General information for g4136.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as General transcription and DNA repair factor IIH helicase subunit XPD.
Parent gene
- The parent gene g4136 is located on chr_3: 30891773..30893551 (+ 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_3 | g4136 | g4136.t1 | TSS | g4136.t1 | 30889217 | 30889217 |
| chr_3 | g4136 | g4136.t1 | isoform | g4136.t1 | 30889371 | 30891773 |
| chr_3 | g4136 | g4136.t1 | exon | g4136.t1.exon1 | 30889371 | 30889375 |
| chr_3 | g4136 | g4136.t1 | cds | g4136.t1.CDS1 | 30889371 | 30889375 |
| chr_3 | g4136 | g4136.t1 | exon | g4136.t1.exon2 | 30889436 | 30889535 |
| chr_3 | g4136 | g4136.t1 | cds | g4136.t1.CDS2 | 30889436 | 30889535 |
| chr_3 | g4136 | g4136.t1 | exon | g4136.t1.exon3 | 30889593 | 30891773 |
| chr_3 | g4136 | g4136.t1 | cds | g4136.t1.CDS3 | 30889593 | 30891773 |
| chr_3 | g4136 | g4136.t1 | TTS | g4136.t1 | 30891836 | 30891836 |
Sequences
>g4136.t1 Gene=g4136 Length=2286
ATGCGTATTTTGGTTGATGGCTTAATTGTTTACTTTCCATACGATTATATTTATCCTGAA
CAATATGCATATATGCTTGAACTTAAAAGAACATTGGATGCTAAAGGACATTGTCTTCTT
GAAATGCCCTCAGGAACCGGCAAAACTGCGACTCTTCTTTCTCTTATTGTTGCTTACATG
ATTGAGAATCCTCATGTTATTCGTAAATTGATTTATTGTTCACGTACAGTTCCCGAGATA
GAAAAAGTTATTGCAGAATTACAAAATCTAATGGAATATTATGAGAAGCATGCACCAGAA
AAACCAAATTTGACAGGCTTAGTGCTTAGTTCACGAAAAAATATGTGTATTCATCCGGAT
GTGTGTAGAGAGAAAGACGGAAAGGTTGTTGATGCAAAATGTTATGGAATGACTGCAAGT
TATGTTCGTGAGAGACAACAATATGATGAAAGTCAACAAGTTTGCCAATATTTTGAAGGT
TTTTCTGCGGAAGGAAAAGAATCCCATCTTCCGAATGGTGTTTACAATTTAGATGACTTA
AAAGAATATGGCAGAATGCGAAATTGGTGTCCTTACTTCTTAGCACGTTATGCAATTGTC
AATGCTCAAGTAATTGTTTACAGTTATTACTACTTACTTGATCCAAAAGTTGCAGATGTT
GTTTCTAAAGAGTTGATAAAAGAATCTGTGGTTGTTTGTGATGAGGCGCACAATATTGAT
AACGTCTGTGTCGATTCAATGAGTGTTCGTATTAATAAGCGTGTGATTGAAAGAGGAACA
CAAGCATTGGGTACATTAGAAAAGCTGGTACAGGAAATGAAAGAAGATGATCAACAGAGA
CTTCAAGATGAATATGCTAAAATGGTTCAAGGACTGCGTGATGCTTATCAAGCTCGTGAG
ACAGATAAAATGCTAGCTAATCCAGTTCTTCCCGATGACATATTGCAAGAAGCAGTTCCA
GGAAATATTCGTCATGCGGATCATTTTCTAGGTTTCTTAAATCGTTTTATTGCATATTTG
AAAACGAGATTGAGAGTTCAGCATGTCGTTCAAGAATCACCAGCAGGTTTTTTAAAAGAC
ATTCATTCGAAAGTATGTATAGATCGAAAACCACTTCGATTTTGTGCCGAAAGATTACAA
TCTCTTTTAAGAACATTAGAAATCACTGATTTAACTGATTATGGTGGTCTTACTGTAATT
ACACATTTTGCAACTCTCGTATCAACATATACGCAAGGATTTACAATTATTATTGAGCCA
TTTGATGATAAAACACCAACTGTTTCAAATCCAATTCTCTACTTCAGCTGTCTTGATTCA
TCGATCGCAATGAGACCAATTTTTAGACGTTTTCAATCAGTTGTTATTACATCAGGTACG
TTAAGTCCTATGGATATGTATCCAAAAATTCTCGATTTTGATCCAGTTGTTATGAGTTCA
TTTACTATGACTTTATCTCGACCATGTTTGCTACCAATGGTTGTTACTCGTGGAAATGAT
CAAGTTGCAATAAGTTCTAAATTTGAATCACGTGAAGATACAGCTGTAACAAGAAATTAT
GGTCAATTACTTGTAGAAACGGCAAAAATTGTGCCTGATGGAATTGTTTGTTTCTTTACA
TCATATTTATATTTAGAATCAGTTGTCGCATCATGGTATGATCAAGGAATCATTGATACA
TTATTAAAATACAAGTTGCTATTTATTGAAACACAAGATGCGGCTGAAACTTCTTATGCG
CTAATGAATTATGTAAAAGCATGTGACTGTGGAAGAGGAGCTGTTTTACTAGCTGTTGCA
AGAGGAAAGGTGTCTGAGGGAGTAGATTTTGATCATCATTTAGGACGAGCTGTTCTTATG
TTTGGCATACCTTATGTCTATACACAATCACGAATTTTGAAAGCACGTTTAGAATATCTT
CGAGATCAATTTCAAATTAAAGAGAATGATTTTCTTACATTTGATGCTCTTCGTCATGCT
GCACAATGTGTCGGTCGTGCTATTAGAGGAAAAACTGATTATGGTATTATGATATTTGCT
GATAAGAGATTCGCTCGTCAAGATAAGCGTGGAAAACTACCAAAGTGGATTCAAGAATAT
CTTACCGATAATTATGTAAATTTGAGCACTGAAGAGGCAATGCAGTTAGCAAAAATATGG
CTTAGACAAATGGCTCAACCTTTCTCACGTGAAGATCAATTAGGCTTATCTTTATTAACT
GTTGAGCAATTAAAAAGTAATGAAAAACAAATCATTGAGAAACATTTAAAACCACAAACT
ATTTGA
>g4136.t1 Gene=g4136 Length=761
MRILVDGLIVYFPYDYIYPEQYAYMLELKRTLDAKGHCLLEMPSGTGKTATLLSLIVAYM
IENPHVIRKLIYCSRTVPEIEKVIAELQNLMEYYEKHAPEKPNLTGLVLSSRKNMCIHPD
VCREKDGKVVDAKCYGMTASYVRERQQYDESQQVCQYFEGFSAEGKESHLPNGVYNLDDL
KEYGRMRNWCPYFLARYAIVNAQVIVYSYYYLLDPKVADVVSKELIKESVVVCDEAHNID
NVCVDSMSVRINKRVIERGTQALGTLEKLVQEMKEDDQQRLQDEYAKMVQGLRDAYQARE
TDKMLANPVLPDDILQEAVPGNIRHADHFLGFLNRFIAYLKTRLRVQHVVQESPAGFLKD
IHSKVCIDRKPLRFCAERLQSLLRTLEITDLTDYGGLTVITHFATLVSTYTQGFTIIIEP
FDDKTPTVSNPILYFSCLDSSIAMRPIFRRFQSVVITSGTLSPMDMYPKILDFDPVVMSS
FTMTLSRPCLLPMVVTRGNDQVAISSKFESREDTAVTRNYGQLLVETAKIVPDGIVCFFT
SYLYLESVVASWYDQGIIDTLLKYKLLFIETQDAAETSYALMNYVKACDCGRGAVLLAVA
RGKVSEGVDFDHHLGRAVLMFGIPYVYTQSRILKARLEYLRDQFQIKENDFLTFDALRHA
AQCVGRAIRGKTDYGIMIFADKRFARQDKRGKLPKWIQEYLTDNYVNLSTEEAMQLAKIW
LRQMAQPFSREDQLGLSLLTVEQLKSNEKQIIEKHLKPQTI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g4136.t1 | CDD | cd18788 | SF2_C_XPD | 488 | 684 | 0.000 |
| 17 | g4136.t1 | Gene3D | G3DSA:3.40.50.300 | - | 16 | 292 | 0.000 |
| 16 | g4136.t1 | Gene3D | G3DSA:3.40.50.300 | - | 498 | 699 | 0.000 |
| 4 | g4136.t1 | PANTHER | PTHR11472 | DNA REPAIR DEAD HELICASE RAD3/XP-D SUBFAMILY MEMBER | 1 | 747 | 0.000 |
| 5 | g4136.t1 | PANTHER | PTHR11472:SF1 | GENERAL TRANSCRIPTION AND DNA REPAIR FACTOR IIH HELICASE SUBUNIT XPD | 1 | 747 | 0.000 |
| 12 | g4136.t1 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 8 | 25 | 0.000 |
| 9 | g4136.t1 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 273 | 292 | 0.000 |
| 14 | g4136.t1 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 308 | 326 | 0.000 |
| 8 | g4136.t1 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 333 | 354 | 0.000 |
| 13 | g4136.t1 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 372 | 394 | 0.000 |
| 6 | g4136.t1 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 403 | 421 | 0.000 |
| 7 | g4136.t1 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 492 | 509 | 0.000 |
| 11 | g4136.t1 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 636 | 658 | 0.000 |
| 10 | g4136.t1 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 707 | 727 | 0.000 |
| 1 | g4136.t1 | Pfam | PF06733 | DEAD_2 | 72 | 254 | 0.000 |
| 3 | g4136.t1 | Pfam | PF06777 | Helical and beta-bridge domain | 270 | 413 | 0.000 |
| 2 | g4136.t1 | Pfam | PF13307 | Helicase C-terminal domain | 524 | 699 | 0.000 |
| 22 | g4136.t1 | ProSiteProfiles | PS51193 | Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. | 7 | 283 | 36.049 |
| 20 | g4136.t1 | SMART | SM00488 | deadxpd | 8 | 280 | 0.000 |
| 19 | g4136.t1 | SMART | SM00491 | Cxpdneu3 | 542 | 686 | 0.000 |
| 15 | g4136.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 32 | 679 | 0.000 |
| 21 | g4136.t1 | TIGRFAM | TIGR00604 | rad3: DNA repair helicase (rad3) | 9 | 708 | 0.000 |
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:0005524 | ATP binding | MF |
| GO:0006139 | nucleobase-containing compound metabolic process | BP |
| GO:0004386 | helicase activity | MF |
| GO:0006289 | nucleotide-excision repair | BP |
| GO:0003676 | nucleic acid binding | MF |
| GO:0016818 | hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides | MF |
| GO:0003678 | DNA helicase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10844 (DNA excision repair protein ERCC-2)
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.
