General information for g9920.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA excision repair protein ERCC-1.
Parent gene
- The parent gene g9920 is located on chr_1: 6047787..6048622 (- 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 | g9920 | g9920.t1 | isoform | g9920.t1 | 6047787 | 6048622 |
| chr_1 | g9920 | g9920.t1 | exon | g9920.t1.exon1 | 6047787 | 6048268 |
| chr_1 | g9920 | g9920.t1 | cds | g9920.t1.CDS1 | 6047787 | 6048268 |
| chr_1 | g9920 | g9920.t1 | exon | g9920.t1.exon2 | 6048331 | 6048622 |
| chr_1 | g9920 | g9920.t1 | cds | g9920.t1.CDS2 | 6048331 | 6048622 |
| chr_1 | g9920 | g9920.t1 | TSS | g9920.t1 | 6048700 | 6048700 |
| chr_1 | g9920 | g9920.t1 | TTS | g9920.t1 | NA | NA |
Sequences
>g9920.t1 Gene=g9920 Length=774
ATGGATTTACTTGATGATTCGTTTGATAAAGTAATATTTGATGTTGAAATTCCAGAAGAT
TCTAAGCAAAAAAGTGAAATTCAAGCCGGTCCATCAACATCGAGTGCATCAGTTTCTAAA
CAAAATGAAAAGTCACAAGAAAATCAACCAGAGAAAGAAGTTGTGATATATGTTGGCAAT
GCAATACAAGTTAATCCCTGTCAAAAGGGAAATCCATTACTTAAATCAATAAATTCAATT
CCTTGGGAATTTAATGAGAAATTAATTCCAGATTATGTTGTAGGCAAAAGAGCATGTGTA
TTATTTCTATCAGTTAAATATCATCAATTGAAACCTGATTACATACATGAGCGATTAAGA
CAGTTAAGGAAAAATTACGAGTTGAGAATTCTACTTGTTCATGTCGATATTAAAGAACCA
CATAATGCACTTAAACATCTTACAAGAATTTGTCTTCTTGCTGATTTTACTTTAATGTTG
GCTTGGTCGTATGAAGAGGCAGGAAAAATTATTGAGACATACAAAATGTTTGAAAATGCA
TCAGCTGAGAGAATTCAAGAAAAACAAGAAACAGATAGCTATCAGAATGTTGTCAATGCA
TTAACGAGTATAAAATCTATAAACAAAACTGATGCAATGACACTTTTAAATAATTTTGGT
ACTCTCGAAAATCTCATTCAAGCTAGTGAAAATCAATTGTATTCTTGCGTCGGACTTGGA
CCAAAGAAAGCACAAAAGCTTCATAAACTTCTCAATCAGAATTTTTTGAAATAA
>g9920.t1 Gene=g9920 Length=257
MDLLDDSFDKVIFDVEIPEDSKQKSEIQAGPSTSSASVSKQNEKSQENQPEKEVVIYVGN
AIQVNPCQKGNPLLKSINSIPWEFNEKLIPDYVVGKRACVLFLSVKYHQLKPDYIHERLR
QLRKNYELRILLVHVDIKEPHNALKHLTRICLLADFTLMLAWSYEEAGKIIETYKMFENA
SAERIQEKQETDSYQNVVNALTSIKSINKTDAMTLLNNFGTLENLIQASENQLYSCVGLG
PKKAQKLHKLLNQNFLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g9920.t1 | Gene3D | G3DSA:3.40.50.10130 | - | 60 | 176 | 7.9E-48 |
| 8 | g9920.t1 | Gene3D | G3DSA:1.10.150.20 | 5’ to 3’ exonuclease | 177 | 257 | 4.1E-28 |
| 7 | g9920.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 20 | 50 | - |
| 6 | g9920.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 25 | 44 | - |
| 3 | g9920.t1 | PANTHER | PTHR12749 | EXCISION REPAIR CROSS-COMPLEMENTING 1 ERCC1 | 24 | 257 | 2.8E-90 |
| 2 | g9920.t1 | Pfam | PF03834 | Binding domain of DNA repair protein Ercc1 (rad10/Swi10) | 62 | 175 | 6.0E-47 |
| 1 | g9920.t1 | Pfam | PF14520 | Helix-hairpin-helix domain | 200 | 247 | 4.8E-9 |
| 5 | g9920.t1 | SUPERFAMILY | SSF52980 | Restriction endonuclease-like | 60 | 188 | 1.39E-47 |
| 4 | g9920.t1 | SUPERFAMILY | SSF47781 | RuvA domain 2-like | 185 | 255 | 1.41E-15 |
| 10 | g9920.t1 | TIGRFAM | TIGR00597 | rad10: DNA repair protein rad10 | 60 | 172 | 2.9E-44 |
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:0006281 | DNA repair | BP |
| GO:0003684 | damaged DNA binding | MF |
KEGG
Orthology
- This transcript has been annotated with K10849 (DNA excision repair protein ERCC-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.
