACTCGCATCATTTTGATAACAAATTTTCAAGTT
GAGGCACACGATGATGAATTGAACGTTGTTGCAGCAAATATCAGTGATAATATGATTGAG
TTGATTGGAGTATCAGATACTGTTCAATATGAAAATAGCAACACTAATTTAACAAGTTGC
CAATTTACACAAAATCCAAACAAAGAAGAAGCTCAAAGCAAGAGTGAAAAAATATTTCAA
GAACTAATTGATCAAATTGAAGATGCAAATTTGTGTCATATCGATTATGTCGAATCTCAA
TTAGCACTTTTTCAAAAGAAAACTACCCGTGCGATGCCATGGAATGCAACTTTATCAATT
GGAAGTCAGTTGTTGATTGAAATTAGTGCATTCGTTTATATTCAAGATGAAAAATTTTTT
GGGAGCTTTAAAACTGAATGTCTCGATCAATTTACTGCTACGAGAATGGTCACAGAATAT
TACAGAAATAATGAGACGATTGAAAAGCCTGATGAAGATGATGTGGTAAAAGCATATATG
TACGGTTCTAAATTCATTGCGATTGATGATCAAGATCTTGCTTACAAAGGAGGAAAAAAA
TGTCTTGCATGCCTAGCATTCTGTAAACGTGATAAAATTCCTCAAGAATATTTCATTGGT
GATGGATGTCACATTGTTGTACCTCAAAAAGATTCAGAGAGAAGTGAAACTCTCTTTTCT
TTATTGGTTCAAGCAATGGCTGTCCGCAATTATCTTATGCTTGCAAGAAAAGTATATCGT
GATGACATAAAACCACAAATTGTTGCTCTTATTCCCCAAATTGAGGATGAAACAAATTAT
TTAATGATGTATGAATTGCCTTATTACGAAGATGTTGAATTCTTTTCCTTTCCAACTCTT
GATCAAATATCAACAAAACCAACTGATCAACAAATGGAAGCAATGAACGAACTTGTTGAA
TTGATGGATTTAACTGATGCAATTGATGATGAAACAGGAATTACTGAAGCATTTACACAA
GATACAATGCAAAATCCTTATCATCAAAATGTATGCAAATCAGTTGCTTATCGTGCACTT
AATCCTACTGAACCTCTGCCACCGATCGACAAAGACTTGTTGAAATTGATTGATACACCA
GAGAAAATCAAACAACGTATTGAAAGTTTTATTATACAATTTGAAGATTTCTTTCCAAGA
GAAATTATACAACGCAAAGATAGAAAGAAACCACTTGGTCAATTACAAAAGGATGGTGAT
ACTGCTATTGATGATACTGAAATTTATGATCATTTGTCATCTGAAAGAACTATAGTTGCC
ATTGGAACAGTAACACCAGCCGAAGATTTTCTTTATTTGCTTAAAAAAGGCGAACGTTTC
AGTGTTTTGTGTGAACAAATGCAATCAATTATTTATGAATACATTTTCAAAAGTATGACA
AAGTTTGAAGATATGGCTGATAAGATAAAGGAAACCATCTTGGCATTTCGTGAGGCAGCA
ACTATTCATGCACCTTTAAATTACAATAAATGGATTGCTGAATTGAAGGCTATGATGACC
AAACGAAATAAAATTGATGAATGGAACTTACTTATCGTAAAAGAAGGCTTAGGTCTAATT
TCACAAAATGAATCGCCTATGTCGACAATTGCACTCGATGAACAAGTTGCATTTTATGAA
ATTATTTCAAAAAATTCATCACGCAATTTCACATCAATTGCTTTAGAAGAAGAAGACGAT
CTTGCTGCATTATTGTAA

>g9372.t1 Gene=g9372 Length=705
MSRTQREALVIIIDVGANTTALSGKSGKTFFERAKECAKKIILRRILTKPEDEIGVILFG
TGETKNDLNSSDLGFENIVEMDFLQCGTWKLVKALDNVKPGNATCDWIDALLVGINYIKN
ETGAKNFCKTRIILITNFQVEAHDDELNVVAANISDNMIELIGVSDTVQYENSNTNLTSC
QFTQNPNKEEAQSKSEKIFQELIDQIEDANLCHIDYVESQLALFQKKTTRAMPWNATLSI
GSQLLIEISAFVYIQDEKFFGSFKTECLDQFTATRMVTEYYRNNETIEKPDEDDVVKAYM
YGSKFIAIDDQDLAYKGGKKCLACLAFCKRDKIPQEYFIGDGCHIVVPQKDSERSETLFS
LLVQAMAVRNYLMLARKVYRDDIKPQIVALIPQIEDETNYLMMYELPYYEDVEFFSFPTL
DQISTKPTDQQMEAMNELVELMDLTDAIDDETGITEAFTQDTMQNPYHQNVCKSVAYRAL
NPTEPLPPIDKDLLKLIDTPEKIKQRIESFIIQFEDFFPREIIQRKDRKKPLGQLQKDGD
TAIDDTEIYDHLSSERTIVAIGTVTPAEDFLYLLKKGERFSVLCEQMQSIIYEYIFKSMT
KFEDMADKIKETILAFREAATIHAPLNYNKWIAELKAMMTKRNKIDEWNLLIVKEGLGLI
SQNESPMSTIALDEQVAFYEIISKNSSRNFTSIALEEEDDLAALL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g9372.t1 CDD cd00873 KU80 233 515 0
11 g9372.t1 Gene3D G3DSA:3.40.50.410 - 2 229 0
12 g9372.t1 Gene3D G3DSA:2.40.290.10 - 230 423 0
10 g9372.t1 Gene3D G3DSA:1.10.1600.10 - 425 526 0
13 g9372.t1 Gene3D G3DSA:1.25.40.240 - 556 690 0
4 g9372.t1 PANTHER PTHR12604 KU AUTOANTIGEN DNA HELICASE 6 668 0
5 g9372.t1 PANTHER PTHR12604:SF4 X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 5 6 668 0
3 g9372.t1 Pfam PF03731 Ku70/Ku80 N-terminal alpha/beta domain 8 172 0
1 g9372.t1 Pfam PF02735 Ku70/Ku80 beta-barrel domain 240 433 0
2 g9372.t1 Pfam PF08785 Ku C terminal domain like 565 679 0
9 g9372.t1 SMART SM00559 ku_4 287 423 0
8 g9372.t1 SUPERFAMILY SSF53300 vWA-like 6 166 0
6 g9372.t1 SUPERFAMILY SSF100939 SPOC domain-like 230 512 0
7 g9372.t1 SUPERFAMILY SSF101420 C-terminal domain of Ku80 554 679 0

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:0043564 Ku70:Ku80 complex CC
GO:0005634 nucleus CC
GO:0003677 DNA binding MF
GO:0042162 telomeric DNA binding MF
GO:0003684 damaged DNA binding MF
GO:0006303 double-strand break repair via nonhomologous end joining BP
GO:0006310 DNA recombination BP
GO:0000723 telomere maintenance 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