General information for g7486.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA repair protein complementing XP-C cells-like protein.
Parent gene
- The parent gene g7486 is located on chr_2: 23978853..23979370 (+ strand)
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_2 | g7486 | g7486.t7 | isoform | g7486.t7 | 23977711 | 23978853 |
| chr_2 | g7486 | g7486.t7 | exon | g7486.t7.exon1 | 23977711 | 23978042 |
| chr_2 | g7486 | g7486.t7 | cds | g7486.t7.CDS1 | 23977798 | 23978042 |
| chr_2 | g7486 | g7486.t7 | exon | g7486.t7.exon2 | 23978106 | 23978460 |
| chr_2 | g7486 | g7486.t7 | cds | g7486.t7.CDS2 | 23978106 | 23978460 |
| chr_2 | g7486 | g7486.t7 | exon | g7486.t7.exon3 | 23978521 | 23978853 |
| chr_2 | g7486 | g7486.t7 | cds | g7486.t7.CDS3 | 23978521 | 23978853 |
| chr_2 | g7486 | g7486.t7 | TSS | g7486.t7 | NA | NA |
| chr_2 | g7486 | g7486.t7 | TTS | g7486.t7 | NA | NA |
Sequences
>g7486.t7 Gene=g7486 Length=1020
ATTTGGGTAGAAGTTTATTCTGAAAAAGATGAGAAATGGATTGCAATAGATGTTTTCCAA
AATAAAATTGATTGTGTAAAAGATATAATGGCAAAGGCAACTCATCCATTAGTGTATGTT
TTCGCTTGGAACAATGATAATTCTCTCAAGGATGTGACAGCTCGTTATTGTCCTAATTTA
AACACAACTGTTAGAAAAATGAGAGTCGATCGTGACTATTTGAACAAAATTTTAATTATG
TATCCTGGAACAAAGACAGCGCGTGATTTGAAAGAAGACGATGAGCTGAATAAATTACAA
TTAGCTCAACCAATGCCAACTTCTATCGCAGAATTTAAAAATCATCCTCTTTATGCACTA
AAACGTCATCTTTTGAAGTATGAAGCTATTTATCCACCTGAACCACCGATTTTGGGCTAC
ATTCGAGATGAACCGATTTATCCTCGAGATTGTGTCTTTGTTTGTCGTTCAAGAGAAACA
TGGTTGAAAGAAGCTCGTGTTGTGAAATTATATGAAGAGCCATATAAAATTGTCAAAACC
ATGAAATGGAACAAGCCAACTAACAAACTCATGAAAGATGTGCCATTAGAATTGTTTGGT
ATATGGCAAACAAAAGATTATGAGCCACCAACAGCTGAAAATGGAATAGTACCACGCAAT
GGCTATGGCAATGTAGAGCTGTTTAAGCCTCAAATGTTACCTTATGGTACAGTGCATTTA
CAACTACCTGGCCTTCAAAAAGTTTGCAAAAAACTAGGCGTTGATTGTGCTCAAGCAGTT
GTTGGATTTGATTCGAGTGGAGGTTGGCCTTATCCGGTTTATGATGGTTTCGTAATTTGC
AAAGAATTCGAGGAAAAAGTTGTTGATGCCTGGAATCGAGAACAAGAAGAAATTGAACGA
AAGGAAAGAGAAAAAATCGAAAAACGTGTTTACGGAAATTGGAAAAAGCTTATTAAAGGA
TTACTTATTCGCGAGCGTTTAAAGTTGAAATATAATTTTGATAATAATTTGGATGATTAA
>g7486.t7 Gene=g7486 Length=310
MAKATHPLVYVFAWNNDNSLKDVTARYCPNLNTTVRKMRVDRDYLNKILIMYPGTKTARD
LKEDDELNKLQLAQPMPTSIAEFKNHPLYALKRHLLKYEAIYPPEPPILGYIRDEPIYPR
DCVFVCRSRETWLKEARVVKLYEEPYKIVKTMKWNKPTNKLMKDVPLELFGIWQTKDYEP
PTAENGIVPRNGYGNVELFKPQMLPYGTVHLQLPGLQKVCKKLGVDCAQAVVGFDSSGGW
PYPVYDGFVICKEFEEKVVDAWNREQEEIERKEREKIEKRVYGNWKKLIKGLLIRERLKL
KYNFDNNLDD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g7486.t7 | Coils | Coil | Coil | 252 | 279 | - |
| 10 | g7486.t7 | Gene3D | G3DSA:3.90.260.10 | Coagulation Factor XIII | 1 | 74 | 5.0E-10 |
| 12 | g7486.t7 | Gene3D | G3DSA:2.20.20.110 | - | 75 | 114 | 4.4E-6 |
| 11 | g7486.t7 | Gene3D | G3DSA:3.30.70.2460 | - | 194 | 265 | 2.4E-19 |
| 4 | g7486.t7 | PANTHER | PTHR12135 | DNA REPAIR PROTEIN XP-C / RAD4 | 3 | 305 | 1.4E-137 |
| 5 | g7486.t7 | PANTHER | PTHR12135:SF0 | DNA REPAIR PROTEIN COMPLEMENTING XP-C CELLS | 3 | 305 | 1.4E-137 |
| 1 | g7486.t7 | Pfam | PF03835 | Rad4 transglutaminase-like domain | 2 | 67 | 6.3E-13 |
| 3 | g7486.t7 | Pfam | PF10403 | Rad4 beta-hairpin domain 1 | 74 | 123 | 4.2E-19 |
| 2 | g7486.t7 | Pfam | PF10405 | Rad4 beta-hairpin domain 3 | 188 | 260 | 3.7E-27 |
| 7 | g7486.t7 | SMART | SM01030 | BHD_1_2 | 72 | 124 | 2.3E-27 |
| 8 | g7486.t7 | SMART | SM01031 | BHD_2_2 | 126 | 181 | 9.0E-20 |
| 9 | g7486.t7 | SMART | SM01032 | BHD_3_2 | 188 | 262 | 7.3E-43 |
| 6 | g7486.t7 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 4 | 87 | 2.21E-14 |
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:0005634 | nucleus | CC |
| GO:0003677 | DNA binding | MF |
| GO:0003684 | damaged DNA binding | MF |
| GO:0006289 | nucleotide-excision repair | BP |
KEGG
Orthology
- This transcript has been annotated with K10838 (xeroderma pigmentosum group C-complementing protein)
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.
