RnoINT0124241 @ rn6
Intron Retention
Gene
ENSRNOG00000059961 | Rapgef3
Description
Rap guanine nucleotide exchange factor 3 [Source:RGD Symbol;Acc:621869]
Coordinates
chr7:139232251-139234394:-
Coord C1 exon
chr7:139234323-139234394
Coord A exon
chr7:139232949-139234322
Coord C2 exon
chr7:139232251-139232948
Length
1374 bp
Sequences
Splice sites
5' ss Seq
CATGTAAGT
5' ss Score
8.31
3' ss Seq
ATGGTTCTCCCTCCCTCCAGGTT
3' ss Score
12.13
Exon sequences
Seq C1 exon
CGCCTCTATCACCACTCAGAAGCCGGGTTTCCCACATCCACGAGGACAGCCAGGCATCAAGAATCTCCACAT
Seq A exon
GTAAGTGGTGGGACAGGGTACTGACAGTTGGCGTAGCTGGGACAGAGCCGGACGCTTACGTGCCGTACGTAAGCGTACGTACGGTACGTACGTGTACAATACGTAAGCGTAGAGTTCGTTGGCACCTGTCTGGGAAAGTTACGGCCGCTAGCTCAAGCTAAGGGGGGAAGTGCTGGAGGTGAAGCTCGTGTGCTAACTCCAACCTATGCACTTATCTGATGGGAGCTCATGCAGTTAAGGAGTAGTCGTAGCCAATGGTTCAGATCACAGTGCCTGCCCTGTGCTCACAGATAGATACATCCATGGTGATAATCCTCCGAGACTTTGGCTCAGTCCAAGGCAGGAAACACAGATGGCGACTTGGTTCTCCACTGTCCTCTGCCTCTCTCTCCACGCAGCAGCCACTATGATGAGTTTTGAGTCACTCCTGTTTTTATTTTATATTTTGCTTATTGGTTGATTGATTTTTATCTGAGACCGGCTTGCCTCATGACCCAGGCTGGGATTCCAAGCCTGAGCCATAGCCTGTGCTTTCATTTAAAAATAATAAAAAGAAAAAAAAAGCCTTATCTCACACCTGCATGCACAATGAACTTTTTGCAAGTTTTATTCTCATCGATGTGTGTATGCACCTGTGCATGTGTGTGAGGACGGATGCCATCCACATGCATATGGGCTCACACGTGTGTGTGCAGTGGTCAAAGAACAGCCTTGGGTGTTCTTCCTTGGGCACCCACTCTCTCTTCTTTGTGAGACAAGCTCTCACTGACCTGGAACATACCAGGCGTCCTAGGCTGTCAGGCTGGCCCCAGTGATCTGACCATTTCTGCCTCACCAGCATGGGAGTTACAGCCGCACAACACAACATGCAGTTTACACCCTGAGCTATCCCTCCAGCTTTTGCTCCTTTCCCTTTTTGGCTTTGCTAGCCTGGACCTCTTTATGTAGCCCAGGCTAACTTCAAGCTCATAAAGATCCCCATGCCTCCACCTCCTGGGTGCTGGGAGCAAAGGCATGTACCACATGTATGGATGTTTTTGCTTTTTTGTTTTGTTTTGTTTTTTGAAACAGGGCCTGGGACTCTCCATCCTCCTGCCTCAGCTCCTGAAGCTCCAGGATTATAAATGTGCACCACCATATCTGTTTTAGTTCCTACTATGCTGAGACTGTGGTGGGGTGTGGGGTCTTCTTTATTCGGACTTTGCAGCCTCTGCCCTCCTGACTCTGTGGTGGGAGAGACAGTGGTCTGGGAACTGGCGTTGAGAGGATGTGAGGTAGGGAAGAAGAGAGAGCTAAGGCTGCTTCCTGGAGAGAGGTAGGCACCGTGAAGTGGCCATGGCGCCTTACCTCTCTGATGGTTCTCCCTCCCTCCAG
Seq C2 exon
GTTCCGAGCAGTCCCTGAGCACCCGGAGTCCAGCCAGCACCTGGGCTTATGTCCAGCAGCTGAAGGTCATTGACAACCAGCGGGAACTGTCCCGCCTCTCCCGGGAACTGGAACCATGAGGAAGGACTGGCTGGAGCAGGCACTTCTCTCAGAGAAAGCCAGAGCCTGTGCAACCAAGAGGTCCAGAGGCCAGCCACAGCTGGGCAGGGCTCTCCACAGAGCGGACTCAAGGCCCTGGAGTGGGCAGTGTCGAGGCAGCTGTCCTCTGTGATGACTGTCAGCTGTGAAGATCTTTGATGTTCACGGCCAAGGAAAAGGGGCCATTGAGGCCCCAGAGGGGTAGGAGAGCTGGGAGGTGCAGGACTCTGGTTCAGTAGAGAGCCCTCCCACCGGGCTTTCTGCATGTCTGTATGTCTGTACATGCAGCTGTGCTGTCCATGGATGCCAGGCCCTGTGCTTGTTTTCACAGGAGCCAGCGAGCTCACATCTGCATGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGCACTGGGTGGTGCCTTGCCTGGGAGAGGGTGGGGAGTTCTGCTATTCTCACCACACATCTGAGATAAACAGCTGGGTGTGGGCAGAGCCGCTGCCTAGAGTGGTGGTCCCTGTGGAGTTGTATTGTTCCCATAAATTAACAAAGATATGTGTGTTCTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000059961:ENSRNOT00000078644:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.400 A=NA C2=0.231
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA

Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACAGCCAGGCATCAAGAAT
R:
TCAATGGCCCCTTTTCCTTGG
Band lengths:
356-1730
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]