General information for g12017.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g12017 is located on chr_1: 20455857..20456953 (+ 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 | g12017 | g12017.t4 | isoform | g12017.t4 | 20455857 | 20456953 |
| chr_1 | g12017 | g12017.t4 | exon | g12017.t4.exon1 | 20455857 | 20456953 |
| chr_1 | g12017 | g12017.t4 | cds | g12017.t4.CDS1 | 20455874 | 20456953 |
| chr_1 | g12017 | g12017.t4 | TTS | g12017.t4 | 20457042 | 20457042 |
| chr_1 | g12017 | g12017.t4 | TSS | g12017.t4 | NA | NA |
Sequences
>g12017.t4 Gene=g12017 Length=1097
TTTATAGATCAGAAAGGATGCAAAACAAAATTGAAAATGAAAATGAAGTCGTTCTTCAAA
AAATGTATGAAAGAGTTCGTCAAAAAGTATTGGATAAAATTCAAGTTGAACTCATAAAAC
GACATAAGGAAATTTTACAATATCCAAAAGGAAGAGAATTGACAATTGATGATTTATGTG
ACTTTTTTGAAGTCGATACAGAAAGTGAATTTGCTTTGAATTTGATTGAAAATTTAAATC
CTTCAGATTTAGCTAAAATCAACAATATCGTTGCAAAACGAAAATCTGAACTTGAAGATA
AAATAAAGATTCTCATGCAGCAGGAATCTGATCGAAGAGTAACCCAAGTCATAAAGTTTC
GCGCAGCTGATGCTGATAATCCAAAATTGGATCGTTTAATTTGTTGGTGGCATCCAAATG
AAGAAGTTTTCGATATTATAAAGATAGGTAAAATGATTGAGCTGATTAAAGCAACGACAG
ATAACATAAATATCATAATAAATCAAAAAACGATTTTTAAAGAACTAAAAAAGAAACCTG
ATTTGACAAAATTTAAATTATACTTTCGCAAAGAGACAAAGTTTCAAGACATCAAAGAAG
ACTTTTCACCATTACATAATGAATTCGATATAGCATGTATAATAATTTACATTGCTGAAC
CATCAATAAATAAAAATCAAGAAGTATTTATTGCAGATGAACATTACAATCTTCTTTGTG
TCAATTTTTACATCGATATTTCTGAATATGCATATGATAATGTATTGACTGAAGGAAGAA
TTCTATACGTTCGTAATCTACAATGGCGAAATTCTTTTCGAAAGCCACATAAAAATATAC
CAGAAGCATTCGCAATTGCTGATTCAACTACCTTCGTTACAAACCCAGGGGAACCAAACG
AGAAACAGCGTATAAATGAATTGACAAACGCAATCAACAGTAATTCAGAATATATGGGAA
AATGCAGAGAGAAAATAATAAGCCTAATTGGTCCAGATATTTTTAAAAAGGAAGGTCTGC
ACAAAAAATATGGATTCTTGAAAAAGATTTCATTACCTGCAAAACCACCAGTAGATTTGT
CTTTCAGTAATGATTAA
>g12017.t4 Gene=g12017 Length=359
MQNKIENENEVVLQKMYERVRQKVLDKIQVELIKRHKEILQYPKGRELTIDDLCDFFEVD
TESEFALNLIENLNPSDLAKINNIVAKRKSELEDKIKILMQQESDRRVTQVIKFRAADAD
NPKLDRLICWWHPNEEVFDIIKIGKMIELIKATTDNINIIINQKTIFKELKKKPDLTKFK
LYFRKETKFQDIKEDFSPLHNEFDIACIIIYIAEPSINKNQEVFIADEHYNLLCVNFYID
ISEYAYDNVLTEGRILYVRNLQWRNSFRKPHKNIPEAFAIADSTTFVTNPGEPNEKQRIN
ELTNAINSNSEYMGKCREKIISLIGPDIFKKEGLHKKYGFLKKISLPAKPPVDLSFSND
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12017.t4 | Coils | Coil | Coil | 82 | 102 | - |
| 5 | g12017.t4 | Gene3D | G3DSA:2.40.50.140 | - | 184 | 328 | 8.4E-24 |
| 2 | g12017.t4 | PANTHER | PTHR11289:SF0 | BREAST CANCER TYPE 2 SUSCEPTIBILITY PROTEIN | 6 | 330 | 2.2E-20 |
| 3 | g12017.t4 | PANTHER | PTHR11289 | BREAST CANCER TYPE 2 SUSCEPTIBILITY PROTEIN BRCA2 | 6 | 330 | 2.2E-20 |
| 1 | g12017.t4 | Pfam | PF09104 | BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 | 184 | 323 | 1.7E-27 |
| 4 | g12017.t4 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 187 | 326 | 2.44E-21 |
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:0006281 | DNA repair | BP |
| GO:0000724 | double-strand break repair via homologous recombination | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
