BtaINT0127296 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005980 | RREB1
Description
ras responsive element binding protein 1 [Source:HGNC Symbol;Acc:HGNC:10449]
Coordinates
chr23:47949285-47950606:-
Coord C1 exon
chr23:47950517-47950606
Coord A exon
chr23:47949449-47950516
Coord C2 exon
chr23:47949285-47949448
Length
1068 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGC
5' ss Score
7.16
3' ss Seq
GTGATCCTTGCTTTCCGCAGCAC
3' ss Score
8.83
Exon sequences
Seq C1 exon
GAGACGAAAGAGGAGAAGTCTTCCTACAACTGCCCCCTGTGCGAGAAGGTCTGCACCACCCAGCACCAGCTAACCATGCACATTCGCCAG
Seq A exon
GTCAGCTAACGCTCCTGTGTTTTTGTTTCACATAGCTCTTCGTTAAGAGGGGAGGCGACTTTTTATCTTAATGGATGAACTGTGGCTGTTTAATTTAAATGTAATACCCTGAGAATTTTGAGGCGCGGCTATGAGACAGTTTTCGTGTGTCCGTGTTACTGTGACAGAGTCCCAGGGCACATGGAACACCTTTTCAGAATTCAGCAAACATCTAGCTAACCGATCACAAATAACAGACTTCTCATCATACGTGAACCAGACTCTTCACAGCACAGAGATTGTAGATGTAGATCCCGATTATCTGCGCTGCTGTAAACTTACATCATGCAGCAGGGAGTTCCCTTGATTTGGGATCTCTTTTGGCTCTTCTTCTTTATTAGGAGATTTGTCCTTCTCCCTTGCCTGCTGTGGATGGTTCATGAGATAGTACTGACCCCAGAACGGTGAAGGACTGACAGTAGTCACATCATAAGTGGTGCTGAGTAATAGCACCGTTTAGTAACTTGGGCTCGGACAGAGATGTTCCTTCGTAACACGTTTCAGAGGCTGGAACCCTAAGCCGGGCGGGTCTCAGCTCTCTTCTCTGACACTAGACTGAGGCGTCAGAGGCCGGAACCCTAAGCCGGGCGGGTCTCAGTTCTCTCTCTGACACTAGACCGAGGCATCAAGCAGAAGAACTCAGTGAGGCCTGTCCTCGCGTTTGCCGCATAGCTCAGTCTTCCTGCTCACGTTCGTTTTTGTGGTCAGTTCATCTACATGTGCCTCTGAAAAAGACCCGCAAAGACCCCACCTTCATTTTGAGCCTGGCGGAAGAAGTGCTCGTCATTCCTGGAACACGGAAACGGAAGAGCGAACCAAAGATTTGTCTCTGGTCCCGATGGATTTTGATATTCGGGAAGACATTTAAAATGAAACAAAAAAACAGCCAAGAAGCATTGCTGGTGTTTTAATACACGTGTGTGTGTGTGCTTATATGTGCGTGTATTTGTGAAGCTCTGAACTTACCCTCCCGATTGCGGAGTCTTGACCCGTCCCCCTCGGTGATGCTGTGATCCTTGCTTTCCGCAG
Seq C2 exon
CACAACACGGACACGGGCGGGGCCGACCACTCGTGCAGCATCTGCGGGAAGTCGCTGAGCTCGGCCAGCTCCCTGGACCGGCACATGCTGGTGCACTCCGGGGAGAGGCCCTACAAGTGCACCGTGTGCGGGCAGTCCTTCACCACCAACGGGAACATGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005980:ENSBTAT00000044565:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.473
Domain overlap (PFAM):
C1:
PF0009621=zf-C2H2=PU(91.3=70.0)
A:
NA
C2:
PF0009621=zf-C2H2=PD(0.1=0.0),PF134651=zf-H2C2_2=WD(100=47.3)
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:
GAGACGAAAGAGGAGAAGTCTTCC
R:
CTGTGCATGTTCCCGTTGGT
Band lengths:
254-1322
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]