Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative UV excision repair protein RAD23 homolog B.

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 g13345 g13345.t4 TSS g13345.t4 29385858 29385858
chr_1 g13345 g13345.t4 isoform g13345.t4 29386455 29387186
chr_1 g13345 g13345.t4 exon g13345.t4.exon1 29386455 29387186
chr_1 g13345 g13345.t4 cds g13345.t4.CDS1 29386629 29387186
chr_1 g13345 g13345.t4 TTS g13345.t4 29387629 29387629

Sequences

>g13345.t4 Gene=g13345 Length=732
AAGAAAAAAGAAGACACACCAGCATCAAAATCAACTACGACCGCATCCAGTACCTCATCA
CCCTCTAAAAGCAGTAGTGAACAATCACAGCAACCGGCAGCAGCGCAAGAAACTGCAAGT
GGCGGTGCTGCAGCAAGCCAGTCACAAATTGCCCAAGCAGAAGCCAACTTAGTGATGGGC
GAAAATTATAATACTATGGTTCAAAACATCATGGAAATGGGTTATGATCGTGATTCAGTA
GTTCGCGCTCTAAATGCCAGTTTTAATAATCCCGAGCGAGCAGTAGAATATTTAATCACA
GGAATACCTGAAATGGCTTTACAAGATCGACCAGCGCCAGTTGGTGGAAACGAACAAAGT
GGTGGCGGTGGTGGCAATATTGGTGCTGCTTTGGATCGATCATCGAATTTAGCAAGCAGT
GGTGAAAGTGGTGGTAATGATGAAAGTCCACTTGCCTTCCTTCGAAGACAAGCTCAATTT
CAACAAATGAGAAATGTAATTCAACAAAATCCTGAAATGTTGAATGCTGTTCTACAACAA
ATTGGTCAAACAAATCCAGCACTATTGCAACTTATTTCAGAAAATCAAGAAGCATTTGTT
AACATGCTTAATGAGTCAGAAGATGGTCGTCAAGCGCCTAGTGGTGGAAATGATGATGAT
GATAGAGGAAATTTCGGTGGATTGTTAGACGTAGGTTCTGTGCCCGAATTTACACAACAA
GATCGTGAAGCC

>g13345.t4 Gene=g13345 Length=186
MGENYNTMVQNIMEMGYDRDSVVRALNASFNNPERAVEYLITGIPEMALQDRPAPVGGNE
QSGGGGGNIGAALDRSSNLASSGESGGNDESPLAFLRRQAQFQQMRNVIQQNPEMLNAVL
QQIGQTNPALLQLISENQEAFVNMLNESEDGRQAPSGGNDDDDRGNFGGLLDVGSVPEFT
QQDREA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g13345.t4 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 1 45 5.3E-22
9 g13345.t4 Gene3D G3DSA:1.10.10.540 - 81 148 2.5E-28
13 g13345.t4 MobiDBLite mobidb-lite consensus disorder prediction 147 186 -
3 g13345.t4 PANTHER PTHR10621 UV EXCISION REPAIR PROTEIN RAD23 2 186 2.0E-42
4 g13345.t4 PANTHER PTHR10621:SF52 RAD23 HOMOLOG A, NUCLEOTIDE EXCISION REPAIR PROTEIN A 2 186 2.0E-42
5 g13345.t4 PRINTS PR01839 DNA repair protein Rad23 signature 119 141 6.5E-8
6 g13345.t4 PRINTS PR01839 DNA repair protein Rad23 signature 177 186 6.5E-8
2 g13345.t4 Pfam PF00627 UBA/TS-N domain 5 40 8.0E-15
1 g13345.t4 Pfam PF09280 XPC-binding domain 93 148 2.0E-24
14 g13345.t4 ProSiteProfiles PS50030 Ubiquitin-associated domain (UBA) profile. 1 43 15.029
11 g13345.t4 SMART SM00165 uba_6 5 42 6.6E-10
12 g13345.t4 SMART SM00727 CBM 91 134 2.8E-6
8 g13345.t4 SUPERFAMILY SSF46934 UBA-like 3 47 1.82E-13
7 g13345.t4 SUPERFAMILY SSF101238 XPC-binding domain 89 154 7.72E-22

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:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process BP
GO:0005515 protein binding MF
GO:0003684 damaged DNA binding MF
GO:0006289 nucleotide-excision repair 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