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.t5 TSS g12076.t5 20813989 20813989
chr_1 g12076 g12076.t5 isoform g12076.t5 20814070 20815926
chr_1 g12076 g12076.t5 exon g12076.t5.exon1 20814070 20814140
chr_1 g12076 g12076.t5 cds g12076.t5.CDS1 20814128 20814140
chr_1 g12076 g12076.t5 exon g12076.t5.exon2 20814234 20814519
chr_1 g12076 g12076.t5 cds g12076.t5.CDS2 20814234 20814519
chr_1 g12076 g12076.t5 exon g12076.t5.exon3 20814588 20814855
chr_1 g12076 g12076.t5 cds g12076.t5.CDS3 20814588 20814855
chr_1 g12076 g12076.t5 exon g12076.t5.exon4 20814922 20815926
chr_1 g12076 g12076.t5 cds g12076.t5.CDS4 20814922 20815176
chr_1 g12076 g12076.t5 TTS g12076.t5 20816005 20816005

Sequences

>g12076.t5 Gene=g12076 Length=1630
ATGTCTATATTAGTTACACTGTGCTTACTAAAAATTGAAATAGTTGATGAAATGGAAAAT
GAAGGTGGTGACAGCAGCATCTTCGGTTGATCAACGAGTCATAAAAGAACGTCGAGGACA
GCGACAACCAAAAACTATTCAAATAGAAACTTATGCAAATGTACTTGCAGGCGAACATCA
ACAAATTAAAGGTGTTTTACCAAAAAATTCAAATACAAACTCAAGGGAGCAAACGCCACT
CACAGAAAATAATTCAGAAACGAGCTCAGTCCCAGATACACCAAATGAAGTGAAATTTTT
CTCTGGTAATCCATTTGTTGAACAAACTAATGGAATTTTGCATCTATACAAAAAGAATGA
ACGAGATTCAATACAAGATGGTCTCTCTCAAACACTTTGTTTGCTTGCTGTTCCAGCAAC
ATTGAGTTGCCATGATATTCTGAATTTTATTGCACCTTGTCATTCAGTCATCAATCATGT
TCGCATTATTCGAGATTCCAATCCAAATCAATATATGGTCATTTTAGATTTTCGTACTGT
CGATGATGCTTACGAGTTTTATAAAACTTTCAATGGTGTTCCATACAATAGTCTTGAACC
AGAACAACTTTGTCATACACTTTGGGTAAGTGCTATTGCATGGGATAACATGGATTCAAC
TCCACCAAATCACACGGAATTGCCGGTTTGTCCTGTTTGCCTCGATCGTATGGACGAAAG
TGTTGATGGTGTGCTGACAATTTTATGTAATCACACATTTCACTGTGGATGTTTAGTAAA
ATGGGGAGATAGTACTTGCCCTATTTGTCGTTATGTACAGACACCAGAACTCACACAAAG
TTCAGTATGCATGGAATGTGAAGGAACTGAAGCACTATAGATTTGTTTAATTTGTGGACA
TGTAGGATGTGGTCGCTATCAAGGTGGACATGCCGCAATACATTACAGAAATACAAACCA
TACATATGCTCTACAATTGGGAACTAATCGAGTATGGGATTATGCTGGCGATAATTTTGT
TCATAGACTTTTGCAAAACAAATCAGATGGAAAACTTGTTGCAACTCAATCACCTAGTGG
AGAAGGAGAGGAGAAAATTGATTCAATGCAATTAGAATTTACATATCTCTTAACTTCTCA
ACTTGATACTCAACGACAACATTATGAAGAGAGACTTGCAAGAATTGAAGCTGCTATGGT
TAATGATAAGCAAGGGATTCTCAAAGAGACAGAAGCTATTAAAGAGAAAAATTCTGAATT
TGAACAAAAATTAAATGCTGTAGTCAAAGAAAAACAGGCAATTGAGAAGAAGTTGAATGC
AATGAGTAGTCGTCTAGCGATAGTACTAAAAGATCTCTCTGAAGAGAAACAATTTTCAAA
AACTCTTCAATTAAATCACAATTCTTGGCAGACAAAGTACTCAAATTTGGAAAAACTTTA
TAAAGAAAAAGAGCAAGAAGTTATTGATTTAAAGGAACAAGTGAGAGATTTAATGTTTTA
TATGGAAGCTCAAAATACAATTTCCAAATCTGAACTGAAAGATGAAATTGCAGAAGGTTC
TGTAACAATAGGTGAAACAAGTGGAAATGGTAAAAACAAAAATCGACGCAAGAAGAAATC
AAGCACATAA

>g12076.t5 Gene=g12076 Length=273
MKVVTAASSVDQRVIKERRGQRQPKTIQIETYANVLAGEHQQIKGVLPKNSNTNSREQTP
LTENNSETSSVPDTPNEVKFFSGNPFVEQTNGILHLYKKNERDSIQDGLSQTLCLLAVPA
TLSCHDILNFIAPCHSVINHVRIIRDSNPNQYMVILDFRTVDDAYEFYKTFNGVPYNSLE
PEQLCHTLWVSAIAWDNMDSTPPNHTELPVCPVCLDRMDESVDGVLTILCNHTFHCGCLV
KWGDSTCPICRYVQTPELTQSSVCMECEGTEAL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g12076.t5 CDD cd12718 RRM_BRAP2 110 193 1.32725E-39
9 g12076.t5 CDD cd16457 RING-H2_BRAP2 209 252 6.54525E-27
7 g12076.t5 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 194 257 5.9E-10
11 g12076.t5 MobiDBLite mobidb-lite consensus disorder prediction 43 73 -
12 g12076.t5 MobiDBLite mobidb-lite consensus disorder prediction 45 73 -
3 g12076.t5 PANTHER PTHR24007 BRCA1-ASSOCIATED PROTEIN 52 273 2.9E-72
4 g12076.t5 PANTHER PTHR24007:SF7 BRCA1-ASSOCIATED PROTEIN 52 273 2.9E-72
1 g12076.t5 Pfam PF07576 BRCA1-associated protein 2 108 196 5.5E-27
2 g12076.t5 Pfam PF13639 Ring finger domain 210 251 5.8E-8
13 g12076.t5 ProSiteProfiles PS50089 Zinc finger RING-type profile. 211 251 12.888
10 g12076.t5 SMART SM00184 ring_2 211 250 8.1E-7
5 g12076.t5 SUPERFAMILY SSF54928 RNA-binding domain, RBD 111 178 5.78E-5
6 g12076.t5 SUPERFAMILY SSF57850 RING/U-box 189 256 1.11E-12

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. There were no conditions that were differentially expressed