BtaINT0122431 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015232 | RAPGEFL1
Description
Rap guanine nucleotide exchange factor (GEF)-like 1 [Source:HGNC Symbol;Acc:HGNC:17428]
Coordinates
chr19:41114592-41116723:+
Coord C1 exon
chr19:41114592-41114689
Coord A exon
chr19:41114690-41116610
Coord C2 exon
chr19:41116611-41116723
Length
1921 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGG
5' ss Score
4.44
3' ss Seq
CCCAGCGGTGTCCACACCAGGAT
3' ss Score
5.46
Exon sequences
Seq C1 exon
GACCTGTACCTGCTGATTATGAAGGATGAGTCCCTTTACCAGGACCTCCGAGAGGACACACTGAGGCTGCACCAGCTTGTGGAAACAGTGGAGCTAAA
Seq A exon
GTGAGGGGAATGGGCTTGGGGAGGGGCCAGGAACGAAGTCCTCCTTGTTCCTCAGTTAGAGGGCTGGGTGCCTCTGGCCTTTGGACTCCAAGATGTCTTGATTTCAGTCCCTTTCTCTTACTGGAGAGGAGCACAAAGCATCATCTCCAGACATTTTGGGGGTCCATTCTCCCATCCACTTATTTGTCAGTCCAGTGGTGTACTGATAAATATTGAACAGCCAGCACTTCAGGAAAAAGAGCCCTGACTTGTAGCTTTTGCTGATTCCCATGGTGTAAATTCGGAGAAGGCAATGGCACCCCACTCCAATACTTTTGCCTGGAAAATCCCACGGACGGAAGAGCCTGGTAGGCTGCAGTCCATGGGGTCGCTACAGTCCGACATGACTGAGCGACTTCACTTTCACTTTTCACTTTTCATGCATTGGAGAAGGAAATGGCAACCCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGGATGGGGAAGCCTGGTGGGCTGCCGTCTATGGGGTCGCACAGAGTCGGACACGGCTGAAGCGACTTAGCAGCAGTAGCAGCAGCATGGTGTAAATTCTCTCACCATGGTTTATTTCAAGCTCCCAACGTGACGTCATTGAATGTGAAGTTGGGAGGAGATGTGTGGTAGCAGGTCATTATGTAGTATCTTCACCATACAAATCCAACAGACGCAAATAACCTGAAGAGCACAGAGAAGAACACGGTGAAACAATTAGGAAATGACTTTTTTTGTATTATAATAATTTGGCTATAAGTTTATAAAACATATATATGTTTATATACAATTATCTATTATAATTAATTTTTTAATGGCTGTGTTTAAAACCAGTTGGCAAAATTTTCCAAAATTTAACAGTCTGCCTTCACGAGCCATTGTGAGCTGACTTCAAGACACCACTGTGTCCATCTGTCCATCTTTTCAGCCCTTTCAGTTTCTCCATTCCACTGTCATAACCCTCATTTAGGCTTCAGTATCTCTCACTTGGATTATGGCTGCAGCCTCTGATCCAGGCCTTTAGCTTATGGTTTTGTGTCTTTCTTATGCTGATGCCAGAGAGATCTTTCAAACTTGACAACCTTGTGCTTCTGTTCCCAAAATAGCCATGCCCCTCCCCCAACAGCATCCTAGCCCCTCTCTGTCTGCCTTCTGCTGATCCTTCCCTCCACATCTCCCACATCCCCCCTTACGCATGACACTCCCTACATACCCACCAATTCCATGAACACCTGTGTGTTCTCAACTTCCTGCTATCACTTATATGGTCCACCCCAGAGTGCCCTCCTCCCACCCCCTTCTCTTCCTGTTGCCCTTCAAGGTCCAGGTCAAATGCCATCTTCTTAGTGAAAGCATCTTTTGGCGGTAGCTGTCCCCTCCTCCCTCCCTGTACCAACAAAACTCTTCTTGTGCCTTTATTATATCATCTAACACCTGTCTGGTGTGAGAAGTAGCTGTACGCAAGTCTGTCTCCCTCCCAGACTGTGAAGTTTTTGTCAGTAAAATTCAGCAAACAGCTGATGACCTATACCTGCCATGTACCAGGCAGGGTGCTAGGCCTGGAGGTTGAAAATAAAATTCAGTCAGCTCTCAATCTTGTAGAAGAGATAAGACACGAAGGTAAACACATATTAGCCCAATGTCCTACAGCCACTGAGACAAAAAGGTGACCTCTGCTGGTGGGTGGGATGGATAGAGAAGAATTCAGGGAGGAGGTGGCATTTGATTCGGTCATTCGGACAGCCATCCCAATGCTGGCCATGGTCCTGTATTCTGACCTCCTTCACCACTCTCTGAACCTGATGCTGGGGCATCCTTGACCCGGTTCTGACATCCCTGCTTGATGCTACCTGCCTGGCATGCAAGATGCCTGGCCGGGCTCTCTGATGCCCAGCGGTGTCCACACCAG
Seq C2 exon
GATCCCGGAGGAGAGCCAGCCACCCAGCAAGCAGGTGAAGCCACTCTTCCGCCACTTCCATCGGATAGACTCCTGTCTGCAGACCCGCGTGGCTTTCCGGGGTTCTGATGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015232:ENSBTAT00000020265:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.077
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0078818=RA=PU(2.6=5.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCTGTACCTGCTGATTATGAAGG
R:
CTCATCAGAACCCCGGAAAGC
Band lengths:
209-2130
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]