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.t1 TSS g12076.t1 20813989 20813989
chr_1 g12076 g12076.t1 isoform g12076.t1 20814070 20815926
chr_1 g12076 g12076.t1 exon g12076.t1.exon1 20814070 20814136
chr_1 g12076 g12076.t1 cds g12076.t1.CDS1 20814070 20814136
chr_1 g12076 g12076.t1 exon g12076.t1.exon2 20814228 20814519
chr_1 g12076 g12076.t1 cds g12076.t1.CDS2 20814228 20814519
chr_1 g12076 g12076.t1 exon g12076.t1.exon3 20814588 20814855
chr_1 g12076 g12076.t1 cds g12076.t1.CDS3 20814588 20814855
chr_1 g12076 g12076.t1 exon g12076.t1.exon4 20814922 20815135
chr_1 g12076 g12076.t1 cds g12076.t1.CDS4 20814922 20815135
chr_1 g12076 g12076.t1 exon g12076.t1.exon5 20815202 20815926
chr_1 g12076 g12076.t1 cds g12076.t1.CDS5 20815202 20815926
chr_1 g12076 g12076.t1 TTS g12076.t1 20816005 20816005

Sequences

>g12076.t1 Gene=g12076 Length=1566
ATGTCTATATTAGTTACACTGTGCTTACTAAAAATTGAAATAGTTGATGAAATGGAAAAT
GAAGGTGAATCAGCAGCAGCATCTTCGGTTGATCAACGAGTCATAAAAGAACGTCGAGGA
CAGCGACAACCAAAAACTATTCAAATAGAAACTTATGCAAATGTACTTGCAGGCGAACAT
CAACAAATTAAAGGTGTTTTACCAAAAAATTCAAATACAAACTCAAGGGAGCAAACGCCA
CTCACAGAAAATAATTCAGAAACGAGCTCAGTCCCAGATACACCAAATGAAGTGAAATTT
TTCTCTGGTAATCCATTTGTTGAACAAACTAATGGAATTTTGCATCTATACAAAAAGAAT
GAACGAGATTCAATACAAGATGGTCTCTCTCAAACACTTTGTTTGCTTGCTGTTCCAGCA
ACATTGAGTTGCCATGATATTCTGAATTTTATTGCACCTTGTCATTCAGTCATCAATCAT
GTTCGCATTATTCGAGATTCCAATCCAAATCAATATATGGTCATTTTAGATTTTCGTACT
GTCGATGATGCTTACGAGTTTTATAAAACTTTCAATGGTGTTCCATACAATAGTCTTGAA
CCAGAACAACTTTGTCATACACTTTGGGTAAGTGCTATTGCATGGGATAACATGGATTCA
ACTCCACCAAATCACACGGAATTGCCGGTTTGTCCTGTTTGCCTCGATCGTATGGACGAA
AGTGTTGATGGTGTGCTGACAATTTTATGTAATCACACATTTCACTGTGGATGTTTAGTA
AAATGGGGAGATAGTACTTGCCCTATTTGTCGTTATGTACAGACACCAGAACTCACACAA
AGATGTGGTCGCTATCAAGGTGGACATGCCGCAATACATTACAGAAATACAAACCATACA
TATGCTCTACAATTGGGAACTAATCGAGTATGGGATTATGCTGGCGATAATTTTGTTCAT
AGACTTTTGCAAAACAAATCAGATGGAAAACTTGTTGCAACTCAATCACCTAGTGGAGAA
GGAGAGGAGAAAATTGATTCAATGCAATTAGAATTTACATATCTCTTAACTTCTCAACTT
GATACTCAACGACAACATTATGAAGAGAGACTTGCAAGAATTGAAGCTGCTATGGTTAAT
GATAAGCAAGGGATTCTCAAAGAGACAGAAGCTATTAAAGAGAAAAATTCTGAATTTGAA
CAAAAATTAAATGCTGTAGTCAAAGAAAAACAGGCAATTGAGAAGAAGTTGAATGCAATG
AGTAGTCGTCTAGCGATAGTACTAAAAGATCTCTCTGAAGAGAAACAATTTTCAAAAACT
CTTCAATTAAATCACAATTCTTGGCAGACAAAGTACTCAAATTTGGAAAAACTTTATAAA
GAAAAAGAGCAAGAAGTTATTGATTTAAAGGAACAAGTGAGAGATTTAATGTTTTATATG
GAAGCTCAAAATACAATTTCCAAATCTGAACTGAAAGATGAAATTGCAGAAGGTTCTGTA
ACAATAGGTGAAACAAGTGGAAATGGTAAAAACAAAAATCGACGCAAGAAGAAATCAAGC
ACATAA

>g12076.t1 Gene=g12076 Length=521
MSILVTLCLLKIEIVDEMENEGESAAASSVDQRVIKERRGQRQPKTIQIETYANVLAGEH
QQIKGVLPKNSNTNSREQTPLTENNSETSSVPDTPNEVKFFSGNPFVEQTNGILHLYKKN
ERDSIQDGLSQTLCLLAVPATLSCHDILNFIAPCHSVINHVRIIRDSNPNQYMVILDFRT
VDDAYEFYKTFNGVPYNSLEPEQLCHTLWVSAIAWDNMDSTPPNHTELPVCPVCLDRMDE
SVDGVLTILCNHTFHCGCLVKWGDSTCPICRYVQTPELTQRCGRYQGGHAAIHYRNTNHT
YALQLGTNRVWDYAGDNFVHRLLQNKSDGKLVATQSPSGEGEEKIDSMQLEFTYLLTSQL
DTQRQHYEERLARIEAAMVNDKQGILKETEAIKEKNSEFEQKLNAVVKEKQAIEKKLNAM
SSRLAIVLKDLSEEKQFSKTLQLNHNSWQTKYSNLEKLYKEKEQEVIDLKEQVRDLMFYM
EAQNTISKSELKDEIAEGSVTIGETSGNGKNKNRRKKKSST

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g12076.t1 CDD cd12718 RRM_BRAP2 130 213 2.47257E-38
16 g12076.t1 CDD cd16457 RING-H2_BRAP2 229 272 2.05072E-29
13 g12076.t1 Coils Coil Coil 357 377 -
14 g12076.t1 Coils Coil Coil 396 423 -
12 g12076.t1 Coils Coil Coil 445 472 -
10 g12076.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 227 270 6.7E-9
11 g12076.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 271 336 2.5E-11
20 g12076.t1 MobiDBLite mobidb-lite consensus disorder prediction 63 93 -
19 g12076.t1 MobiDBLite mobidb-lite consensus disorder prediction 65 93 -
21 g12076.t1 MobiDBLite mobidb-lite consensus disorder prediction 499 521 -
4 g12076.t1 PANTHER PTHR24007 BRCA1-ASSOCIATED PROTEIN 72 282 2.7E-134
6 g12076.t1 PANTHER PTHR24007:SF7 BRCA1-ASSOCIATED PROTEIN 72 282 2.7E-134
5 g12076.t1 PANTHER PTHR24007 BRCA1-ASSOCIATED PROTEIN 282 518 2.7E-134
7 g12076.t1 PANTHER PTHR24007:SF7 BRCA1-ASSOCIATED PROTEIN 282 518 2.7E-134
1 g12076.t1 Pfam PF07576 BRCA1-associated protein 2 128 216 1.7E-26
3 g12076.t1 Pfam PF13639 Ring finger domain 230 271 1.4E-7
2 g12076.t1 Pfam PF02148 Zn-finger in ubiquitin-hydrolases and other protein 280 321 1.2E-9
22 g12076.t1 ProSiteProfiles PS50089 Zinc finger RING-type profile. 231 271 12.888
23 g12076.t1 ProSiteProfiles PS50271 Zinc finger UBP-type profile. 256 321 11.228
18 g12076.t1 SMART SM00184 ring_2 231 270 8.1E-7
17 g12076.t1 SMART SM00290 Zf_UBP_1 266 310 0.0073
8 g12076.t1 SUPERFAMILY SSF57850 RING/U-box 247 331 2.91E-16
9 g12076.t1 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:0008270 zinc ion 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