Gene loci information

Transcript annotation

  • This transcript has been annotated as BRCA1-associated protein.

Parent gene

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.t4 TSS g12076.t4 20813989 20813989
chr_1 g12076 g12076.t4 isoform g12076.t4 20814070 20815926
chr_1 g12076 g12076.t4 exon g12076.t4.exon1 20814070 20814133
chr_1 g12076 g12076.t4 cds g12076.t4.CDS1 20814070 20814133
chr_1 g12076 g12076.t4 exon g12076.t4.exon2 20814228 20814519
chr_1 g12076 g12076.t4 cds g12076.t4.CDS2 20814228 20814519
chr_1 g12076 g12076.t4 exon g12076.t4.exon3 20814588 20814855
chr_1 g12076 g12076.t4 cds g12076.t4.CDS3 20814588 20814855
chr_1 g12076 g12076.t4 exon g12076.t4.exon4 20814922 20815926
chr_1 g12076 g12076.t4 cds g12076.t4.CDS4 20814922 20815176
chr_1 g12076 g12076.t4 TTS g12076.t4 20816005 20816005

Sequences

>g12076.t4 Gene=g12076 Length=1629
ATGTCTATATTAGTTACACTGTGCTTACTAAAAATTGAAATAGTTGATGAAATGGAAAAT
GAAGAATCAGCAGCAGCATCTTCGGTTGATCAACGAGTCATAAAAGAACGTCGAGGACAG
CGACAACCAAAAACTATTCAAATAGAAACTTATGCAAATGTACTTGCAGGCGAACATCAA
CAAATTAAAGGTGTTTTACCAAAAAATTCAAATACAAACTCAAGGGAGCAAACGCCACTC
ACAGAAAATAATTCAGAAACGAGCTCAGTCCCAGATACACCAAATGAAGTGAAATTTTTC
TCTGGTAATCCATTTGTTGAACAAACTAATGGAATTTTGCATCTATACAAAAAGAATGAA
CGAGATTCAATACAAGATGGTCTCTCTCAAACACTTTGTTTGCTTGCTGTTCCAGCAACA
TTGAGTTGCCATGATATTCTGAATTTTATTGCACCTTGTCATTCAGTCATCAATCATGTT
CGCATTATTCGAGATTCCAATCCAAATCAATATATGGTCATTTTAGATTTTCGTACTGTC
GATGATGCTTACGAGTTTTATAAAACTTTCAATGGTGTTCCATACAATAGTCTTGAACCA
GAACAACTTTGTCATACACTTTGGGTAAGTGCTATTGCATGGGATAACATGGATTCAACT
CCACCAAATCACACGGAATTGCCGGTTTGTCCTGTTTGCCTCGATCGTATGGACGAAAGT
GTTGATGGTGTGCTGACAATTTTATGTAATCACACATTTCACTGTGGATGTTTAGTAAAA
TGGGGAGATAGTACTTGCCCTATTTGTCGTTATGTACAGACACCAGAACTCACACAAAGT
TCAGTATGCATGGAATGTGAAGGAACTGAAGCACTATAGATTTGTTTAATTTGTGGACAT
GTAGGATGTGGTCGCTATCAAGGTGGACATGCCGCAATACATTACAGAAATACAAACCAT
ACATATGCTCTACAATTGGGAACTAATCGAGTATGGGATTATGCTGGCGATAATTTTGTT
CATAGACTTTTGCAAAACAAATCAGATGGAAAACTTGTTGCAACTCAATCACCTAGTGGA
GAAGGAGAGGAGAAAATTGATTCAATGCAATTAGAATTTACATATCTCTTAACTTCTCAA
CTTGATACTCAACGACAACATTATGAAGAGAGACTTGCAAGAATTGAAGCTGCTATGGTT
AATGATAAGCAAGGGATTCTCAAAGAGACAGAAGCTATTAAAGAGAAAAATTCTGAATTT
GAACAAAAATTAAATGCTGTAGTCAAAGAAAAACAGGCAATTGAGAAGAAGTTGAATGCA
ATGAGTAGTCGTCTAGCGATAGTACTAAAAGATCTCTCTGAAGAGAAACAATTTTCAAAA
ACTCTTCAATTAAATCACAATTCTTGGCAGACAAAGTACTCAAATTTGGAAAAACTTTAT
AAAGAAAAAGAGCAAGAAGTTATTGATTTAAAGGAACAAGTGAGAGATTTAATGTTTTAT
ATGGAAGCTCAAAATACAATTTCCAAATCTGAACTGAAAGATGAAATTGCAGAAGGTTCT
GTAACAATAGGTGAAACAAGTGGAAATGGTAAAAACAAAAATCGACGCAAGAAGAAATCA
AGCACATAA

>g12076.t4 Gene=g12076 Length=292
MSILVTLCLLKIEIVDEMENEESAAASSVDQRVIKERRGQRQPKTIQIETYANVLAGEHQ
QIKGVLPKNSNTNSREQTPLTENNSETSSVPDTPNEVKFFSGNPFVEQTNGILHLYKKNE
RDSIQDGLSQTLCLLAVPATLSCHDILNFIAPCHSVINHVRIIRDSNPNQYMVILDFRTV
DDAYEFYKTFNGVPYNSLEPEQLCHTLWVSAIAWDNMDSTPPNHTELPVCPVCLDRMDES
VDGVLTILCNHTFHCGCLVKWGDSTCPICRYVQTPELTQSSVCMECEGTEAL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g12076.t4 CDD cd12718 RRM_BRAP2 129 212 4.70149E-39
10 g12076.t4 CDD cd16457 RING-H2_BRAP2 228 271 8.28806E-27
8 g12076.t4 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 213 276 6.6E-10
13 g12076.t4 MobiDBLite mobidb-lite consensus disorder prediction 21 41 -
12 g12076.t4 MobiDBLite mobidb-lite consensus disorder prediction 62 92 -
14 g12076.t4 MobiDBLite mobidb-lite consensus disorder prediction 64 92 -
3 g12076.t4 PANTHER PTHR24007 BRCA1-ASSOCIATED PROTEIN 66 292 3.4E-72
4 g12076.t4 PANTHER PTHR24007:SF7 BRCA1-ASSOCIATED PROTEIN 66 292 3.4E-72
1 g12076.t4 Pfam PF07576 BRCA1-associated protein 2 127 215 6.3E-27
2 g12076.t4 Pfam PF13639 Ring finger domain 229 270 6.4E-8
15 g12076.t4 ProSiteProfiles PS50089 Zinc finger RING-type profile. 230 270 12.888
11 g12076.t4 SMART SM00184 ring_2 230 269 8.1E-7
5 g12076.t4 SUPERFAMILY SSF54928 RNA-binding domain, RBD 130 197 6.53E-5
6 g12076.t4 SUPERFAMILY SSF57850 RING/U-box 208 275 1.37E-12
7 g12076.t4 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

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.

Raw TPM values