General information for g12017.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Breast cancer type 2 susceptibility protein.
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.t1 | TSS | g12017.t1 | 20452783 | 20452783 |
| chr_1 | g12017 | g12017.t1 | isoform | g12017.t1 | 20452972 | 20456953 |
| chr_1 | g12017 | g12017.t1 | exon | g12017.t1.exon1 | 20452972 | 20453008 |
| chr_1 | g12017 | g12017.t1 | cds | g12017.t1.CDS1 | 20452972 | 20453008 |
| chr_1 | g12017 | g12017.t1 | exon | g12017.t1.exon2 | 20453074 | 20453729 |
| chr_1 | g12017 | g12017.t1 | cds | g12017.t1.CDS2 | 20453074 | 20453729 |
| chr_1 | g12017 | g12017.t1 | exon | g12017.t1.exon3 | 20453794 | 20454216 |
| chr_1 | g12017 | g12017.t1 | cds | g12017.t1.CDS3 | 20453794 | 20454216 |
| chr_1 | g12017 | g12017.t1 | exon | g12017.t1.exon4 | 20454275 | 20455793 |
| chr_1 | g12017 | g12017.t1 | cds | g12017.t1.CDS4 | 20454275 | 20455793 |
| chr_1 | g12017 | g12017.t1 | exon | g12017.t1.exon5 | 20455857 | 20456953 |
| chr_1 | g12017 | g12017.t1 | cds | g12017.t1.CDS5 | 20455857 | 20456953 |
| chr_1 | g12017 | g12017.t1 | TTS | g12017.t1 | 20457042 | 20457042 |
Sequences
>g12017.t1 Gene=g12017 Length=3732
ATGGATACCAGTTGGTTAGATTATGATTCGGATGAAGACGATAAAAACATTCAAATTTCA
AAGTTAGGTATAGATGAATCAATTGAATTTGAAGAATCTTTTGAGAGAAACAAGAAAATA
AGGACTAAGAAAAGAACTGGTAAACGTTCAAGTACACGACAAGCTCACAAACGTCGTAAA
AAAGAAGAAATTGATGAACCAAAACAGGAACAAGAAGGTCAAAGTGTGATTGATGCATCA
AATGATGATGAACAAGAAGCTCAAAATGTAATCGATGCATTAAATGATGATGAACAAGAA
GCTCAAAGTGTGAACGATTCATCAAATGATGACGAACAAAAATTATCTGAGGCACAATGG
GAAAAGGAATTTATTGATGAATTGAGTCAAACTGTTGTGGATTTTTCACCAGGAGCATCA
CCAGAACAAATAAAAGATTGTATTGACAAATCATTTTTAGAAGTATCACATGAATCAAAT
TTCGATGATTTAAATCAATCAATTCATGAATTGTCACAAAAATTGGAAAGTTCTGTAAAC
GGTGTACAATTAGTCAATAATGTCATTGGAACTGTTACTTCAAATCGTTACAATCAGGAT
GATATTGTGCACCACAAAGATATACAGGAACCACAAGAAGAAAATAAAAAACCACAAGAT
GAAGATTCAAAAGAAGAAGATACAGTAGTAACAATCAATAAAAAAAAGACTGTCAGATTT
AAAGAACTAGATGTTGCATCATCTAGCAATTCCCGTACAAAAAATGATTTAAAATTCAAT
GAGACAACACTTATACCAAAAATTCAACAACCATTTGGTTTTGCATTCGCATCTGGGAAA
AATATTGCTCTGGATGAAAAGGTCTTGTCAAACATTAAAAACAGATTTCAAAAAGAAGAA
GAAAATATAAATTACAATGAAATAAGTGAAACTTCTATAGATGATTTTAATCACACTGCT
GCAAATACCACAATTCAATCACCGAAAACTCCACTTATGACATCAACGCCCATTGTTAAA
AAATCATTTCGAAAAACTTCGTTGTATAATCGTGTAGCAAATAATTTTTTGCTTACACAG
CACGATTTGGAAATTGATTATGATCATATCGATCAGATTGATAGAGAGCAATCATTTAAA
AATAGTAAATCTGATAATAATGAGCAACAAAATTTCGTTGGATTCGCTTTTGCATCTGGA
AAGCATATTGCTGTAGATGAAAAAGTTTTATCAAATATGAAAAACAAATTTCAAATAGAA
GACAACACTGATATCAATAATATTGAAATAGATGAAACTGAGACTAATCTAAATGAAAGT
GAGATTAAAAAAGATGCAACTGAAATTATTCAAAATGAAAATGAGATTGAAATAGATGAA
AATGATTTTAAAAACGTTGATCCTCAACCTATTGCAATCAATACTATTCAATCACAAAAA
GAAGCCTATCAAAAATCTCTGTTTTCAAAATACGAAGATGAGAATTATGATAAATCAAAT
GCGATACCATCGAACTCAAACAGAATGCCATCACAGCCTCGTACTAATGATTTCAATCAA
ATTCCTGACTGTGCAACTCAAATAAAATATGAAGAAATTAATGATTTAATAACAAAAGTT
GAGATAGCTGAAAGTATAAGAATCGCTCGAGTGGAAGAGCTCAAAAAACAAATTGAATTT
ATATCAAAAAAGTCAAAAGATGATCTTAATTTCAGTTTTGGAAAACTTTTCATTCAGAAA
AGTCAAACAAATCGACTTAAATTGAGAGACTATCATTCTAGTTCTTTAATCACATTGAAA
GAATCCATGGCTAATAGATTTATTCCATATGATCAAATAACACAACACTTATTTGATATG
AGTTGCTATACGAATGTTCCGCATAATGAAGTTTTCGTAACAATTGCTGATGATGCAAAA
TTGGTGTTTAATTCGAAAAATTCTGGAACAGTAAGTTTTAACGAAATAAAACATAGCTTT
CTTGCCATGAAAGGAATAAAACCCAAATTGTTACCTGAAGCATGGGTTCAAAATGCCTAT
GAAATGATATTTTGGAAGTTAAATTTCATGGAGAATTTTCTTGAGAAAATTGATAAGGAT
ATGGTTCTTAATCCTGAGAATATCTTACTTCAAATGAAATATCGTTATGATCGTGAAATA
CATAAATTCCAATCACCCCCATTGCGTCGAATTTTAGAAAAGGATGTACCAGCTGGTCAT
CGTATCGTGTTAAAAGTTGTAAATATATCTTACACTTCTGAAAATGGTTATGAACTAGAA
TTATCTGATGGCTGGTACAAAATTAGAACTCTCATTGATTCATGTCTCGCTGAAGCAATT
ACTAAGCGTAAAATACAAGTTCATTCTAAACTTTTGATATGCAATATGGAACTTAAACAA
ACTATTAATGATACAAACGTATTTGTGTTATTAGAAGCATCAAAATTAAAAATTTCTGGA
AATTCTACACGATTAGTAGAATGGAACACAAAAATGGGTTTCTGCAAAATTCCTTTCCCT
TTTCAAATTACTTTAGATTCTGTTAAAAATAATGGTGGTATTATTGGAAAATTACGAATT
GTAATAACACATGTTTATAATCCAATTTATGTTGAGACAGTAGAAGATAAACGAGTTTAT
AGATCAGAAAGGATGCAAAACAAAATTGAAAATGAAAATGAAGTCGTTCTTCAAAAAATG
TATGAAAGAGTTCGTCAAAAAGTATTGGATAAAATTCAAGTTGAACTCATAAAACGACAT
AAGGAAATTTTACAATATCCAAAAGGAAGAGAATTGACAATTGATGATTTATGTGACTTT
TTTGAAGTCGATACAGAAAGTGAATTTGCTTTGAATTTGATTGAAAATTTAAATCCTTCA
GATTTAGCTAAAATCAACAATATCGTTGCAAAACGAAAATCTGAACTTGAAGATAAAATA
AAGATTCTCATGCAGCAGGAATCTGATCGAAGAGTAACCCAAGTCATAAAGTTTCGCGCA
GCTGATGCTGATAATCCAAAATTGGATCGTTTAATTTGTTGGTGGCATCCAAATGAAGAA
GTTTTCGATATTATAAAGATAGGTAAAATGATTGAGCTGATTAAAGCAACGACAGATAAC
ATAAATATCATAATAAATCAAAAAACGATTTTTAAAGAACTAAAAAAGAAACCTGATTTG
ACAAAATTTAAATTATACTTTCGCAAAGAGACAAAGTTTCAAGACATCAAAGAAGACTTT
TCACCATTACATAATGAATTCGATATAGCATGTATAATAATTTACATTGCTGAACCATCA
ATAAATAAAAATCAAGAAGTATTTATTGCAGATGAACATTACAATCTTCTTTGTGTCAAT
TTTTACATCGATATTTCTGAATATGCATATGATAATGTATTGACTGAAGGAAGAATTCTA
TACGTTCGTAATCTACAATGGCGAAATTCTTTTCGAAAGCCACATAAAAATATACCAGAA
GCATTCGCAATTGCTGATTCAACTACCTTCGTTACAAACCCAGGGGAACCAAACGAGAAA
CAGCGTATAAATGAATTGACAAACGCAATCAACAGTAATTCAGAATATATGGGAAAATGC
AGAGAGAAAATAATAAGCCTAATTGGTCCAGATATTTTTAAAAAGGAAGGTCTGCACAAA
AAATATGGATTCTTGAAAAAGATTTCATTACCTGCAAAACCACCAGTAGATTTGTCTTTC
AGTAATGATTAA
>g12017.t1 Gene=g12017 Length=1243
MDTSWLDYDSDEDDKNIQISKLGIDESIEFEESFERNKKIRTKKRTGKRSSTRQAHKRRK
KEEIDEPKQEQEGQSVIDASNDDEQEAQNVIDALNDDEQEAQSVNDSSNDDEQKLSEAQW
EKEFIDELSQTVVDFSPGASPEQIKDCIDKSFLEVSHESNFDDLNQSIHELSQKLESSVN
GVQLVNNVIGTVTSNRYNQDDIVHHKDIQEPQEENKKPQDEDSKEEDTVVTINKKKTVRF
KELDVASSSNSRTKNDLKFNETTLIPKIQQPFGFAFASGKNIALDEKVLSNIKNRFQKEE
ENINYNEISETSIDDFNHTAANTTIQSPKTPLMTSTPIVKKSFRKTSLYNRVANNFLLTQ
HDLEIDYDHIDQIDREQSFKNSKSDNNEQQNFVGFAFASGKHIAVDEKVLSNMKNKFQIE
DNTDINNIEIDETETNLNESEIKKDATEIIQNENEIEIDENDFKNVDPQPIAINTIQSQK
EAYQKSLFSKYEDENYDKSNAIPSNSNRMPSQPRTNDFNQIPDCATQIKYEEINDLITKV
EIAESIRIARVEELKKQIEFISKKSKDDLNFSFGKLFIQKSQTNRLKLRDYHSSSLITLK
ESMANRFIPYDQITQHLFDMSCYTNVPHNEVFVTIADDAKLVFNSKNSGTVSFNEIKHSF
LAMKGIKPKLLPEAWVQNAYEMIFWKLNFMENFLEKIDKDMVLNPENILLQMKYRYDREI
HKFQSPPLRRILEKDVPAGHRIVLKVVNISYTSENGYELELSDGWYKIRTLIDSCLAEAI
TKRKIQVHSKLLICNMELKQTINDTNVFVLLEASKLKISGNSTRLVEWNTKMGFCKIPFP
FQITLDSVKNNGGIIGKLRIVITHVYNPIYVETVEDKRVYRSERMQNKIENENEVVLQKM
YERVRQKVLDKIQVELIKRHKEILQYPKGRELTIDDLCDFFEVDTESEFALNLIENLNPS
DLAKINNIVAKRKSELEDKIKILMQQESDRRVTQVIKFRAADADNPKLDRLICWWHPNEE
VFDIIKIGKMIELIKATTDNINIIINQKTIFKELKKKPDLTKFKLYFRKETKFQDIKEDF
SPLHNEFDIACIIIYIAEPSINKNQEVFIADEHYNLLCVNFYIDISEYAYDNVLTEGRIL
YVRNLQWRNSFRKPHKNIPEAFAIADSTTFVTNPGEPNEKQRINELTNAINSNSEYMGKC
REKIISLIGPDIFKKEGLHKKYGFLKKISLPAKPPVDLSFSND
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 22 | g12017.t1 | Coils | Coil | Coil | 77 | 97 | - |
| 21 | g12017.t1 | Coils | Coil | Coil | 966 | 986 | - |
| 17 | g12017.t1 | Gene3D | G3DSA:2.40.50.140 | - | 725 | 839 | 1.0E-22 |
| 18 | g12017.t1 | Gene3D | G3DSA:2.40.50.140 | - | 840 | 1050 | 2.9E-21 |
| 20 | g12017.t1 | Gene3D | G3DSA:1.10.132.40 | - | 872 | 992 | 2.9E-21 |
| 19 | g12017.t1 | Gene3D | G3DSA:2.40.50.140 | - | 1072 | 1212 | 7.1E-23 |
| 13 | g12017.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 119 | - |
| 15 | g12017.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 10 | 39 | - |
| 11 | g12017.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 40 | 56 | - |
| 16 | g12017.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 57 | 72 | - |
| 12 | g12017.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 73 | 88 | - |
| 10 | g12017.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 95 | 109 | - |
| 14 | g12017.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 204 | 230 | - |
| 4 | g12017.t1 | PANTHER | PTHR11289:SF0 | BREAST CANCER TYPE 2 SUSCEPTIBILITY PROTEIN | 48 | 1214 | 1.1E-110 |
| 5 | g12017.t1 | PANTHER | PTHR11289 | BREAST CANCER TYPE 2 SUSCEPTIBILITY PROTEIN BRCA2 | 48 | 1214 | 1.1E-110 |
| 2 | g12017.t1 | Pfam | PF09169 | BRCA2, helical | 556 | 722 | 6.4E-23 |
| 1 | g12017.t1 | Pfam | PF09103 | BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 | 728 | 836 | 1.9E-25 |
| 3 | g12017.t1 | Pfam | PF09104 | BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 | 1068 | 1207 | 1.4E-26 |
| 23 | g12017.t1 | ProSiteProfiles | PS50138 | BRCA2 repeat profile. | 267 | 301 | 8.639 |
| 6 | g12017.t1 | SUPERFAMILY | SSF81872 | BRCA2 helical domain | 563 | 721 | 2.49E-17 |
| 8 | g12017.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 726 | 841 | 6.94E-24 |
| 7 | g12017.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 843 | 1079 | 7.8E-10 |
| 9 | g12017.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 1071 | 1210 | 1.68E-20 |
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 transcript has been annotated with K08775 (breast cancer 2 susceptibility protein)
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.
