BtaINT0122310 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020791 | RAPGEF1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:HGNC Symbol;Acc:HGNC:4568]
Coordinates
chr11:101791006-101791829:-
Coord C1 exon
chr11:101791690-101791829
Coord A exon
chr11:101791120-101791689
Coord C2 exon
chr11:101791006-101791119
Length
570 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGC
5' ss Score
7.31
3' ss Seq
CCAGGTTTCCTCTCTTCCAGGAG
3' ss Score
9.2
Exon sequences
Seq C1 exon
ACTCTCAGCGTTCTCATCTCTCCTCCTTCACCATGAAGCTGAAGGACAAATTCCACTCGCCCAAAATCAAGAGGACGCCATCAAAGAAGGGAAAACCAGCCGAGGTGTCTGTGAAGATTCCAGAGAAGCCCGTGAACAAA
Seq A exon
GTAAGCTGACTCCAGGTGTTTCTGCTGGCCTGCACCTGCTTTGAACAATGTGTTTGTGCTGTTTCTGAGTTCATGCCCTGGGGACTGAGCTTTCAGTACAGAGCACCTTTCCGGTAGCGCTCCACAGTTCCAGGTGGGGCCTTCTGTGTCCTTGTGAAATAGAAACTTTTAGGATGGGTGAGTGTTTCTCCCATTAATAAGAGTCCAGATCAGTTGGCTAGAACAGTTCTTTTCCAGATGTCATCCTCTGGGCATTTAACACAGCTCAGAGCATCACATTCACACCCCAGGACGCAGCCTCCATGCCCCTAGAGAGGCCCATGTTGCCCCCCGACACACACACGTAGATTTGTGATGTCCAGAACATCCATCATTTGGTTCCAGGGTCCACGCTCTGAAACTTGCTAAACCCTTGAAACCCAACTGAAGATGCCCTCAAACACCAGGAACCTCAGCAGGGCCAGTCAAGCCAGATGTGTTGCAACAGCTGTTGATTTTCATCAACCCCTTCCCTTCAGCTTAAAACGGCCATTTCAAGCTCTGTAGGAATCCAGGTTTCCTCTCTTCCAG
Seq C2 exon
GAGGCAACAGACAGATTTCTACCAGAGGGCTACCCTATCCCCTTGGATCTGGAGCAGCAGGCAGTAGAGTTTATGTCCACCAGTGCTGTGGCTTCCAGGTCTCAAAGGCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020791:ENSBTAT00000032663:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.532 A=NA C2=0.053
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
ACTCTCAGCGTTCTCATCTCTCC
R:
CTTCTGCCTTTGAGACCTGGA
Band lengths:
254-824
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development