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.t3 TSS g13345.t3 29385858 29385858
chr_1 g13345 g13345.t3 isoform g13345.t3 29385956 29387366
chr_1 g13345 g13345.t3 exon g13345.t3.exon1 29385956 29387195
chr_1 g13345 g13345.t3 cds g13345.t3.CDS1 29386251 29387195
chr_1 g13345 g13345.t3 exon g13345.t3.exon2 29387256 29387366
chr_1 g13345 g13345.t3 cds g13345.t3.CDS2 29387256 29387366
chr_1 g13345 g13345.t3 TTS g13345.t3 29387629 29387629

Sequences

>g13345.t3 Gene=g13345 Length=1351
ATGTGGATAACAATCAAGAACTTACAGCAGCAAACAATTAAATTAGAGTTTGATGAATCG
CAAACGGTAAGTAATCAAATATCGGTCAAAATGCAAATTCCATAAGCATGTGAAAAAATA
AATTTAAAATGTTATTTTGATCTCATTATTCTTCTTTCTATTCTATCTTTGACCTAATTA
GGTTCAAAAACTCAAGGAGAAGATTGAATCAGAGTTAGGAAAGGAATATCCAGCATCACA
ACAAAAGCTTATTTATGCAGGTGAGTGACCGCTTTAAATATCGACGCATTACCGAATGTT
TCACAACATACTTTGTTTTTATTCGCAACTTTCTCTAAACACAGGATGTATTCTTGACGA
TGATAAAACCATCGAAAGTTATAAAGTGGATGAAAAGAAATTCATTGTAGTGATGGTAAA
AAAAGCGACTGTTGCAGCAGCTGCAGCTCCTGAAAAAGAAGAAGCGGGTAAAACAATAAC
AAATGAATCAACGACTGAAAAGAAAAAAGAAGACACACCAGCATCAAAATCAACTACGAC
CGCATCCAGTACCTCATCACCCTCTAAAAGCAGTAGTGAACAATCACAGCAACCGGCAGC
AGCGCAAGAAACTGCAAGTGGCGGTGCTGCAGCAAGCCAGTCACAAATTGCCCAAGCAGA
AGCCAACTTAGTGATGGGCGAAAATTATAATACTATGGTTCAAAACATCATGGAAATGGG
TTATGATCGTGATTCAGTAGTTCGCGCTCTAAATGCCAGTTTTAATAATCCCGAGCGAGC
AGTAGAATATTTAATCACAGGAATACCTGAAATGGCTTTACAAGATCGACCAGCGCCAGT
TGGTGGAAACGAACAAAGTGGTGGCGGTGGTGGCAATATTGGTGCTGCTTTGGATCGATC
ATCGAATTTAGCAAGCAGTGGTGAAAGTGGTGGTAATGATGAAAGTCCACTTGCCTTCCT
TCGAAGACAAGCTCAATTTCAACAAATGAGAAATGTAATTCAACAAAATCCTGAAATGTT
GAATGCTGTTCTACAACAAATTGGTCAAACAAATCCAGCACTATTGCAACTTATTTCAGA
AAATCAAGAAGCATTTGTTAACATGCTTAATGAGTCAGAAGATGGTCGTCAAGCGCCTAG
TGGTGGAAATGATGATGATGATAGAGGAAATTTCGGTGGATTGTTAGACGTAGGTTCTGT
GCCCGAATTTACACAACAAGATCGTGAAGCCATTGAAAGATTAAAGGCACTCGGTTTTCC
AGATGAACTGGTTGTTCAAGCTTACATTGCTTGTGAAAAAAATGAAAATTTGGCCGCCAA
CTTTTTACTTTCACAGACCTTTGATGACTAA

>g13345.t3 Gene=g13345 Length=351
MFHNILCFYSQLSLNTGCILDDDKTIESYKVDEKKFIVVMVKKATVAAAAAPEKEEAGKT
ITNESTTEKKKEDTPASKSTTTASSTSSPSKSSSEQSQQPAAAQETASGGAAASQSQIAQ
AEANLVMGENYNTMVQNIMEMGYDRDSVVRALNASFNNPERAVEYLITGIPEMALQDRPA
PVGGNEQSGGGGGNIGAALDRSSNLASSGESGGNDESPLAFLRRQAQFQQMRNVIQQNPE
MLNAVLQQIGQTNPALLQLISENQEAFVNMLNESEDGRQAPSGGNDDDDRGNFGGLLDVG
SVPEFTQQDREAIERLKALGFPDELVVQAYIACEKNENLAANFLLSQTFDD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g13345.t3 CDD cd14380 UBA2_Rad23 308 346 1.11469E-18
14 g13345.t3 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 124 171 6.3E-23
13 g13345.t3 Gene3D G3DSA:1.10.10.540 - 207 274 8.0E-28
15 g13345.t3 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 306 349 1.1E-21
20 g13345.t3 MobiDBLite mobidb-lite consensus disorder prediction 49 115 -
21 g13345.t3 MobiDBLite mobidb-lite consensus disorder prediction 57 76 -
22 g13345.t3 MobiDBLite mobidb-lite consensus disorder prediction 77 115 -
4 g13345.t3 PANTHER PTHR10621 UV EXCISION REPAIR PROTEIN RAD23 14 351 2.0E-84
5 g13345.t3 PANTHER PTHR10621:SF52 RAD23 HOMOLOG A, NUCLEOTIDE EXCISION REPAIR PROTEIN A 14 351 2.0E-84
7 g13345.t3 PRINTS PR01839 DNA repair protein Rad23 signature 245 267 4.3E-27
9 g13345.t3 PRINTS PR01839 DNA repair protein Rad23 signature 303 319 4.3E-27
8 g13345.t3 PRINTS PR01839 DNA repair protein Rad23 signature 320 334 4.3E-27
6 g13345.t3 PRINTS PR01839 DNA repair protein Rad23 signature 335 350 4.3E-27
2 g13345.t3 Pfam PF00627 UBA/TS-N domain 131 166 2.1E-14
1 g13345.t3 Pfam PF09280 XPC-binding domain 219 274 6.0E-24
3 g13345.t3 Pfam PF00627 UBA/TS-N domain 309 344 3.7E-11
24 g13345.t3 ProSiteProfiles PS50030 Ubiquitin-associated domain (UBA) profile. 126 169 14.619
25 g13345.t3 ProSiteProfiles PS50030 Ubiquitin-associated domain (UBA) profile. 307 347 13.27
17 g13345.t3 SMART SM00165 uba_6 131 168 6.6E-10
19 g13345.t3 SMART SM00727 CBM 217 260 2.8E-6
18 g13345.t3 SMART SM00165 uba_6 309 346 1.6E-9
12 g13345.t3 SUPERFAMILY SSF46934 UBA-like 109 172 3.11E-14
10 g13345.t3 SUPERFAMILY SSF101238 XPC-binding domain 215 280 2.35E-21
11 g13345.t3 SUPERFAMILY SSF46934 UBA-like 295 350 1.24E-12
23 g13345.t3 TIGRFAM TIGR00601 rad23: UV excision repair protein Rad23 14 351 5.1E-98

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