BtaINT0152104 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001697 | TRA2B
Description
Bos taurus transformer 2 beta homolog (Drosophila) (TRA2B), mRNA. [Source:RefSeq mRNA;Acc:NM_001034776]
Coordinates
chr1:81892813-81894986:+
Coord C1 exon
chr1:81892813-81893001
Coord A exon
chr1:81893002-81894870
Coord C2 exon
chr1:81894871-81894986
Length
1869 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGT
5' ss Score
9.82
3' ss Seq
ACAACTCATATCTTTTGAAGGCA
3' ss Score
5.42
Exon sequences
Seq C1 exon
GCAAATCCTGATCCCAACTGTTGTCTTGGAGTATTTGGATTGAGCTTGTACACTACAGAAAGAGATCTAAGAGAAGTGTTCTCTAAATATGGCCCAATTGCTGATGTATCTATTGTATATGACCAGCAATCTAGACGTTCAAGAGGATTTGCCTTTGTATACTTTGAAAATGTAGATGATGCCAAGGAA
Seq A exon
GTAAGTAAAAAGTCTTGTACCTTTGTGTTAAAAAAAAAAAAGGTATATACACATGCTTTCACTTTTACACACACGCTCAGAGTCTTTAACTATTCTTCCTTGGATGACTTTTGCTTTAGTAATTCCATCAGTCGTGTCAGACTCTTTGCAATCCCATGGACTATGCAGTCCATGGAATTCTCCAGGCCAGAATATTGAAGTGAGTAGCATATCTTTTAATGTGGAAATTTCAAAGATTTGTAGCATAACAGCAAAGTGACAGTTTGGTTCTAAATTCCAACTCAGTCTCTTCCACCATTTTATTTGAAGTAAATTCAAACATAGTCAACTGTTCTCAGATGTGTGCCTAGATACAGATATTTCTAAAATAGAAGAATATTAATAGTCCAGTTTGGAATATTTAATGAGTGTTTACATCAGATTACTTTCTAAAATGAAAACATTAAGAAGTGATAAAACCATGACTCAGGATAAAGGAACTGGTTTTGATTGTATACTGTATACTGGCAAGTGATTTTATGTTTTGGATGTTGAGGTAGAACATAGGAAGTAACTTTTTTTGGCCTTGAGGCTTATGGGATCTTAGTTTCCCAACCAGGGATTGAACCTGGGCCACGGCAGTGAAAGCACCAAGTCCTAAACATTGGACCTGTAAAATTTTTTTTACAGAGGCTAAAGTAAAAATTCGATGTGTGACTCCTGGCCCATTTAAGAAATTTGAACTTCAGATACATGGGGGTGATTGCTAAAGTCATCTCCGAGGACAGTAATAAGGAGGGGAGAATCTTGAGAAACTTAATGACAAGCCATCTGAGGTTAATATTGAGATTAATAATTTTGAGCTCTAAATAAAATTAAATGAATAGAGTAAGCCCATCTACTAAAGGAAGAATTAAAAGCTGAATGCAGGTGGTTATAATTTAAGAGATTTAAGGAATGCTATGTCATTCAACTTCATTTTGGTAATAATTGATGTCAAAAATGTTAATAACATTTGTCCAAGGTTACTTACGGAATCGGCTTCTTTGTTTTTCTACTTTGTGTGTGTGTGTCCTACAGAACCACAGTTCCCTTTCTGAAAGATAGTATATTTTGTATCTAAATCAGTAATGCCAAAAACTGCCTTGAGGCCTAAAACAATCAAACTAGAAAATAGCATAATTGGAATTAGAAATCTAAATTCTATTTAGATAGAGAGGTATTTGTTTAAATTGTGAATAAACTGCTATGTCTTTGGGATGGGGTATTTTTTTTCTTTAGTACAGTATATTTTCATTTTAATGTTTGAAACTATATGTAATTCAAGCTTTCAACCCAGCTCTTTGCTTCCATAGCAGGGGTCCTCAAATTTGTGTAAAGGATTAGACAGTAACTATTTTGGGCTTTGGGAGCCATAAGAGCTCAATGACGGCTTTTCAACCCTACCATTGTAATGTAAAAGCCATATAAAATGCAAATTAATGAGGGGCTTTGTTTCAGTAAAACATGGTCACTTAATTTTGAATTTCATTTCTGATGAAATACTACTTTGACACCCACACCTGTTTAAATTCTTAGCTCGTGGGTCATAGTTTGCCAACTGTGTACTATTTTATAGACTTATAGGTACTGTCAAATCTATAGTTGGTACAGTAATTTCAAATAGTTCATGGCTTAAGTTGGTGCTCACAGGTGGCTTTTTTTTTTTTTTAATGAACTTTTCTAGGCTAGCTTTTGTAAGTAAAGATTTGATAGGCAGAAAAACTTATTAATAAGCTGTCAGATATAATGCTCAGGCCTAACTGAAACATCTAGTTGGGTTTTATATATAGATAATAGTTAATTTGGGGCTTTGTTCATGATTTATATAACAACTCATATCTTTTGAAG
Seq C2 exon
GCAAAAGAGCGTGCCAATGGAATGGAGCTTGATGGACGTAGGATCAGAGTTGACTTCTCCATAACGAAAAGACCACATACTCCAACACCAGGAATTTACATGGGGAGACCTACCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001697:ENSBTAT00000002225:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.111 A=NA C2=0.667
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(76.1=85.7)
A:
NA
C2:
PF0007617=RRM_1=PD(21.1=38.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAAATCCTGATCCCAACTGT
R:
AGGTAGGTCTCCCCATGTAAA
Band lengths:
304-2173
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development