General information for g12076.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as BRCA1-associated protein.
Parent gene
- The parent gene g12076 is located on chr_1: 20814940..20815926 (+ 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 | g12076 | g12076.t3 | TSS | g12076.t3 | 20813989 | 20813989 |
| chr_1 | g12076 | g12076.t3 | isoform | g12076.t3 | 20814070 | 20815926 |
| chr_1 | g12076 | g12076.t3 | exon | g12076.t3.exon1 | 20814070 | 20814136 |
| chr_1 | g12076 | g12076.t3 | cds | g12076.t3.CDS1 | 20814070 | 20814136 |
| chr_1 | g12076 | g12076.t3 | exon | g12076.t3.exon2 | 20814234 | 20814519 |
| chr_1 | g12076 | g12076.t3 | cds | g12076.t3.CDS2 | 20814234 | 20814519 |
| chr_1 | g12076 | g12076.t3 | exon | g12076.t3.exon3 | 20814588 | 20814855 |
| chr_1 | g12076 | g12076.t3 | cds | g12076.t3.CDS3 | 20814588 | 20814855 |
| chr_1 | g12076 | g12076.t3 | exon | g12076.t3.exon4 | 20814922 | 20815926 |
| chr_1 | g12076 | g12076.t3 | cds | g12076.t3.CDS4 | 20814922 | 20815176 |
| chr_1 | g12076 | g12076.t3 | TTS | g12076.t3 | 20816005 | 20816005 |
Sequences
>g12076.t3 Gene=g12076 Length=1626
ATGTCTATATTAGTTACACTGTGCTTACTAAAAATTGAAATAGTTGATGAAATGGAAAAT
GAAGGTGCAGCAGCATCTTCGGTTGATCAACGAGTCATAAAAGAACGTCGAGGACAGCGA
CAACCAAAAACTATTCAAATAGAAACTTATGCAAATGTACTTGCAGGCGAACATCAACAA
ATTAAAGGTGTTTTACCAAAAAATTCAAATACAAACTCAAGGGAGCAAACGCCACTCACA
GAAAATAATTCAGAAACGAGCTCAGTCCCAGATACACCAAATGAAGTGAAATTTTTCTCT
GGTAATCCATTTGTTGAACAAACTAATGGAATTTTGCATCTATACAAAAAGAATGAACGA
GATTCAATACAAGATGGTCTCTCTCAAACACTTTGTTTGCTTGCTGTTCCAGCAACATTG
AGTTGCCATGATATTCTGAATTTTATTGCACCTTGTCATTCAGTCATCAATCATGTTCGC
ATTATTCGAGATTCCAATCCAAATCAATATATGGTCATTTTAGATTTTCGTACTGTCGAT
GATGCTTACGAGTTTTATAAAACTTTCAATGGTGTTCCATACAATAGTCTTGAACCAGAA
CAACTTTGTCATACACTTTGGGTAAGTGCTATTGCATGGGATAACATGGATTCAACTCCA
CCAAATCACACGGAATTGCCGGTTTGTCCTGTTTGCCTCGATCGTATGGACGAAAGTGTT
GATGGTGTGCTGACAATTTTATGTAATCACACATTTCACTGTGGATGTTTAGTAAAATGG
GGAGATAGTACTTGCCCTATTTGTCGTTATGTACAGACACCAGAACTCACACAAAGTTCA
GTATGCATGGAATGTGAAGGAACTGAAGCACTATAGATTTGTTTAATTTGTGGACATGTA
GGATGTGGTCGCTATCAAGGTGGACATGCCGCAATACATTACAGAAATACAAACCATACA
TATGCTCTACAATTGGGAACTAATCGAGTATGGGATTATGCTGGCGATAATTTTGTTCAT
AGACTTTTGCAAAACAAATCAGATGGAAAACTTGTTGCAACTCAATCACCTAGTGGAGAA
GGAGAGGAGAAAATTGATTCAATGCAATTAGAATTTACATATCTCTTAACTTCTCAACTT
GATACTCAACGACAACATTATGAAGAGAGACTTGCAAGAATTGAAGCTGCTATGGTTAAT
GATAAGCAAGGGATTCTCAAAGAGACAGAAGCTATTAAAGAGAAAAATTCTGAATTTGAA
CAAAAATTAAATGCTGTAGTCAAAGAAAAACAGGCAATTGAGAAGAAGTTGAATGCAATG
AGTAGTCGTCTAGCGATAGTACTAAAAGATCTCTCTGAAGAGAAACAATTTTCAAAAACT
CTTCAATTAAATCACAATTCTTGGCAGACAAAGTACTCAAATTTGGAAAAACTTTATAAA
GAAAAAGAGCAAGAAGTTATTGATTTAAAGGAACAAGTGAGAGATTTAATGTTTTATATG
GAAGCTCAAAATACAATTTCCAAATCTGAACTGAAAGATGAAATTGCAGAAGGTTCTGTA
ACAATAGGTGAAACAAGTGGAAATGGTAAAAACAAAAATCGACGCAAGAAGAAATCAAGC
ACATAA
>g12076.t3 Gene=g12076 Length=291
MSILVTLCLLKIEIVDEMENEGAAASSVDQRVIKERRGQRQPKTIQIETYANVLAGEHQQ
IKGVLPKNSNTNSREQTPLTENNSETSSVPDTPNEVKFFSGNPFVEQTNGILHLYKKNER
DSIQDGLSQTLCLLAVPATLSCHDILNFIAPCHSVINHVRIIRDSNPNQYMVILDFRTVD
DAYEFYKTFNGVPYNSLEPEQLCHTLWVSAIAWDNMDSTPPNHTELPVCPVCLDRMDESV
DGVLTILCNHTFHCGCLVKWGDSTCPICRYVQTPELTQSSVCMECEGTEAL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g12076.t3 | CDD | cd12718 | RRM_BRAP2 | 128 | 211 | 3.24595E-39 |
| 10 | g12076.t3 | CDD | cd16457 | RING-H2_BRAP2 | 227 | 270 | 8.03819E-27 |
| 8 | g12076.t3 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 212 | 275 | 6.6E-10 |
| 12 | g12076.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 61 | 91 | - |
| 13 | g12076.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 63 | 91 | - |
| 3 | g12076.t3 | PANTHER | PTHR24007 | BRCA1-ASSOCIATED PROTEIN | 70 | 291 | 3.0E-72 |
| 4 | g12076.t3 | PANTHER | PTHR24007:SF7 | BRCA1-ASSOCIATED PROTEIN | 70 | 291 | 3.0E-72 |
| 1 | g12076.t3 | Pfam | PF07576 | BRCA1-associated protein 2 | 126 | 214 | 6.2E-27 |
| 2 | g12076.t3 | Pfam | PF13639 | Ring finger domain | 228 | 269 | 6.4E-8 |
| 14 | g12076.t3 | ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 229 | 269 | 12.888 |
| 11 | g12076.t3 | SMART | SM00184 | ring_2 | 229 | 268 | 8.1E-7 |
| 5 | g12076.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 129 | 196 | 6.53E-5 |
| 6 | g12076.t3 | SUPERFAMILY | SSF57850 | RING/U-box | 207 | 274 | 1.34E-12 |
| 7 | g12076.t3 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 17 | - |
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:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K10632 (BRCA1-associated 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.
