General information for g10260.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA repair endonuclease XPF.
Parent gene
- The parent gene g10260 is located on chr_1: 8562644..8568181 (+ 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_1 | g10260 | g10260.t1 | isoform | g10260.t1 | 8559642 | 8562644 |
| chr_1 | g10260 | g10260.t1 | exon | g10260.t1.exon1 | 8559642 | 8559850 |
| chr_1 | g10260 | g10260.t1 | cds | g10260.t1.CDS1 | 8559642 | 8559850 |
| chr_1 | g10260 | g10260.t1 | exon | g10260.t1.exon2 | 8559911 | 8562644 |
| chr_1 | g10260 | g10260.t1 | cds | g10260.t1.CDS2 | 8559911 | 8562644 |
| chr_1 | g10260 | g10260.t1 | TSS | g10260.t1 | NA | NA |
| chr_1 | g10260 | g10260.t1 | TTS | g10260.t1 | NA | NA |
Sequences
>g10260.t1 Gene=g10260 Length=2943
ATGGAAGGAAACAGTATCGAAGAAGATTCTAAAGTTGAAACTAATGAACAAAAGGAGAAG
AACATAGAAGATGATATTAATGTTGAAGAAATTAACTTTATGGAGAAGATTTTAGAAAAA
GATGCAAGTGATGAATTAAAATGTCTTGATTTTGAACGTCAAATGTTTCTTGATTGCGTT
TTTAGTGATGGTCTAATGATTTGTGCAAAAGGAGTGAGTTATGAAAAAGTCATAATAAAC
TTATTCAAAGTTTATTTGAATCCAGCAAATTTAATTTTAATTCTCAATTGTGATGAATAC
GAAGAAAATTACTTGACAAAGCTACTCAATTCGCCTCTTGTTAGAGCTGCATCTACTAAC
AGCAATGAACGTGAAAAAATATACTTATCAGGCGGCATTCAGTTCATTTCGACTCAAGTT
TTAGTCCTAGATTTGTTAAAAAATAAAATTCCTACTGAACTTATTACCGGTATATTTGTG
CTTAGAGCACATCAAGTAATTGAATCATGTCAAGAAGCATTTGCATTAAGACTATATAGA
CAAAAAAATAAGACAGGATTTATCAAAGCCTTTACAAATTCAGCTGAAGCTTTCACTTTT
GGATATGGTCACGTTGAAAAAGTAATGCGGAATTTATTTGTTCGTGAATTATTCTTATGG
CCAAGATTCCATGCAGTAATTCAACGCTCTCTTAAAACATACGAACCGGTATCTGTAGAA
TTTCATGTTCCGCTTTCGTCTAAATTAGCTCAAATTCAAACGAATATATTGGATATCATG
AATTTTATTGTAAAAGAATTAAAAAGAATCAATCCTACCGTTGATCTTGAGGAAGTCACA
GTGGAAAATTGTGTAACAAAGAGATTTCAAAAAATTTTACAAACCCAATTGGATTCAATT
TGGCATCAATTAAACGCTAAAACAAAATTGCTCATAACTGATTTGAAAATTCTACGAAGT
TTAATGTTTAGTGCTATCTATTCTGATTCTGTGACATTTTATAGTACATTAAAGAATTAT
CGTGGTGCTGAATATGCAATGCACAACAGTGGTTGGACTTTATTAGATGCAGCTGAAAGA
ATATTTAAGTTTTCTAAGGAACGTGTTTTTAATAATCAAGATGAATTTGAGCCAGAACCG
AATGCAAAATGGAGAGCTGTTAGCGAAATTCTTCGAATCGAAATACCAGCTGATATTAAA
GACGTTATAAGTGATGAACGTAATGAATTTGATAAACAAAAGCCAATTAAAATTCTCATT
CTATGTAATGATGCTCGAACTTGCTATCAATTAAATCAATATCTCACACAAGGTGCTGAA
AAAACTTTATTTTGGACAGCTCTTAAGAATGAAGTCAAAGTTAAAAAATTAAGCAAAAGT
TATAAATCATTTAATATCCATGAAAGTGGAATAGTGAAAAATCCTGTTGAAGTAAATAAT
CCTGATTTCAAGCATAAACCATCGACAAGTGGTAAAGCAGTTAGAAACGAAAAAATTTCT
TTAAAATTCAATGACACAAGTCGAAAGCGTAAGCATACAAACGATGAGACAAATGAAAGC
AAGACAGATGATAATAACAAAGTGATGGTTAATGATGAAAACGAAGAAGAGGAGGAATAC
ATAAAAGATACTTATCTTCTTACAATGACTCAACGCATCGATGGTAATGAAAGTTTTTCT
GCAGCAGATTTTGACTTGACTAAAGCTGAAAATGTAACTTTTGAAGTTTGTGATGAATAT
AATGAGAAGAATCCATCTTTGAATGCAACTGCAATTTTGTCTTCTATGCAGAAGCCTACT
GTCTTTATTCAGACTTTCAAAAGTGATAGAAATAGAATGTCATCTTTAGATCAAACACTG
CAGGATATGTCTCCAGATTATATAATTTTATATAATATTAATATTACTGCAATTAGACAA
ATTGAAATTTTCGAAGCACGTCATCAAAGGCATGTACGCAGACGTCTTAAAGTCTATGTT
ATAATGCATGCTAAAACGGTTGAAGAACAGAGCTTCTTGACAGCATTACGACGTGAAAAA
CAAGCTTTTGAATTGTTGATTGAAACCAAAAGAACAATGGTTGTGCCTGAATATCAAGAT
GGTAAAACAGATGTTGAAATTGAAGATCAACTTGATGATGAAGAAGAAGAGGATACAAGA
AATGCTGGCGGTCAGGAAAAAGCCTTAAAGAAAGAAAAGTCAAAAGTTATTGTTGATTCA
CGAGAATTTAGAAGTGAACTACCATGTCTTATTCATAAGAGAGGTCTAGATGTTATTCCC
GCAATGATTACGATTGGTGATTATATATTAACACCTGATATTTGTGTTGAACGAAAATCT
ATTTCCGATCTTATTGGATCATTGCAAAGCGGACGATTATACAATCAATGTTTTCAAATG
ACCAGACACTATTCCATGGCTATATTATTAATTGAATTTGATCAAAATAAGTCATTTCAT
TTACAAGGTCGCTATATGCTTTCACGTGATTCTGACACTATGAATATGGAAATAGTTCAA
AAAATTCAATTGCTAACTATACATTTCCCAAAATTAAGATTGGTTTGGTCACCATCACCT
TATGCAACTGCTCAACTTTTTGAGGAACTCAAGCTCAATAGAGAAGAACCGAATTTGGAA
GAAATTATGCAGACGGGCACAGATGAAACAATGCAGGAATTAGCTGTAATAACTGATAGA
TACAATACTAATATTCATGATTTTCTTCTCAAACTTCCTGGAATAACACCAAAAAATATT
CATCAAGTAATGAAGAAAGGAAAGAATTTGAAAAACCTTTTGAAAATGTCGGACATTGAT
CTTGTTGAATTACTTGGCAACATTAAAGATGCTAGACTTTTACATAACATTCTACATAAA
GCACATGAAGCAAACAAGCAAGATCAAAAAACTATTAAAGGAAGAAAATTTCTTAAAAAG
TAA
>g10260.t1 Gene=g10260 Length=980
MEGNSIEEDSKVETNEQKEKNIEDDINVEEINFMEKILEKDASDELKCLDFERQMFLDCV
FSDGLMICAKGVSYEKVIINLFKVYLNPANLILILNCDEYEENYLTKLLNSPLVRAASTN
SNEREKIYLSGGIQFISTQVLVLDLLKNKIPTELITGIFVLRAHQVIESCQEAFALRLYR
QKNKTGFIKAFTNSAEAFTFGYGHVEKVMRNLFVRELFLWPRFHAVIQRSLKTYEPVSVE
FHVPLSSKLAQIQTNILDIMNFIVKELKRINPTVDLEEVTVENCVTKRFQKILQTQLDSI
WHQLNAKTKLLITDLKILRSLMFSAIYSDSVTFYSTLKNYRGAEYAMHNSGWTLLDAAER
IFKFSKERVFNNQDEFEPEPNAKWRAVSEILRIEIPADIKDVISDERNEFDKQKPIKILI
LCNDARTCYQLNQYLTQGAEKTLFWTALKNEVKVKKLSKSYKSFNIHESGIVKNPVEVNN
PDFKHKPSTSGKAVRNEKISLKFNDTSRKRKHTNDETNESKTDDNNKVMVNDENEEEEEY
IKDTYLLTMTQRIDGNESFSAADFDLTKAENVTFEVCDEYNEKNPSLNATAILSSMQKPT
VFIQTFKSDRNRMSSLDQTLQDMSPDYIILYNINITAIRQIEIFEARHQRHVRRRLKVYV
IMHAKTVEEQSFLTALRREKQAFELLIETKRTMVVPEYQDGKTDVEIEDQLDDEEEEDTR
NAGGQEKALKKEKSKVIVDSREFRSELPCLIHKRGLDVIPAMITIGDYILTPDICVERKS
ISDLIGSLQSGRLYNQCFQMTRHYSMAILLIEFDQNKSFHLQGRYMLSRDSDTMNMEIVQ
KIQLLTIHFPKLRLVWSPSPYATAQLFEELKLNREEPNLEEIMQTGTDETMQELAVITDR
YNTNIHDFLLKLPGITPKNIHQVMKKGKNLKNLLKMSDIDLVELLGNIKDARLLHNILHK
AHEANKQDQKTIKGRKFLKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g10260.t1 | Gene3D | G3DSA:3.40.50.10130 | - | 735 | 882 | 1.2E-49 |
| 10 | g10260.t1 | Gene3D | G3DSA:1.10.150.20 | 5’ to 3’ exonuclease | 892 | 973 | 3.0E-21 |
| 7 | g10260.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 21 | - |
| 6 | g10260.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 479 | 526 | - |
| 9 | g10260.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 488 | 526 | - |
| 8 | g10260.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 708 | 728 | - |
| 2 | g10260.t1 | PANTHER | PTHR10150 | DNA REPAIR ENDONUCLEASE XPF | 47 | 964 | 7.8E-255 |
| 1 | g10260.t1 | Pfam | PF02732 | ERCC4 domain | 738 | 867 | 5.4E-18 |
| 5 | g10260.t1 | SMART | SM00891 | ERCC4_2 | 735 | 815 | 1.1E-26 |
| 4 | g10260.t1 | SUPERFAMILY | SSF52980 | Restriction endonuclease-like | 734 | 872 | 6.17E-36 |
| 3 | g10260.t1 | SUPERFAMILY | SSF47781 | RuvA domain 2-like | 898 | 965 | 3.33E-14 |
| 12 | g10260.t1 | TIGRFAM | TIGR00596 | rad1: DNA repair protein (rad1) | 124 | 963 | 2.4E-265 |
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:0004520 | endodeoxyribonuclease activity | MF |
| GO:0003697 | single-stranded DNA binding | MF |
| GO:0003677 | DNA binding | MF |
| GO:0006281 | DNA repair | BP |
| GO:0004518 | nuclease activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10848 (DNA excision repair protein ERCC-4 [EC:3.1.-.-])
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.
