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.t1 TSS g13345.t1 29385858 29385858
chr_1 g13345 g13345.t1 isoform g13345.t1 29385956 29387366
chr_1 g13345 g13345.t1 exon g13345.t1.exon1 29385956 29386021
chr_1 g13345 g13345.t1 cds g13345.t1.CDS1 29385956 29386021
chr_1 g13345 g13345.t1 exon g13345.t1.exon2 29386137 29386215
chr_1 g13345 g13345.t1 cds g13345.t1.CDS2 29386137 29386215
chr_1 g13345 g13345.t1 exon g13345.t1.exon3 29386300 29387195
chr_1 g13345 g13345.t1 cds g13345.t1.CDS3 29386300 29387195
chr_1 g13345 g13345.t1 exon g13345.t1.exon4 29387256 29387366
chr_1 g13345 g13345.t1 cds g13345.t1.CDS4 29387256 29387366
chr_1 g13345 g13345.t1 TTS g13345.t1 29387629 29387629

Sequences

>g13345.t1 Gene=g13345 Length=1152
ATGTGGATAACAATCAAGAACTTACAGCAGCAAACAATTAAATTAGAGTTTGATGAATCG
CAAACGGTTCAAAAACTCAAGGAGAAGATTGAATCAGAGTTAGGAAAGGAATATCCAGCA
TCACAACAAAAGCTTATTTATGCAGGATGTATTCTTGACGATGATAAAACCATCGAAAGT
TATAAAGTGGATGAAAAGAAATTCATTGTAGTGATGGTAAAAAAAGCGACTGTTGCAGCA
GCTGCAGCTCCTGAAAAAGAAGAAGCGGGTAAAACAATAACAAATGAATCAACGACTGAA
AAGAAAAAAGAAGACACACCAGCATCAAAATCAACTACGACCGCATCCAGTACCTCATCA
CCCTCTAAAAGCAGTAGTGAACAATCACAGCAACCGGCAGCAGCGCAAGAAACTGCAAGT
GGCGGTGCTGCAGCAAGCCAGTCACAAATTGCCCAAGCAGAAGCCAACTTAGTGATGGGC
GAAAATTATAATACTATGGTTCAAAACATCATGGAAATGGGTTATGATCGTGATTCAGTA
GTTCGCGCTCTAAATGCCAGTTTTAATAATCCCGAGCGAGCAGTAGAATATTTAATCACA
GGAATACCTGAAATGGCTTTACAAGATCGACCAGCGCCAGTTGGTGGAAACGAACAAAGT
GGTGGCGGTGGTGGCAATATTGGTGCTGCTTTGGATCGATCATCGAATTTAGCAAGCAGT
GGTGAAAGTGGTGGTAATGATGAAAGTCCACTTGCCTTCCTTCGAAGACAAGCTCAATTT
CAACAAATGAGAAATGTAATTCAACAAAATCCTGAAATGTTGAATGCTGTTCTACAACAA
ATTGGTCAAACAAATCCAGCACTATTGCAACTTATTTCAGAAAATCAAGAAGCATTTGTT
AACATGCTTAATGAGTCAGAAGATGGTCGTCAAGCGCCTAGTGGTGGAAATGATGATGAT
GATAGAGGAAATTTCGGTGGATTGTTAGACGTAGGTTCTGTGCCCGAATTTACACAACAA
GATCGTGAAGCCATTGAAAGATTAAAGGCACTCGGTTTTCCAGATGAACTGGTTGTTCAA
GCTTACATTGCTTGTGAAAAAAATGAAAATTTGGCCGCCAACTTTTTACTTTCACAGACC
TTTGATGACTAA

>g13345.t1 Gene=g13345 Length=383
MWITIKNLQQQTIKLEFDESQTVQKLKEKIESELGKEYPASQQKLIYAGCILDDDKTIES
YKVDEKKFIVVMVKKATVAAAAAPEKEEAGKTITNESTTEKKKEDTPASKSTTTASSTSS
PSKSSSEQSQQPAAAQETASGGAAASQSQIAQAEANLVMGENYNTMVQNIMEMGYDRDSV
VRALNASFNNPERAVEYLITGIPEMALQDRPAPVGGNEQSGGGGGNIGAALDRSSNLASS
GESGGNDESPLAFLRRQAQFQQMRNVIQQNPEMLNAVLQQIGQTNPALLQLISENQEAFV
NMLNESEDGRQAPSGGNDDDDRGNFGGLLDVGSVPEFTQQDREAIERLKALGFPDELVVQ
AYIACEKNENLAANFLLSQTFDD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g13345.t1 CDD cd01805 Ubl_Rad23 1 72 2.31737E-31
19 g13345.t1 CDD cd14380 UBA2_Rad23 340 378 1.89944E-18
15 g13345.t1 Gene3D G3DSA:3.10.20.90 - 1 78 1.2E-22
18 g13345.t1 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 156 203 7.1E-23
16 g13345.t1 Gene3D G3DSA:1.10.10.540 - 239 306 9.2E-28
17 g13345.t1 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 338 381 1.2E-21
26 g13345.t1 MobiDBLite mobidb-lite consensus disorder prediction 81 147 -
27 g13345.t1 MobiDBLite mobidb-lite consensus disorder prediction 89 108 -
25 g13345.t1 MobiDBLite mobidb-lite consensus disorder prediction 109 147 -
5 g13345.t1 PANTHER PTHR10621 UV EXCISION REPAIR PROTEIN RAD23 1 383 8.2E-106
6 g13345.t1 PANTHER PTHR10621:SF52 RAD23 HOMOLOG A, NUCLEOTIDE EXCISION REPAIR PROTEIN A 1 383 8.2E-106
9 g13345.t1 PRINTS PR01839 DNA repair protein Rad23 signature 277 299 5.8E-27
8 g13345.t1 PRINTS PR01839 DNA repair protein Rad23 signature 335 351 5.8E-27
10 g13345.t1 PRINTS PR01839 DNA repair protein Rad23 signature 352 366 5.8E-27
7 g13345.t1 PRINTS PR01839 DNA repair protein Rad23 signature 367 382 5.8E-27
4 g13345.t1 Pfam PF00240 Ubiquitin family 3 75 1.7E-21
2 g13345.t1 Pfam PF00627 UBA/TS-N domain 163 198 2.3E-14
1 g13345.t1 Pfam PF09280 XPC-binding domain 251 306 6.8E-24
3 g13345.t1 Pfam PF00627 UBA/TS-N domain 341 376 4.2E-11
29 g13345.t1 ProSiteProfiles PS50053 Ubiquitin domain profile. 1 75 20.74
31 g13345.t1 ProSiteProfiles PS50030 Ubiquitin-associated domain (UBA) profile. 158 201 14.619
30 g13345.t1 ProSiteProfiles PS50030 Ubiquitin-associated domain (UBA) profile. 339 379 13.27
23 g13345.t1 SMART SM00213 ubq_7 1 74 4.2E-20
21 g13345.t1 SMART SM00165 uba_6 163 200 6.6E-10
24 g13345.t1 SMART SM00727 CBM 249 292 2.8E-6
22 g13345.t1 SMART SM00165 uba_6 341 378 1.6E-9
11 g13345.t1 SUPERFAMILY SSF54236 Ubiquitin-like 1 80 4.84E-22
13 g13345.t1 SUPERFAMILY SSF46934 UBA-like 141 204 3.78E-14
12 g13345.t1 SUPERFAMILY SSF101238 XPC-binding domain 247 312 2.75E-21
14 g13345.t1 SUPERFAMILY SSF46934 UBA-like 327 382 1.42E-12
28 g13345.t1 TIGRFAM TIGR00601 rad23: UV excision repair protein Rad23 1 383 1.3E-116

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

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