BtaINT0122380 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020984 | RAPGEF4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:HGNC Symbol;Acc:HGNC:16626]
Coordinates
chr2:23679247-23680601:-
Coord C1 exon
chr2:23680523-23680601
Coord A exon
chr2:23679394-23680522
Coord C2 exon
chr2:23679247-23679393
Length
1129 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TGTTGCTCTCTTCCCAATAGTTC
3' ss Score
9.42
Exon sequences
Seq C1 exon
CACAAAGTTCTTTTGCAACAGTTCAACACAGGCGATGAGAGAGCCCAGAAGCGCCAGCCTATCCGTGGCTCTGATGAAG
Seq A exon
GTGAGATTTCTTTTCCAGCATGTGTAGATTATTTAAAGTCAGAATGAAATCTTCCCTCTGGGTGTCACCCCTTGGGCCCACAGAATAGCTTTTCTTGGCTCTCTGTGCACTCCAGATGGTTTGCTTGGAGGTGCCCTTTGGCATTCCAATTATTTTTGTCCTTGAACTTGGTACCTGGAGCCAAGGTGCTTATTCACACTTCTCTGATTCTGCCTCTACCCCACTGCCACCTTTCCTTGAAGGAGAGAAAGATTATCTCAGGGGCCAGTTGTCAAGGTGGCTGGAAGGTGGTTGGTGTTTTGCAGATGCCTCTCAGAGGTGGAGCACCAGGGTCAGCTGCTCACCTGCCGAGCAGGGCTCCCGCCCAGGAAGAGTGCCCCCAGCCCTGAGCACTACCTCGTTAGCACCCATCGGGAAGGCCCAAATACCAGCTGCTATTGTTTGCTTGGTTAAGATTTCTTCGAAGAGTCACAGGCAAAATAAAATGATCATGATGAAATTTTCATCTTCAGCCACAGATGAATGTTGTAATTTAGGGGTGCCCCAAACTCAAGAATTACAGGAGGTGGAATTACTTCCAGGACTTGTGTGTTCAGAGCTGAACATGTGGATAACCACATGCAGATTTACTGAACTGAACACCACCCAAGCCATGTGCCCAGGCCTCAGAGTACATACACCAGTGGACAAGTGAACAGGAATCTTAGCGAATGTTCATGACCCCAGGCAGAAGCATTCCTGTTTGCAAGAGTGTTCATGCTGACTCCCTACCACTGAACTAGGCAGTGGGAAACTAGTGATCTGCCTGCCACATAACACTCACAGACAAGGGCAGACCCTGAAAACTTGCCTAAACATGCCTCTCATTCTTTCCCCATGACCTGTGTGTGGGCTTTCCACAACTATCTGTTGTGGTTTTTGTAACTGGGATTGGCAGTCATGGACTGTTCTAAGGTAAGTTTTAGAGGAGGACAAGTGTAGGCATCCATGAGCACAAATCAATACAAGTCATAAGAATGGCAAGGCGATGCACATTTTGGAGGGTGCGTCCAAACATTTTGCATAGCTTAAGTTTTTTTTTAAGAACTCCCAAGATCAATTCATCTTATTGTTGCTCTCTTCCCAATAG
Seq C2 exon
TTCTGTTTAAAGTCTATTGCGTGGACCACACCTACACAACCATCCGGGTACCGGTGGCCGCCTCGGTGAAGGAAGTCCTCAGCGCCGTTGCCGACAAACTGGGCTCCGGGGAAGGCCTGATCATCGTCAAGATGAGTTCCGGGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020984:ENSBTAT00000061074:21
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=0.000
Domain overlap (PFAM):
C1:
PF0078818=RA=PU(2.5=7.4)
A:
NA
C2:
PF0078818=RA=FE(61.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGTTCTTTTGCAACAGTTCAACACA
R:
CTCCCCCGGAACTCATCTTGA
Band lengths:
222-1351
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]