General information for g6462.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA repair protein complementing XP-G cells-like protein.
Parent gene
- The parent gene g6462 is located on chr_2: 17159791..17161893 (- 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 | g6462 | g6462.t1 | isoform | g6462.t1 | 17158077 | 17161893 |
| chr_2 | g6462 | g6462.t1 | exon | g6462.t1.exon1 | 17158077 | 17161505 |
| chr_2 | g6462 | g6462.t1 | cds | g6462.t1.CDS1 | 17158077 | 17161505 |
| chr_2 | g6462 | g6462.t1 | exon | g6462.t1.exon2 | 17161568 | 17161743 |
| chr_2 | g6462 | g6462.t1 | cds | g6462.t1.CDS2 | 17161568 | 17161743 |
| chr_2 | g6462 | g6462.t1 | exon | g6462.t1.exon3 | 17161806 | 17161893 |
| chr_2 | g6462 | g6462.t1 | cds | g6462.t1.CDS3 | 17161806 | 17161893 |
| chr_2 | g6462 | g6462.t1 | TSS | g6462.t1 | 17161991 | 17161991 |
| chr_2 | g6462 | g6462.t1 | TTS | g6462.t1 | NA | NA |
Sequences
>g6462.t1 Gene=g6462 Length=3693
ATGGGTGTAACTGGTCTTTGGAAATTAATTGAATCATCAGGAAAACCTGTGCCAGTCGAA
ACACTTGAAAATAAAGTACTTGCAATAGATATTTCGATTTGGCTGCATCAAGTTGTAAAA
GGATATCAGGATAATAAAGGAGGTCATGTTCAAAATGCGCACATTATAGGTTTATTTAAT
CGAATTTGTAAATTACTGTATTATCGTATCAAACCAATATTTGTTTTCGACGGTGCTGCT
TGCAGTCTCAAACATGATACTATTAGAAAACGTTCACAACAAAAATCTAAAATCCAGACC
GAAGCTGAAAGAATTGAAAAACTTTTACTTGAATCATTAGCTAAAGAACATGTTTTGAAA
GAAAAATTAGAAATCGCTAGTACATCTACATCACCAGTTAAAAATGTTAAACCACTCAAC
AAAAATGAAGAATTCAAAGATGAAATGTTTATGCTTCCTCCAACTAAAGCAATTAAAGTT
GAAAGCATTAAGAAAGAACTCGAAGAAGATGATGAATGGAACTGTCCAAAAAAGTCATAT
AGCAGAAATATCACAAGTATCGATGTGAACAGTCAATATTTCAAAAGTTTACCAGCTGAC
AAAAGACATGAGATTCTTATGGATATAAAAGATACTCGTAAACAAAGTAGTTGGAATAAA
ATGAAAGAACTTCCTGTTGAATCAGATGATTTTTCAAAATATCAAATGGCAGGATTACTT
AAACGTCGTCAAGTTCAAGTTTCATTAGAAGAGGCAGAAAAAGAGATGGGAGGTAAAAAT
TGGAGTTTGAGTGAATTGGAATCTTTATTATCAGAAGATGGTGTGATAGAGACAAGTTCA
AAGAAAGCTCAAAAAATTGCAGCCAATGAAAATGTAAGATTTTTACTCGTTCGTGATATT
GCAAAAGTCATAAGTGAAGCTAAAAAAGAAGAAGAAAATCGACCATCGACATCAAAACAA
ATGGAAATAAAGAAAGAAGAACTTCTTGATGAAGATTATGATTTAGAATTACAAAAAGCA
ATACAAATGTCGTTAGGACATGATGTCGATGATGAGCAAGCTGATGAAGAAGAGCCTAAA
AAATGTGACGAACCTATTAAATTGAATACACAACAACGTAAAAAGTTTGGTAATACAGTT
CAAACACATGGACTAGTTCGAGGTTTTATGATGGAATATGCGGAAATGAATGATGATGAT
ATTCATGATATGATAAATGAAACACAGCAAGAACCAAATGAAGATGATTTAAATGATTCA
TGGAGTGAGAAATTTCCAAATACTGATCGTTATGTACTCTATGGAACACAAAAAGAAAAT
CAAACTCAAAGCAAAGAAGAAAGTCAAGAAAACTCAAAAGAACTCGTCATTTTAGTTGAT
TCAAAAATATCGAAGTTTGAAGAGAACGAAGACTTATTTGCAGATGTGTTTAATACAGAA
GAACAAGTTGATTTATCACATGACAAAAAAGAAGACATTCCAGATGTAGAAGTAGCTTCG
ATAGCTTCATCTGATGATGACACTATTGAATATGAAGTTCCTGAAGAGATAACACAAAAT
GAAACAGAAAAACGTAGTGAAACTGAATTCGACTCAGGTTTTGTATCTGAAGAGAGCAAC
AAAAAATTATCTACTATCAATGAAAAAACAAATTTAAATCAACTTTCTGAAAACGATAAA
TTCTGGGATATTTTGAATGATGATGAAGATAAATCGAAGCCAGTTCTCGAAAAACAATCG
CAACATAAGTTACCTGATATAGTTATGTCTACACACAAAGAGTTACATGAAACAAAGGAA
ATAGATGCACAAACTGAAAAAGAAATTTCTGTTATAATTGAAAATGCAGCAGACAAATCT
GATAAAGAAACAAATATGAATCAAGTTTCCGAAAATGATAAATTTTGGAATCTTTTGAAT
GATGATGATGAAAAATCTTTGCCAATATTTAAAAAAGATGTCGATAAAAATTCACAAAAA
GAAGAAGAAGAACTAAAGATAGCACAATTTCATGAGGATGAAAATATGCCCCAAAATATT
GAAGAATCGGAAAAAATTGAAGACAAAATATCAATTGATATTCAAGAAACGATTACAGTT
GAGAAAAAAATTGAAATTTCACAAGATGAAGTTGTTTCCTCACAAAAAGAAGTATCAATT
TCACATGATATAAAAGAACCTCAGGAAAAAAGTACACAAGATGAACACAAGTTGTCATTA
GAAGACCAAAAAGATATGGAAAATGCTCTAAAAGCATTAGAACAAGATTATACGAAAGAA
GAGCTTGAACAATTGCAAACTGATGTAAAGAAACAAACGAAAGATTTTGAACATGAACGA
AACAAATTAAATCGAATGGGAATGTCAATCACACAATCAATGACACGAGATTGCAAAGAA
TTGCTAAAACTTTTTGGTATTCCTTATATTAAATCACCAACAGAAGCTGAAGCTCAATGT
GCATTTTTAAATCATATAGGTATGATTGATGGAATTATTACAGATGATTCAGATGTATGG
CTTTTCGGTGCAAAGACAGTTTATAAGAATTTCTTCGTTCAAAAAAAGAGTGTTATGGAA
TTTAGAATGGATAATGTTCAAGAAATGTATCATCTTGATAGATATAAACTTATTCAACTT
GCAATGCTTGTAGGTTCTGATTATACATTAGGCTTACATGGTGTTGGTGCAGTTACTGCT
CTAGAAATTCTTGCAGCTTTTCCTCCTACACCTCAAGTTGAAGGGGAAACAGATCAATAT
CAATCATTGCTTTCAAGCTTGAGAAAATTTCGTGATTGGTTCATTGGTGGACGTGAAGCT
GGAACGAATGGTAAATCAGCTCTGAAAAGCAAATTAAAAAATGTTGAGATAATTGAAGGA
TTTCCAAGCATTGCTGTTATGCAAGCATATTTAGAGCCGAGAATCAATACAAGTAAAAAA
CCTTTCTCTTGGGGAACGCCTGATTTTGAATCAATAGTTGAATATACACGACAAAAACTT
GGTTGGACTCGATTAAAGACTGAAGAAATTTTGAATCCAGTAATAAAAAAATTAAATGAG
AAAAAGCAAACAACGATTCGAGATTATTTCAAATCACAAATGTCGAAAAAGGTGTTTGAT
AATCAAAAGATGAGTAAAAGAGTACAAAAAGCAGTAGTAAAATTGGGCGGTGAAGAAGAT
CAGGTTGATGAAAAGATTGAGAAACAGAAACCAGCACCAAGAAAAAGAAAGACTACATCG
AAAACATCAAAAAAGAAACAGACAATGGAAGAAGAAGAAAAAGAAAAGAAAGAAATTGAA
GACCTTGTTTTATTATTAAGTGATGAGGATGAAAATGATATGAAACCACCACCTGTTAAA
AAATCATCTCCTTCGCCCAATTCGAAAGTCAATGCATTTGACCTTCTTAAACAGCCTGAA
CCTTCAAAATCTAAATCACCAACAAAGTCCAAAAAACCAGGAGCAGCTCTAACAAGAAAA
CGAAAAGTCAAGAAAGATGAATCACAACCTAGTACAAGCAATGCAAATAATAATGATGAT
GATGATGATATTCTACCTCCTAAACGAGCACCAAGAATTCCTGATACAAAGCAAGTTATT
CCACAAAAAGAGCGTGAAAAAGAAGAACAAGAGAAACTTAAGCAAAAAGCAATCGAAATA
TTTAAAAAGTCAAAGTCAGCGAGACGAAAGTAA
>g6462.t1 Gene=g6462 Length=1230
MGVTGLWKLIESSGKPVPVETLENKVLAIDISIWLHQVVKGYQDNKGGHVQNAHIIGLFN
RICKLLYYRIKPIFVFDGAACSLKHDTIRKRSQQKSKIQTEAERIEKLLLESLAKEHVLK
EKLEIASTSTSPVKNVKPLNKNEEFKDEMFMLPPTKAIKVESIKKELEEDDEWNCPKKSY
SRNITSIDVNSQYFKSLPADKRHEILMDIKDTRKQSSWNKMKELPVESDDFSKYQMAGLL
KRRQVQVSLEEAEKEMGGKNWSLSELESLLSEDGVIETSSKKAQKIAANENVRFLLVRDI
AKVISEAKKEEENRPSTSKQMEIKKEELLDEDYDLELQKAIQMSLGHDVDDEQADEEEPK
KCDEPIKLNTQQRKKFGNTVQTHGLVRGFMMEYAEMNDDDIHDMINETQQEPNEDDLNDS
WSEKFPNTDRYVLYGTQKENQTQSKEESQENSKELVILVDSKISKFEENEDLFADVFNTE
EQVDLSHDKKEDIPDVEVASIASSDDDTIEYEVPEEITQNETEKRSETEFDSGFVSEESN
KKLSTINEKTNLNQLSENDKFWDILNDDEDKSKPVLEKQSQHKLPDIVMSTHKELHETKE
IDAQTEKEISVIIENAADKSDKETNMNQVSENDKFWNLLNDDDEKSLPIFKKDVDKNSQK
EEEELKIAQFHEDENMPQNIEESEKIEDKISIDIQETITVEKKIEISQDEVVSSQKEVSI
SHDIKEPQEKSTQDEHKLSLEDQKDMENALKALEQDYTKEELEQLQTDVKKQTKDFEHER
NKLNRMGMSITQSMTRDCKELLKLFGIPYIKSPTEAEAQCAFLNHIGMIDGIITDDSDVW
LFGAKTVYKNFFVQKKSVMEFRMDNVQEMYHLDRYKLIQLAMLVGSDYTLGLHGVGAVTA
LEILAAFPPTPQVEGETDQYQSLLSSLRKFRDWFIGGREAGTNGKSALKSKLKNVEIIEG
FPSIAVMQAYLEPRINTSKKPFSWGTPDFESIVEYTRQKLGWTRLKTEEILNPVIKKLNE
KKQTTIRDYFKSQMSKKVFDNQKMSKRVQKAVVKLGGEEDQVDEKIEKQKPAPRKRKTTS
KTSKKKQTMEEEEKEKKEIEDLVLLLSDEDENDMKPPPVKKSSPSPNSKVNAFDLLKQPE
PSKSKSPTKSKKPGAALTRKRKVKKDESQPSTSNANNNDDDDDILPPKRAPRIPDTKQVI
PQKEREKEEQEKLKQKAIEIFKKSKSARRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 24 | g6462.t1 | CDD | cd09868 | PIN_XPG_RAD2 | 2 | 109 | 4.95809E-51 |
| 23 | g6462.t1 | CDD | cd09868 | PIN_XPG_RAD2 | 789 | 1016 | 2.7751E-48 |
| 20 | g6462.t1 | Coils | Coil | Coil | 743 | 782 | - |
| 22 | g6462.t1 | Coils | Coil | Coil | 1082 | 1109 | - |
| 21 | g6462.t1 | Coils | Coil | Coil | 1203 | 1223 | - |
| 18 | g6462.t1 | Gene3D | G3DSA:3.40.50.1010 | - | 1 | 143 | 8.7E-31 |
| 19 | g6462.t1 | Gene3D | G3DSA:3.40.50.1010 | - | 764 | 1048 | 5.1E-54 |
| 30 | g6462.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 518 | 541 | - |
| 32 | g6462.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 518 | 536 | - |
| 35 | g6462.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 711 | 737 | - |
| 33 | g6462.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 719 | 737 | - |
| 29 | g6462.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1058 | 1230 | - |
| 34 | g6462.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1058 | 1073 | - |
| 31 | g6462.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1083 | 1117 | - |
| 28 | g6462.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1198 | 1222 | - |
| 3 | g6462.t1 | PANTHER | PTHR16171 | DNA REPAIR PROTEIN COMPLEMENTING XP-G CELLS-RELATED | 1 | 1179 | 4.6E-185 |
| 4 | g6462.t1 | PANTHER | PTHR16171:SF7 | DNA REPAIR PROTEIN COMPLEMENTING XP-G CELLS | 1 | 1179 | 4.6E-185 |
| 15 | g6462.t1 | PRINTS | PR00066 | Xeroderma pigmentosum group G protein signature | 2 | 19 | 6.2E-25 |
| 7 | g6462.t1 | PRINTS | PR00853 | Xeroderma pigmentosum group G/yeast RAD superfamily signature | 24 | 38 | 1.9E-33 |
| 14 | g6462.t1 | PRINTS | PR00066 | Xeroderma pigmentosum group G protein signature | 54 | 77 | 6.2E-25 |
| 9 | g6462.t1 | PRINTS | PR00853 | Xeroderma pigmentosum group G/yeast RAD superfamily signature | 72 | 91 | 1.9E-33 |
| 11 | g6462.t1 | PRINTS | PR00066 | Xeroderma pigmentosum group G protein signature | 176 | 194 | 6.2E-25 |
| 13 | g6462.t1 | PRINTS | PR00066 | Xeroderma pigmentosum group G protein signature | 218 | 243 | 6.2E-25 |
| 12 | g6462.t1 | PRINTS | PR00066 | Xeroderma pigmentosum group G protein signature | 753 | 769 | 6.2E-25 |
| 6 | g6462.t1 | PRINTS | PR00853 | Xeroderma pigmentosum group G/yeast RAD superfamily signature | 802 | 819 | 1.9E-33 |
| 5 | g6462.t1 | PRINTS | PR00853 | Xeroderma pigmentosum group G/yeast RAD superfamily signature | 823 | 843 | 1.9E-33 |
| 8 | g6462.t1 | PRINTS | PR00853 | Xeroderma pigmentosum group G/yeast RAD superfamily signature | 877 | 892 | 1.9E-33 |
| 10 | g6462.t1 | PRINTS | PR00066 | Xeroderma pigmentosum group G protein signature | 1013 | 1033 | 6.2E-25 |
| 2 | g6462.t1 | Pfam | PF00752 | XPG N-terminal domain | 1 | 97 | 3.6E-29 |
| 1 | g6462.t1 | Pfam | PF00867 | XPG I-region | 803 | 887 | 2.5E-24 |
| 26 | g6462.t1 | SMART | SM00485 | xpgn3 | 1 | 98 | 2.0E-41 |
| 25 | g6462.t1 | SMART | SM00484 | xpgineu | 803 | 872 | 3.8E-28 |
| 27 | g6462.t1 | SMART | SM00279 | HhH_4 | 874 | 907 | 8.5E-8 |
| 16 | g6462.t1 | SUPERFAMILY | SSF88723 | PIN domain-like | 3 | 887 | 9.25E-60 |
| 17 | g6462.t1 | SUPERFAMILY | SSF47807 | 5’ to 3’ exonuclease, C-terminal subdomain | 872 | 1031 | 7.92E-22 |
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:0003697 | single-stranded DNA binding | MF |
| GO:0003677 | DNA binding | MF |
| GO:0003824 | catalytic activity | MF |
| GO:0004519 | endonuclease activity | MF |
| GO:0006289 | nucleotide-excision repair | BP |
| GO:0004518 | nuclease activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10846 (DNA excision repair protein ERCC-5)
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.
