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.t5 TSS g13345.t5 29385858 29385858
chr_1 g13345 g13345.t5 isoform g13345.t5 29386776 29387686
chr_1 g13345 g13345.t5 exon g13345.t5.exon1 29386776 29387195
chr_1 g13345 g13345.t5 cds g13345.t5.CDS1 29386941 29387195
chr_1 g13345 g13345.t5 exon g13345.t5.exon2 29387262 29387686
chr_1 g13345 g13345.t5 cds g13345.t5.CDS2 29387262 29387366
chr_1 g13345 g13345.t5 TTS g13345.t5 29387787 29387787

Sequences

>g13345.t5 Gene=g13345 Length=845
CAAGATCGACCAGCGCCAGTTGGTGGAAACGAACAAAGTGGTGGCGGTGGTGGCAATATT
GGTGCTGCTTTGGATCGATCATCGAATTTAGCAAGCAGTGGTGAAAGTGGTGGTAATGAT
GAAAGTCCACTTGCCTTCCTTCGAAGACAAGCTCAATTTCAACAAATGAGAAATGTAATT
CAACAAAATCCTGAAATGTTGAATGCTGTTCTACAACAAATTGGTCAAACAAATCCAGCA
CTATTGCAACTTATTTCAGAAAATCAAGAAGCATTTGTTAACATGCTTAATGAGTCAGAA
GATGGTCGTCAAGCGCCTAGTGGTGGAAATGATGATGATGATAGAGGAAATTTCGGTGGA
TTGTTAGACGTAGGTTCTGTGCCCGAATTTACACAACAAGATCGTGAAGCCATTGAAAGA
GCACTCGGTTTTCCAGATGAACTGGTTGTTCAAGCTTACATTGCTTGTGAAAAAAATGAA
AATTTGGCCGCCAACTTTTTACTTTCACAGACCTTTGATGACTAAAAATCTGCTTCTATG
TTTCGCCATCACTGCTTAACTTTCTTTTTTATGATGATAATAATAAAGTTAGAAAGAGAA
GACGAAATTCAACACCAAACAACACTTAAATAATTATCGTGAATTCATCATTACTATTGT
TGATGGCATAACTATACAGACATCAAATCTTTTTTTTTTCATTTTTCCCTTGTCAAGACA
TTGCTTCTTGTACATAAAAAGCAAGAAAAAGAACTTGATATAAATATGCTCACACATACA
CATACTACACACATGCATCTTTTGCTCTATGTTTTTATTTTATAATATTTTGTTAATTAT
GAACT

>g13345.t5 Gene=g13345 Length=119
MRNVIQQNPEMLNAVLQQIGQTNPALLQLISENQEAFVNMLNESEDGRQAPSGGNDDDDR
GNFGGLLDVGSVPEFTQQDREAIERALGFPDELVVQAYIACEKNENLAANFLLSQTFDD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g13345.t5 Gene3D G3DSA:1.10.10.540 - 1 45 9.4E-20
11 g13345.t5 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 76 117 2.5E-18
13 g13345.t5 MobiDBLite mobidb-lite consensus disorder prediction 42 65 -
3 g13345.t5 PANTHER PTHR10621 UV EXCISION REPAIR PROTEIN RAD23 1 119 2.5E-35
4 g13345.t5 PANTHER PTHR10621:SF52 RAD23 HOMOLOG A, NUCLEOTIDE EXCISION REPAIR PROTEIN A 1 119 2.5E-35
7 g13345.t5 PRINTS PR01839 DNA repair protein Rad23 signature 15 37 2.1E-21
6 g13345.t5 PRINTS PR01839 DNA repair protein Rad23 signature 88 102 2.1E-21
5 g13345.t5 PRINTS PR01839 DNA repair protein Rad23 signature 103 118 2.1E-21
1 g13345.t5 Pfam PF09280 XPC-binding domain 1 44 7.4E-19
2 g13345.t5 Pfam PF00627 UBA/TS-N domain 86 112 8.8E-8
14 g13345.t5 ProSiteProfiles PS50030 Ubiquitin-associated domain (UBA) profile. 87 115 9.125
12 g13345.t5 SMART SM00165 uba_6 79 114 1.8E-4
8 g13345.t5 SUPERFAMILY SSF101238 XPC-binding domain 1 51 2.88E-17
9 g13345.t5 SUPERFAMILY SSF46934 UBA-like 64 118 1.53E-9

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