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.t2 TSS g13345.t2 29385858 29385858
chr_1 g13345 g13345.t2 isoform g13345.t2 29385956 29387186
chr_1 g13345 g13345.t2 exon g13345.t2.exon1 29385956 29386021
chr_1 g13345 g13345.t2 cds g13345.t2.CDS1 29385956 29386021
chr_1 g13345 g13345.t2 exon g13345.t2.exon2 29386137 29386215
chr_1 g13345 g13345.t2 cds g13345.t2.CDS2 29386137 29386215
chr_1 g13345 g13345.t2 exon g13345.t2.exon3 29386300 29387186
chr_1 g13345 g13345.t2 cds g13345.t2.CDS3 29386300 29387186
chr_1 g13345 g13345.t2 TTS g13345.t2 29387629 29387629

Sequences

>g13345.t2 Gene=g13345 Length=1032
ATGTGGATAACAATCAAGAACTTACAGCAGCAAACAATTAAATTAGAGTTTGATGAATCG
CAAACGGTTCAAAAACTCAAGGAGAAGATTGAATCAGAGTTAGGAAAGGAATATCCAGCA
TCACAACAAAAGCTTATTTATGCAGGATGTATTCTTGACGATGATAAAACCATCGAAAGT
TATAAAGTGGATGAAAAGAAATTCATTGTAGTGATGGTAAAAAAAGCGACTGTTGCAGCA
GCTGCAGCTCCTGAAAAAGAAGAAGCGGGTAAAACAATAACAAATGAATCAACGACTGAA
AAGAAAAAAGAAGACACACCAGCATCAAAATCAACTACGACCGCATCCAGTACCTCATCA
CCCTCTAAAAGCAGTAGTGAACAATCACAGCAACCGGCAGCAGCGCAAGAAACTGCAAGT
GGCGGTGCTGCAGCAAGCCAGTCACAAATTGCCCAAGCAGAAGCCAACTTAGTGATGGGC
GAAAATTATAATACTATGGTTCAAAACATCATGGAAATGGGTTATGATCGTGATTCAGTA
GTTCGCGCTCTAAATGCCAGTTTTAATAATCCCGAGCGAGCAGTAGAATATTTAATCACA
GGAATACCTGAAATGGCTTTACAAGATCGACCAGCGCCAGTTGGTGGAAACGAACAAAGT
GGTGGCGGTGGTGGCAATATTGGTGCTGCTTTGGATCGATCATCGAATTTAGCAAGCAGT
GGTGAAAGTGGTGGTAATGATGAAAGTCCACTTGCCTTCCTTCGAAGACAAGCTCAATTT
CAACAAATGAGAAATGTAATTCAACAAAATCCTGAAATGTTGAATGCTGTTCTACAACAA
ATTGGTCAAACAAATCCAGCACTATTGCAACTTATTTCAGAAAATCAAGAAGCATTTGTT
AACATGCTTAATGAGTCAGAAGATGGTCGTCAAGCGCCTAGTGGTGGAAATGATGATGAT
GATAGAGGAAATTTCGGTGGATTGTTAGACGTAGGTTCTGTGCCCGAATTTACACAACAA
GATCGTGAAGCC

>g13345.t2 Gene=g13345 Length=344
MWITIKNLQQQTIKLEFDESQTVQKLKEKIESELGKEYPASQQKLIYAGCILDDDKTIES
YKVDEKKFIVVMVKKATVAAAAAPEKEEAGKTITNESTTEKKKEDTPASKSTTTASSTSS
PSKSSSEQSQQPAAAQETASGGAAASQSQIAQAEANLVMGENYNTMVQNIMEMGYDRDSV
VRALNASFNNPERAVEYLITGIPEMALQDRPAPVGGNEQSGGGGGNIGAALDRSSNLASS
GESGGNDESPLAFLRRQAQFQQMRNVIQQNPEMLNAVLQQIGQTNPALLQLISENQEAFV
NMLNESEDGRQAPSGGNDDDDRGNFGGLLDVGSVPEFTQQDREA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g13345.t2 CDD cd01805 Ubl_Rad23 1 72 1.2011E-31
11 g13345.t2 Gene3D G3DSA:3.10.20.90 - 1 78 9.9E-23
13 g13345.t2 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 156 203 6.1E-23
12 g13345.t2 Gene3D G3DSA:1.10.10.540 - 239 306 7.8E-28
20 g13345.t2 MobiDBLite mobidb-lite consensus disorder prediction 81 147 -
21 g13345.t2 MobiDBLite mobidb-lite consensus disorder prediction 89 108 -
19 g13345.t2 MobiDBLite mobidb-lite consensus disorder prediction 109 147 -
18 g13345.t2 MobiDBLite mobidb-lite consensus disorder prediction 305 344 -
4 g13345.t2 PANTHER PTHR10621:SF53 RAD23 HOMOLOG B, NUCLEOTIDE EXCISION REPAIR PROTEIN 1 317 2.0E-80
5 g13345.t2 PANTHER PTHR10621 UV EXCISION REPAIR PROTEIN RAD23 1 317 2.0E-80
7 g13345.t2 PRINTS PR01839 DNA repair protein Rad23 signature 277 299 1.7E-7
6 g13345.t2 PRINTS PR01839 DNA repair protein Rad23 signature 335 344 1.7E-7
3 g13345.t2 Pfam PF00240 Ubiquitin family 3 75 1.4E-21
2 g13345.t2 Pfam PF00627 UBA/TS-N domain 163 198 2.0E-14
1 g13345.t2 Pfam PF09280 XPC-binding domain 251 306 5.8E-24
23 g13345.t2 ProSiteProfiles PS50053 Ubiquitin domain profile. 1 75 20.74
24 g13345.t2 ProSiteProfiles PS50030 Ubiquitin-associated domain (UBA) profile. 158 201 14.619
16 g13345.t2 SMART SM00213 ubq_7 1 74 4.2E-20
15 g13345.t2 SMART SM00165 uba_6 163 200 6.6E-10
17 g13345.t2 SMART SM00727 CBM 249 292 2.8E-6
8 g13345.t2 SUPERFAMILY SSF54236 Ubiquitin-like 1 80 4.14E-22
10 g13345.t2 SUPERFAMILY SSF46934 UBA-like 141 204 3.57E-14
9 g13345.t2 SUPERFAMILY SSF101238 XPC-binding domain 247 312 2.35E-21
22 g13345.t2 TIGRFAM TIGR00601 rad23: UV excision repair protein Rad23 1 342 3.2E-91

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