DreINT0124557 @ danRer10
Intron Retention
Gene
ENSDARG00000079291 | rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:ZFIN;Acc:ZDB-GENE-090312-38]
Coordinates
chr23:33494236-33496319:+
Coord C1 exon
chr23:33494236-33494330
Coord A exon
chr23:33494331-33496230
Coord C2 exon
chr23:33496231-33496319
Length
1900 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAAT
5' ss Score
4.44
3' ss Seq
CTATAGTTTGAATTATCCAGGTA
3' ss Score
3.12
Exon sequences
Seq C1 exon
GACGTCGAGGCAAACACCGTCCGTCTGGAGGAGCATGGTAAAGTCGTTCTGGTTCTTGAGAAGAGCTCGGCGCAGGATACACCAAGCTGCAACAA
Seq A exon
GTAAATCATTTTGTCAGTTTTTATACTATAGTGCACATATCAAATATTTAACTTGAGCTAAATAATTAAAACTGGCATCACCTGACAGAATAAAAAGAAGTGTGTTTATGCATTTAACTTTTGTACTGTATTATAAGCATTTTTAGCAATTAGATTCATCTTTAATTTTTATGGGAAAACAGCATGTTTTATCCTAAGCCAAAACACGTCAACTTAAGCAGATGATGTTAGATTAAAGGTTTTTATTTAGTTTTGAGGGTCTCATACAATAGGTTTACATGCAACTAAGATAAAAAATGTAGCGTATACTTTTTTCAGCCAGCAAAATTTAATCTGCATTTTCAAATTTTTGGTCAAAAGATAAAAATGAGCAAAAAAAAGCTGATTTACCACACTGCCCATCAGTGTTCAGCACAGAGGTTCTACTCTCCATCTAACCATTGCTACTGTAGGGTCTAAAGTGGTTTTCACACCAGACATAGAAAGTATTGTGCTATGAAACCCATTCTTTTCAATGGCATGCACCAAGCATAGTTGCTGCACCAACCAAAGCACAAGAGCAGCTGACCACACGTTTGACTACCTTGCACATTGGGATGGGTACCGAAACCTAAATTAGTGTAATATTAATAGTTAAATAAACACGCACATTCGGTTACAATGAAAACAGTCTTTTCTTTCTGCAGTAGCCTAAATAAATCTTAAAAATTAAAAAATCTTTTACATCAGCTGTATTTACAAATATAGCCTATGAATAGCCTAATAATAAACTATGCTTATTAGAAAATTATATTTAAAAAAAAATGCTTATTTTTACATTGCAAGATGCTCCAAAACTGTTTTAAAAACAAAGTTAACTCCCAAAACACCGTTTTCACTCATTTATGTGACCTCATTTATGTGAATGCATTAGTGAAAAATCATATATGTATAATGCTGGGACATTTATGTAGTATATTTGTTTCTGATGCTTGCAACATCGCTAGTTTTTTGTCATGGCAAACCAGGTAAAGGTCACCTTATGACTCATTTACTGTCTAATTTAGTTTAATGGTGTGTGATTATTTTAATTACATTACATATTATTAAGTTTTTATAATTTATCTTTTTAAAATCTATTTATTAAATATTTATTAAAAAGCTTTGATTTCGGTTTTTGGTCAAATGCATCCATAATTTTCAGTACATCCCTAAATAAAATTAAAAAAAATTAAATTTGCTCATAATATACATTTCATATTATCTTATTTCACAAATAGTGAAATGAGCGGGATATTTTACTGCTAATAGAGTAATAATTAATCACACTTAAAAATAAGCAATGAAAACATTCCTCCAGATCGATATTCTCCGTAACACATACTGTAACTAAAGAGGACTCTACTATCTATATTTAAGCAAACTTTCTATAAGAATCTACAAACTACATATGCTTGTCTTTGTCCAGCTCACCAATCAACATTCACAACACAGTTTACAACCTCACATTTAATGTATCAACACTGGGATGGTTATGTATCATGTATTGAAGGAGCATTCTTTCAATAAAAAGATTGCATTTGCTTTTGTACGGAATGTCTCCACCTCACAACACTGGGCTCATTTTAGCATTCCTGCGTGTAAATCAAATCATCCAGCATCTTTATAAACCATTTATATAACATCAGCAAGTGAAACAATCCCTGAATAACGAATATCGAGCATCGCTAAAGCTGTCCGCAAGGAAAGTGCAACTACTGATTCATTCAAGTACGTTACCAACATACAGTATGAGTGCTGTTGTACAATGAAATGCAAGCTCAATCCTTATTAGTCATCACTATTATTTGATTTCAAGTGCACTAATTCAATTATGAACAACAGAAATGGAGGACGCCTAACTATAGTTTGAATTATCCAG
Seq C2 exon
GTACACGGTAATGTCAGGAACGCCGGAAAAGATCCTGGAGCACATGCTGGAGGCCATAAAACTGGAAACCAACGGAGCTGACTTCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079291:ENSDART00000142328:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.094 A=NA C2=0.032
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=PD(2.3=6.2)
A:
NA
C2:
PF0061815=RasGEF_N=PU(25.9=90.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACGTCGAGGCAAACACCG
R:
ATGAAGTCAGCTCCGTTGGTT
Band lengths:
182-2082
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]