BtaINT0122400 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015539 | RAPGEF5
Description
Rap guanine nucleotide exchange factor (GEF) 5 [Source:HGNC Symbol;Acc:HGNC:16862]
Coordinates
chr4:31054290-31056112:-
Coord C1 exon
chr4:31055968-31056112
Coord A exon
chr4:31054388-31055967
Coord C2 exon
chr4:31054290-31054387
Length
1580 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATG
5' ss Score
8.99
3' ss Seq
CCCCCCACCCCCGCCCCCAGACC
3' ss Score
9.02
Exon sequences
Seq C1 exon
CTATTCTGCTAAGAAGTATCAAGGCAAAGAAGAAAATTCAGATGTTCCTTGTCGGAAACGGAAGGTCTTGCATCTTGTTTCCCAGTGGATTGCTCTATACAAAGACTGGTTACATGAAGATGAACATTCAAAAATGTTTTTAAAG
Seq A exon
GTAATGTAAAACTTCCAGTTATTCAGTTACTCTTTGATGCTGAATGACTGATTTTATTTTCAGTTGTGCATTTCAGTAATCTCATTCCTATGTTACAGTCCTCTAACTTGTTTGTAATATTGAAGTTATGATTCAAAGTATTTGTTTGTTTTGACTTCTGAAGCCAAATATTTGGAGAAGGCAATGGCACCCCACTCCAGTACTCCTCCCATGGACGGAGGAGCCTGGTAGGCTGCAGTCCAAGAGGTCACTAAGAGTCGGACATGACTGAGCGACTTCACTTTCACTTTTCACTTTCATGCATTGGAGAAGGAAATGGCAACCCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGGATGGGGGAGCCTGGTGGGCTGCCGTCTATGGGGTTGCACAGAGTCGGACACGACTGAAGTGACTTGCAGCAGCAGCCAAATATTATTTACATAGTTAGAAATTTTTAACTTTAAATAATTCTATGTCAATAAATGTAGAAGGCAAGTTTTAAAGTCGCTCATTTAAAGTTATTTATTTTACTTGTCATGGGAATTTTTATTGCAAATGAAATAATTAAGGAAGATTAAATAAAACATACTTTAAAATTTGATAACTGCCTAATATGTTGAGATGTATTATAGGTTTAAACTAACCAGTCCCATATCTACAATAGTGGGATAAAACATTATTTTTATCATATAAGAACTATATTGACAATGTATACATTATGAAACTTTATCAGGACCTGGTGTATATTGAGACATTAAAACAATCATAACTAATAAAATTGATGCTAAACCTCGATTTACATTTTAAGTTATGTTCTTGCCTGGAGAGTCCCAGGGACGCCAGAGCCTGGTGGGCTGCCATCTATGGGGTCGCACAGAGTCGGACACGACTGAAGCGACTTAGCAGCAGCAGCAGCAAGCTGATATGTGTTTCTAATCATGAGTAGGCTGCAGTGTCTTTTCAACACAGATGATTCTCTGGAGACAGTTTGTAGACAGCTGGACTCTTTTGGCCACCAAAAGCATGTTAGCTGTGCAGGTCAATACAGAGAAGGGGTGCAGTGGAATCCGTGTGGGGGAAGAGTTCTATTTCAGAATAGGCAAGTGTCTAAACTGACTTTGTCTTCAAGAAAGAAATCACTTTGATTTCAAAATTCAAATATCTTTTAGACATCCAGTTAAAAACTGATTTAAACCAAGTCTCTGGCTAAACTACTGTTATTTTCAAAACAACTGGTTAGTTTAATTCAATAGATTTCTTTTCCTTCCCAAATGATTATGTGGCTATTATTTCTAAAAATATATTGTAGAACAGGCCTGGGAATTTCGAGTAGCTCCTACCCATAGCCCCTAAGAGCTGCCAGAGAGCCACACAGTTGAGCAAGGGGGTCTGAGGTGGAACCCCCACTCAGGAGCTCTGTGGTGCCTGGTTTAACCCCTTGCATTGTTCTGGATCCCACTTCTCTCTCTGATCAGGTTACCCACTGTTTGAGTCTTAATCCTTATAAAATAGACACCAGACCAATTCAGCTGCCATTTTCTGCCCCCCCCACCCCCCCCACCCCCGCCCCCAG
Seq C2 exon
ACCATATACAGGAATGTGCTGGATGATGTCTATGAATACCCAATACTTGAAAAAGAGCTGAAAGAATTTCAGAAGATACTTGGAATGCACCGTCGTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015539:ENSBTAT00000033832:14
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=0.000
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=FE(43.6=100)
A:
NA
C2:
PF0061815=RasGEF_N=PD(5.5=18.2)
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:
TCTGCTAAGAAGTATCAAGGCAA
R:
GACGACGGTGCATTCCAAGTA
Band lengths:
238-1818
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]