General information for g4555.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA repair protein XRCC1.
Parent gene
- The parent gene g4555 is located on chr_2: 3231409..3232228 (+ 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 | g4555 | g4555.t1 | TSS | g4555.t1 | 3230058 | 3230058 |
| chr_2 | g4555 | g4555.t1 | isoform | g4555.t1 | 3230121 | 3232228 |
| chr_2 | g4555 | g4555.t1 | exon | g4555.t1.exon1 | 3230121 | 3230171 |
| chr_2 | g4555 | g4555.t1 | cds | g4555.t1.CDS1 | 3230121 | 3230171 |
| chr_2 | g4555 | g4555.t1 | exon | g4555.t1.exon2 | 3230230 | 3231419 |
| chr_2 | g4555 | g4555.t1 | cds | g4555.t1.CDS2 | 3230230 | 3231419 |
| chr_2 | g4555 | g4555.t1 | exon | g4555.t1.exon3 | 3231481 | 3232228 |
| chr_2 | g4555 | g4555.t1 | cds | g4555.t1.CDS3 | 3231481 | 3232228 |
| chr_2 | g4555 | g4555.t1 | TTS | g4555.t1 | 3232356 | 3232356 |
Sequences
>g4555.t1 Gene=g4555 Length=1989
ATGCCACAGATTAAAAATATAAAAATTCACAGTTTTAGTAGCGAAGATCCAAATTTCCCG
GCAAAAAATTTAATAAACACTGATGTTACAAAAAGATGGAAATGCGCAAAACCTGGTGAA
AAGAGTGCTTTTGTGGTACTAAAATTAGACAAACCTTATCAAATTACACAAATTGACATT
GGAAATGAATTTTCATCAATGATAGAAATTTTGGTCGGTAATAGCCAACAAGAACCACCT
GATTTTCGAGAAATTTTAATGTCAACAAGCTTTATGACTTTAATTGAAGCCAGAAATGAA
ACAAATCCTCATAGATTGAGAATCTTTAATAAAGGCTTATTTGTTTCTGGTGTGGCTGAG
AAAAAATGGGATTTAATTAAAATTTTGTGTGTTCAAAATTATAACAATCGAAAACAATAC
GGCATCTCTTTTATTAATCTATTTACAAATGATGAAGTGACTTCAAAAGAGGAAGAATCT
CCAATTAAGCTTAATCATATTATACATCAAACACCCAAGCCAATGTCTGCATCTAAACCA
GTTAAAACTCTTGGCAAATTTCATTTTCGTGATTCAAGTTCAGATGAAGAAAAAGATGAA
GACTCGTCGCCCTTTGCAAAATGGAAGGCCAAAAAAAATGAGTTTAAAAATTCTACTAAC
GATTTAGACAAATTGCCAGAAAATTCTAAATCTGGTCTAAAGGAGCATTTAAAAGAAAAA
CTAGCATCTGAAAATCGTAAACGAAATCGGTCAATTGATGAGAAAGATGAGAAAGAAATT
GTGAAAAATCGCAATCGTTCTAAAGGCTTAATGTATGAAAGTAGTGACGATGAACCAAAT
GAAAAATTACAAAAGAAAATTGACAAAGATAAAGAATTAAAAGAAAAGGAAAAACATGTG
CCTAAATTCAATAATAGTACAAAAATTACTACAATTTCTCCACCAAAATCTAATAATAAA
TTTGCAAGTTTCACTTCATCATCTTTTGGTTCATCATCAAAAAGTTTAAATGTCGAATTG
GATAAAAAACAAACTAATAAATCACCAGAGAAGCAAATCACCAAATCACCAGAAAAAGAA
TTAAAAGCTGTTCAATATAAGCCGTTTAATAAATTACTTGAAGGTGTAATTTTTGTTTTG
AGCGGCTATCAAAATCCAGAGCGAGGTGTGATTCGACAGAAAGCTATTGATATGGGTGCT
GTATATAAACCAGATTGGGACAGTTCTTGTACTCATTTAGTTTGTTCCTATAACAACACA
CCTAAGTATCATCAAGTAAAAGGCAAAGGAAAGATAATTACAAAGAAATGGATAGAGCGC
TGTTTCACTGAGCAGAAGCGATTGCCTTGGCGTCGATTTGCAGTAGATAAAAGTGAACAG
GACGAGTCAGAGAGCGAAGAAGAAATTTTTAGTGAATGGCACAAACCAAAAACATCCTCA
AATAATGATGATGATAAAGAAAGTATTAATTCAAATAGCTGTGACATCGATGATGATTAT
GACATGCTTATTGTTGATAAAAGAAATGAAAAAAATCCAAGTCCCATGAAAAAAGTTATT
GCTTCAATGACAATCGATGATAGTGAATCGGATAATGATATGAAAACTGTAAAAATAGAA
AAGAGTGAAATTGACAGTGAAAGCAAAGATAATAACAATGACTTCCAGGAAAACGTGGAG
TGCTATTCAGAAGATTCAATCAGTTCAGTTGATATTACAAAAATTGAATGTGAAGTATTC
AAAGATAAAAAATTTTATTTGAATACAGATCTCAGTGCTACAGATAAAATTTTATTGAAA
GATCATATTAAAAATATGTTGGGTGTTGTTACGAAAAACCCTCATAAGGCAGATTATATA
ATTGTCAAAAAAGCTAAGTCGTTGCCAATCAAAGTATCAGCAGAAATCGTAAAAGAAGTT
TGGATACGAGAGTGTTTCGAATTGCAGGCATTTATACCAACATCACGTTACAGAATTGCT
AAATCATAA
>g4555.t1 Gene=g4555 Length=662
MPQIKNIKIHSFSSEDPNFPAKNLINTDVTKRWKCAKPGEKSAFVVLKLDKPYQITQIDI
GNEFSSMIEILVGNSQQEPPDFREILMSTSFMTLIEARNETNPHRLRIFNKGLFVSGVAE
KKWDLIKILCVQNYNNRKQYGISFINLFTNDEVTSKEEESPIKLNHIIHQTPKPMSASKP
VKTLGKFHFRDSSSDEEKDEDSSPFAKWKAKKNEFKNSTNDLDKLPENSKSGLKEHLKEK
LASENRKRNRSIDEKDEKEIVKNRNRSKGLMYESSDDEPNEKLQKKIDKDKELKEKEKHV
PKFNNSTKITTISPPKSNNKFASFTSSSFGSSSKSLNVELDKKQTNKSPEKQITKSPEKE
LKAVQYKPFNKLLEGVIFVLSGYQNPERGVIRQKAIDMGAVYKPDWDSSCTHLVCSYNNT
PKYHQVKGKGKIITKKWIERCFTEQKRLPWRRFAVDKSEQDESESEEEIFSEWHKPKTSS
NNDDDKESINSNSCDIDDDYDMLIVDKRNEKNPSPMKKVIASMTIDDSESDNDMKTVKIE
KSEIDSESKDNNNDFQENVECYSEDSISSVDITKIECEVFKDKKFYLNTDLSATDKILLK
DHIKNMLGVVTKNPHKADYIIVKKAKSLPIKVSAEIVKEVWIRECFELQAFIPTSRYRIA
KS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g4555.t1 | Coils | Coil | Coil | 234 | 254 | - |
| 11 | g4555.t1 | Coils | Coil | Coil | 280 | 300 | - |
| 10 | g4555.t1 | Gene3D | G3DSA:2.60.120.260 | - | 1 | 149 | 1.5E-53 |
| 9 | g4555.t1 | Gene3D | G3DSA:3.40.50.10190 | - | 366 | 454 | 4.9E-22 |
| 8 | g4555.t1 | Gene3D | G3DSA:3.40.50.10190 | - | 572 | 661 | 1.3E-9 |
| 18 | g4555.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 219 | 314 | - |
| 20 | g4555.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 219 | 303 | - |
| 16 | g4555.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 337 | 359 | - |
| 19 | g4555.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 340 | 359 | - |
| 15 | g4555.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 456 | 492 | - |
| 17 | g4555.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 468 | 492 | - |
| 4 | g4555.t1 | PANTHER | PTHR11370 | DNA-REPAIR PROTEIN XRCC1 | 1 | 661 | 2.8E-106 |
| 1 | g4555.t1 | Pfam | PF01834 | XRCC1 N terminal domain | 1 | 147 | 1.8E-49 |
| 3 | g4555.t1 | Pfam | PF00533 | BRCA1 C Terminus (BRCT) domain | 370 | 442 | 3.7E-8 |
| 2 | g4555.t1 | Pfam | PF16589 | BRCT domain, a BRCA1 C-terminus domain | 579 | 658 | 7.4E-8 |
| 21 | g4555.t1 | ProSiteProfiles | PS50172 | BRCT domain profile. | 368 | 455 | 15.204 |
| 22 | g4555.t1 | ProSiteProfiles | PS50172 | BRCT domain profile. | 575 | 659 | 12.867 |
| 13 | g4555.t1 | SMART | SM00292 | BRCT_7 | 370 | 445 | 6.5E-11 |
| 14 | g4555.t1 | SMART | SM00292 | BRCT_7 | 577 | 649 | 2.1E-4 |
| 5 | g4555.t1 | SUPERFAMILY | SSF49785 | Galactose-binding domain-like | 1 | 148 | 1.11E-48 |
| 7 | g4555.t1 | SUPERFAMILY | SSF52113 | BRCT domain | 367 | 457 | 1.74E-22 |
| 6 | g4555.t1 | SUPERFAMILY | SSF52113 | BRCT domain | 579 | 658 | 5.82E-9 |
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:0003684 | damaged DNA binding | MF |
| GO:0000012 | single strand break repair | BP |
KEGG
Orthology
- This transcript has been annotated with K10803 (DNA-repair protein XRCC1)
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.
