DreINT0124607 @ danRer10
Intron Retention
Gene
ENSDARG00000074307 | rapgef5b
Description
Rap guanine nucleotide exchange factor (GEF) 5b [Source:ZFIN;Acc:ZDB-GENE-061215-2]
Coordinates
chr16:19320673-19322597:+
Coord C1 exon
chr16:19320673-19320817
Coord A exon
chr16:19320818-19322499
Coord C2 exon
chr16:19322500-19322597
Length
1682 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGT
5' ss Score
10.75
3' ss Seq
TGTTGTTCTCATGTTTTCAGACC
3' ss Score
9.79
Exon sequences
Seq C1 exon
CTATTGTTCCAAAAAAGGCCGGATGAAGGAGGAGTGGAGAGAGAGTCTGCTTAGGAAACGGAAAGTGCTGCACCTGCTGTCCCAGTGGAGCTCACTGTGCACAGAGCTGCCGCAGGACGATGACAACACCAAACTCTTCCTCAAG
Seq A exon
GTACGTATGCCGAGAGAGGAATGTGGAATTATTTTTGGAAATACTAAAATGCCATGGCCGCCCCTAAAGCTTTTGATTTCTTAATGCCACCTAATGAGGATGGCATCACATGATTATTACTGCCTTCAGAGGCTTGCAAACTCCCAGTAGTAAGTTTACATATTACAGACGAGTGTTGCAAGTTTGTAACACAACTGCACACTTTCATATTGAAATTCTAAGACATTTTCACAATTGTTAGAGAGCAATTTGGAAAAAACACACTACTGGTCAAAAACTTGGGGCAGTTAGTTATTTTTTTAAAGAAAATTATACTGTTCATCATTTAATAAATGCAAAAAAAAAAGTGAAATTGTTGAATGTTTGTTAGAATTTTAAATAACTGCCTTCTTATTGTATGTATTTTCAAATGAAGTTATTACTTCAGTCATTTTTGCTTTTATTACTATTATCATTAGTAATAATAATAATAACAATAATAATAATAATTAATGTTATAGTGATTTCTGAGGTATTATGTGACCCTGAAGACTAGAGAAATGAAGCTGAAAATTCATCTTTAAAATCACTGGAATAAATGATTAAATTAAAAGATAAACTACACATTTTATAGCGCACTTTACACATTATATAGTGCAATAACATTTCACAATTTTACACTTTGTACTGTTTGTTTGACTAAATAAAAGCAGCCCTGGTGAGCAAGAGCTTATATTAAAATATTTAAAAATCGTACCGACCACAAACGTTTGACTGCTAGTGTAGATTTTAAAAAAGTCAATTACAAAGTTACAAGATGTAAAGTCAGTTTTACACAATATAACATCAGAAACATAAGCTCAAGAGGTCTTATAAAGAAAAGTCAAAATTGTGATGACTGAATTTTTTTTTCTTCTTAGAATTCAGAGAAATTTTATGAAGTTCAGAATAGCAAATACAGACTGAGAATTTATTAACATAAAAAAGGCAATTGTATCAGTTTGTGTGACCTTTCTTATCAGAATTTCTGATGAAAAGAAAGTTTGAATTGTGGGATAAACTTTCTAATTCTAATTTTATTAGTCACATACACAGTCAAACAAGGTATGATATGCAGTGAAATGCTTACACAACTTGGGACCTAAAATAATGACATTAATCATACAAAAATATTAATAATAACAGTAAGACTAATTACTGTTTTTATTATTATTTTTCCATAACAACTACAAGAAATGCTCCAGTTTCCCCCCATAGTCCAAAGATATGCACTATAGATGAATTGAATAAGCTAAATTTGCCATAGTGTATGTATGTATGGGTGGTATCCAGTGTTAGGTTGTGGCTGGAAGGTCATCCGCTGCGTAAAACAAATGCTGGATAAGTTGCTGGTTCATTCCTCTGTGGCGACCCCAGAAAAAATCTAATAAATAAACTAAGCCGAAAAGAAAATTTTAGTTCTTGTTCTTTAAAAAAAAAAAAATATTGCCTTTACAATCAAATTAGAAGTAATAGTCAAAATAATGCATATTTATGTGTGTGTGTGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCATGCGTGTGCATGTGTGTGTGTGTGTGCACGAGTATTTTTATTTTTTGCCATATAAAGTATTGCAACGAATCCACAAACTAAAATGTGAATGTTGTTCTCATGTTTTCAG
Seq C2 exon
ACCCTGTACAGACACGTTCTAGATGATCTCTACGAGTTCCCCCCGCTAGAGAAGGATCTCAAAGAACTTCAGAAACTTCTACGGATGCAAAGGAGACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074307:ENSDART00000114954:13
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(41.7=100)
A:
NA
C2:
PF0061815=RasGEF_N=PD(7.8=27.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAAAGGCCGGATGAAGGAGG
R:
TGTCTCCTTTGCATCCGTAGA
Band lengths:
232-1914
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]