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.t6 TSS g13345.t6 29385858 29385858
chr_1 g13345 g13345.t6 isoform g13345.t6 29386776 29387686
chr_1 g13345 g13345.t6 exon g13345.t6.exon1 29386776 29387195
chr_1 g13345 g13345.t6 cds g13345.t6.CDS1 29386941 29387195
chr_1 g13345 g13345.t6 exon g13345.t6.exon2 29387256 29387585
chr_1 g13345 g13345.t6 cds g13345.t6.CDS2 29387256 29387366
chr_1 g13345 g13345.t6 exon g13345.t6.exon3 29387662 29387686
chr_1 g13345 g13345.t6 TTS g13345.t6 29387787 29387787

Sequences

>g13345.t6 Gene=g13345 Length=775
CAAGATCGACCAGCGCCAGTTGGTGGAAACGAACAAAGTGGTGGCGGTGGTGGCAATATT
GGTGCTGCTTTGGATCGATCATCGAATTTAGCAAGCAGTGGTGAAAGTGGTGGTAATGAT
GAAAGTCCACTTGCCTTCCTTCGAAGACAAGCTCAATTTCAACAAATGAGAAATGTAATT
CAACAAAATCCTGAAATGTTGAATGCTGTTCTACAACAAATTGGTCAAACAAATCCAGCA
CTATTGCAACTTATTTCAGAAAATCAAGAAGCATTTGTTAACATGCTTAATGAGTCAGAA
GATGGTCGTCAAGCGCCTAGTGGTGGAAATGATGATGATGATAGAGGAAATTTCGGTGGA
TTGTTAGACGTAGGTTCTGTGCCCGAATTTACACAACAAGATCGTGAAGCCATTGAAAGA
TTAAAGGCACTCGGTTTTCCAGATGAACTGGTTGTTCAAGCTTACATTGCTTGTGAAAAA
AATGAAAATTTGGCCGCCAACTTTTTACTTTCACAGACCTTTGATGACTAAAAATCTGCT
TCTATGTTTCGCCATCACTGCTTAACTTTCTTTTTTATGATGATAATAATAAAGTTAGAA
AGAGAAGACGAAATTCAACACCAAACAACACTTAAATAATTATCGTGAATTCATCATTAC
TATTGTTGATGGCATAACTATACAGACATCAAATCTTTTTTTTTTCATTTTTCCCTTGTC
AAGACATTGCTTCTTGTACATAAAAAGCAATATAATATTTTGTTAATTATGAACT

>g13345.t6 Gene=g13345 Length=121
MRNVIQQNPEMLNAVLQQIGQTNPALLQLISENQEAFVNMLNESEDGRQAPSGGNDDDDR
GNFGGLLDVGSVPEFTQQDREAIERLKALGFPDELVVQAYIACEKNENLAANFLLSQTFD
D

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g13345.t6 CDD cd14380 UBA2_Rad23 78 116 8.9592E-20
11 g13345.t6 Gene3D G3DSA:1.10.10.540 - 1 45 9.8E-20
12 g13345.t6 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 76 119 1.7E-22
15 g13345.t6 MobiDBLite mobidb-lite consensus disorder prediction 42 65 -
3 g13345.t6 PANTHER PTHR10621 UV EXCISION REPAIR PROTEIN RAD23 1 121 2.4E-39
4 g13345.t6 PANTHER PTHR10621:SF52 RAD23 HOMOLOG A, NUCLEOTIDE EXCISION REPAIR PROTEIN A 1 121 2.4E-39
6 g13345.t6 PRINTS PR01839 DNA repair protein Rad23 signature 15 37 1.8E-28
8 g13345.t6 PRINTS PR01839 DNA repair protein Rad23 signature 73 89 1.8E-28
7 g13345.t6 PRINTS PR01839 DNA repair protein Rad23 signature 90 104 1.8E-28
5 g13345.t6 PRINTS PR01839 DNA repair protein Rad23 signature 105 120 1.8E-28
1 g13345.t6 Pfam PF09280 XPC-binding domain 1 44 7.7E-19
2 g13345.t6 Pfam PF00627 UBA/TS-N domain 79 114 6.7E-12
16 g13345.t6 ProSiteProfiles PS50030 Ubiquitin-associated domain (UBA) profile. 77 117 13.27
14 g13345.t6 SMART SM00165 uba_6 79 116 1.6E-9
9 g13345.t6 SUPERFAMILY SSF101238 XPC-binding domain 1 51 3.01E-17
10 g13345.t6 SUPERFAMILY SSF46934 UBA-like 64 120 2.01E-13

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