GgaINT0124536 @ galGal3
Intron Retention
Gene
ENSGALG00000003712 | RAPGEF1
Description
NA
Coordinates
chr17:6903463-6905070:-
Coord C1 exon
chr17:6904947-6905070
Coord A exon
chr17:6903647-6904946
Coord C2 exon
chr17:6903463-6903646
Length
1300 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TTGGTTTTTTTTTGCTTCAGGAT
3' ss Score
9.84
Exon sequences
Seq C1 exon
CCCTCCTCCAGCCTTGCCCCCTAAAAAACGGCAGTCGGCGCCTTCCCCAACCAGAGTGGCAGTTGTGGCCCCCATGAGTCGAGCCACCAGTGGGTCTAGTTTGCCTGTTGGAATCAACAGACAG
Seq A exon
GTAAGGGCATAACCCCTTTGTGAAATCCAAGGGCAATGTGCTGCAGAGTGTAGCAAAAGCTCAGGGAAACACTGTGACCTGAGCAGTGCAGTTCCCAGTACGTTCCTACCGTCCCAGGCAGCCCCATATGGAACGATGCTGGGATGGGAATTCTGGCAGCAGGAACATCAATGGAGTGAATGGTGCAAAGAGCTGATTTAGTTTTTTGTTGTTGGATTTGAATAATGAATGATCTGCTACCAAACTTTGTTGCCTTGAGGTGTAGCAGAATGTGAAAATCTGGGAGGCTGAGTGTCTCAGTGTTGGGTAGGTCAGGGTGTACAGTGGTTTGCTGTGCTTACAAGATCTTAGCAAGGTTTACTTGCAAGCCAGGGATCATGTAGCAGGTTGACATCAGAAGCCTATATTTTTCCATTTCCAGTTTAACATGTCAATTAACCTAAGCAGTAGTTTAAGCATCTGCTCTGACTGCTGCTGGTGCTTTGGGAAAATTTGTAAATTTTCTGGTAGAGCTACAGAGAACTTGTGGCAGTGTGTATTAGTCATGCTCTATCACTTGTGCTAATGTAGAGTTTACAAGATTGTAAATAAATGGTTTTGCTTTACACCTTCAGGAACTTACTGACTCAGCAGTGAGAACTCGAATCGTGTTAAAGTGCACCAAAATCAAATCTCACACTCAATCCCCAGAGCTCTGACTTAGGGAGCCTCTGCTGTCAGTTGGCTGACCCAGATAAAGCTGTGGAGGTTTTGCAGTTACTGGTGCAATCTCACTTAGATTGATCTGCAGGGATGGGAATACCTGCAAGGTTCACTTGCAGCTTGATGAGCTTGAGGTAATTTCTGAAACTGAAACATAGTCAATAGGCACCGAAAGTTTGCATAAGCTGTATCCCATTATCACCTGTTTACCCTTTGCATGCACAAAACTAACCAAATATTTAATAAAGCCCCAATTATTTAGTGAGAGTTCTCGTCTTCTAGTTACCCAGTACCAATGTCAACAGCTGGTGACATCGGCTGTGCATCACAGCATGCCCTGGCCTCCAGCAGGTGCATGCAGGGCTCCCTTTGGGGGCTGCTCTTCCGTGTGCCCTTTACCCAGTGGGAAGCTTTCTGGCTTCCTGGTGGGCTTGTCTAACTAGGGAGGGCTAGCAGCACTGATCTGCTCCCTTCCTAGTTTTCTTACAGTAGCTGCAAGGTGTATGTTCCTTGAGCTGTATCTTATTACTAGCAAGCTGCCAAGAATGATGGTAATTTGTTGTTTTGGTTGTTTGGGGTTGGTTTTTTTTTGCTTCAG
Seq C2 exon
GATTTTGATGTTGACTGCTATGCCCAGAGAAGGCTGTCAGGTGGCAGCCACTCCTACGGGGGAGAATCTCCTCGCCTCTCACCGTGCAGCAGCATTGGCAAACTCAGCAAGTCCGATGAGCAGCTCTCTTCTCTGGACCGTGACAGTGGTCAGTGCTCCCGCAACACAAGCTGTGAAACATTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003712:ENSGALT00000005891:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.905 A=NA C2=0.839
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCAGCCTTGCCCCCTAAAA
R:
CACAGCTTGTGTTGCGGGAG
Band lengths:
294-1594
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]