BtaINT0122370 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020984 | RAPGEF4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:HGNC Symbol;Acc:HGNC:16626]
Coordinates
chr2:23711292-23713802:-
Coord C1 exon
chr2:23713742-23713802
Coord A exon
chr2:23711369-23713741
Coord C2 exon
chr2:23711292-23711368
Length
2373 bp
Sequences
Splice sites
5' ss Seq
TGTGTAAGT
5' ss Score
7.65
3' ss Seq
TTTTTTCTTTTTGTATCTAGTAT
3' ss Score
7.87
Exon sequences
Seq C1 exon
GTGAAACGGGAGTTGGCAGCGGTTCTCATTTTTGAGTCTCATGCCAAAGGAGGGACTGTGT
Seq A exon
GTAAGTGAAGGCTGTAATGGTGCACGGCGCCTGGCTTGCCCCGTCCCGAGCATGTGCCCCTGGAGCCTGACTGTAAATGCTCCCCTTTCTTAGGCCTGAGACAGACTTGCCAGGATGTCACGTGGCATGTTTTTGTTTTTCTGGACCCGTGATTATTCCCAGCATGGCTGTGGCTTTGCAGCCTGGTGGGTGTCAGGTACCAGCCTGGGAGCGTTTACCAGCCAGCATCTCTACTTGCTCCCTCCCCTGCTGGCTCAAGATCGTGTTTAAAGAGGGTGGGATGAAGTCATACTGTCTTCAGGGAAAACCTTCACACAGTGACCTCACTTCAATTTTGTGGCTTGGGAAGACCTAATCTGTCTCTTGAGAGGCTAGTTAGAATAGCGTACTCTCCTGCTTGCTTCTCACGCTTCCACTATCAGCTGCAAGCCTGAGAGAATTTCTTTGCCCAGATATTTATGCAGGACTACTATGTAGTGGAGAAGGAAAATGGCAGCCCACTCCAGTACTCTTGCCTGGAAAATTCCATGGACTGAGCAGCCTGGTAGGCTACAGTCCATGGGGTCGCAAAGAGTCGGACACGACTGAGCAACTTCACTTCACGTTCACTATGTAGTATCTCTCCAGTAAGTACGTCGTAGTTTAGTTCTATGACCATATATGGGAGCAAGAAATTGAAAGTGAAAGTCTTAAGTCGTTCAGTTGTGTCTGACTCCTTGCGACATGGACTGTAGCCTGCCAGGCTCCTCTGTCCATGGGATGCTCCATGCAAGAATACTGGAGTGGGTTGCCATTTCCTTCTCCAGGGGATCTTCCTGACCCAGGAGTCGAACCCAGGTCTCCCACATTGCAGGTGGATTCTTTACTGTGTGAGCCCACTGGGGAAGCCAGAAGGCCTCTTAAGAAATTGAAATTTCATATTATAAATGTGAGCAGAATTATTTTGACTAGCATTTCCCACTCATCCTACAAAACCATTCTTGGAAAACATGGTGAGTGGGGTATTCAGGACACGAAATGCCTCCTCTAATTTCTCTTGGAGAATTGTAAGACACAAGCATGCTCTGTTTCTCAGGAGTTCTACAATAAGGAAAAATTTCACACCACTTAAACTGATACCGCCTTAACCTAATGAAACATAGAAAACATTTTTAATGGATACCTATTAACTTTTCAAGAGACCATCTTTGGAAAATCTTGCTCTTTCTTCAGATTGAGCTGTGTTAGTCAAATAAACAGAGACCATGAATTGTAAAAGCAAAAAGAGTTAACATCGATGTTTCAAATATTTTACTTTTAGTCCTCAAAAGTGTATATCTAATATTGCTAGTTACTTTAAAAAGAATGTTTTTTCTTTACTTTTTAAAGGTTCACATTAACATTTAAAAAATGTTTATATTACTGGTGACTTACAACTTCTTTTGTGCTTTTCCTTCTATCTTTCTGACAGTTTTCATTTTATTATGAAATATTTAAGTATTTCAGACAAATCACTAGAGATTGTTACAAACCCCTTTTTATTTATTTATTTATTTTTACAAACCCCTTCTTAAAAAACACTTTTATCAAGTACTAACCTGACACTCTATTTTTTAATATTTTCATTTTTTATATTTTCTAAAAAATGAAATCCTACATTTGAAGAGTCTCTGTTTCCTTTTTTATCTCATTCTTCTCTTTTCCTCTCCAAGGTAACTCATACCCTATATCATGTGATTATCATTCCAACCCATTTTTTAAAAATATATGTAGATATGTATCCATCAACAATATGTAGTGCTGATTTGCATGTTTTCAGACTTCACATTGGGCTTCCTGGTGGCTCAGTGGTAAAGAATCCGCCTGCTGATGTAGAAGATGTGGGTTTGACCCCTGGGTCAGGAAGATCCCCTGGAGAAGGAAATGGCAACCCACTCTAGTATTCTTGCCTGGAGAATTCCATGGACAGAGGAGCCTGTCGGGCTACAGTCCATGGGGCCGGAAAAGAATAAAACACGACTGAGCAACTAAACGACAACAAATTTCATGTTATTGGTCAGATTACTTTTAAAAATGATGTTCTATAGCTTAGTAAGTTTTGATGAGTTGTGGGGGGAAGTGGATTGCTTTAAGGAATGGATTGCTGGAGAATTAATAGTAAATATATATCTGTAGGACATAGCAAGGAGTGCAGTGTTCCTGTTTCTTTCATGTTCTAAAGAAAAGAAGTAATATTCCACCTGAATAAGTTAGCATTTGCTAGTTTTTTTTTTTTTTCCCTCCTGGAATTAAATGCATAATTCTGAGGCCTTTAAAATGATGATTTGATAAGCTGTAATTTATATTGATGTGCTTCTATTCTTGTCATAAGTCTTTTTTTCTTTTTGTATCTAG
Seq C2 exon
TATTTAACCAAGGGGAAGAAGGCACCTCCTGGTACATTATTCTAAAAGGATCAGTGAATGTAGTCATTTATGGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020984:ENSBTAT00000061074:12
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:
PF0002724=cNMP_binding=PU(10.3=42.9)
A:
NA
C2:
PF0002724=cNMP_binding=FE(28.7=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]