DreINT0132872 @ danRer10
Intron Retention
Gene
ENSDARG00000000189 | sema6e
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6E [Source:ZFIN;Acc:ZDB-GENE-040724-119]
Coordinates
chr16:30282302-30284010:+
Coord C1 exon
chr16:30282302-30282433
Coord A exon
chr16:30282434-30283854
Coord C2 exon
chr16:30283855-30284010
Length
1421 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
CTCTCTCTCTCTTTCTCCAGGCC
3' ss Score
13.33
Exon sequences
Seq C1 exon
CATCACTGGTTCTGCTGTATGTGCATTTTACATGGATGACATAGAGAAAGTGTTCAATGGGAAGTTTAAGGAGCAGCGAAACAGCGAGTCCGCCTGGACACCAGTTCCTGATGAAGCGGTGCCCAAACCCCG
Seq A exon
GTAAGTCATGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTTTGGTTTTAGTTTTGTTTTTGTTTTTAGTTTTGTTTTTGTTTTTAGTTTTGTTTTTGTTTTTAGTTTTGTTTAGTTTTTTTGTTTTGTTTTGTTTTGTTTTTCGTTTTGTTTTTGTTTTTCGTTTTGTTTTAGTTTTGTTTAGTTGTTTTGTTTTGTTTTTGTTGTTAGTTTTGTTTTTAGTTTTGTTTATTTTTTGTTTTGTTTTTGTTTTTAGTTTTGTTTTGTTTTTTGTGTTTGTTGTTAGTTTTGTTTTTAGTTTTGTTTAGTTTTTTTGTTTTGTTTTGTTTTGTTTTTTGTTTTGTTAAAAACCCTGAAAACAGTTACTGGCTTTTGCACAAACCAAAAAATAAATAACTTTACTTTTGTTGCTTTTGCTACATGTTATAGTTATAACAATTAATTTGAAAAAAATAGAACTTTTTATTTTAATGAAACACAAATACAAAGTTTAGACTGAAAGAAATATTGCTAATATTTTTGATTAGGAAAAAAACTAATGAAATATAAGCAAAAGCACAAATAAATTCAATAAAATGAATGTACAATTAAAAAACAATTTATTATTCAAATGCTTTTTTTTTTCTTTTATTAACATTTAACACATATACCAGATTTCATATTAGGATGCAATCAGTTTAAGATGTATGGATCCAATATAGTAATAGATTCACATCCAGTTCATTTCTTAGTTGCTTACATTCACCTATCATAACCAACTGTATTTGATACTGCTTTCCAAGATTATTGGCATGATTTTGTACTTTTTGTCCCTACTTAAACAAAAAGATCTGCATGCTGTATGAAACCTGGCTCGCTCTGTGTGTGTTTTTCTTGTTCACATCATTGTATCATAATAGTATTGCAATAACATGTCACAAGATTACAGTTTAGACAACATTATAGTTTACTGTATTTTTGATTAAAAAAAAAAAAACTGCAACATCCCTAGAGTAGCATGAGCACATCACACAAAGGAATATATTCATGAACTTATCAAACAAAATGAAATCTCACTTACACACTCAGCTGACAAAGAATAGACTTCCTTGTCATCTTGCTTCGCGTGATATGCCTGTTTTCTGGAGCTCAGAGAGCAGCTTGTTTGGCCTGACGGACTCTTAAAACAGCTTCTATTTAACAGCGGCAGATGGCTGGAACGGATCTTGTTAACTGTATGTGTACGATCTGTTTTTGTTGATCATTTCACTGAGCCACAGTAAAGTCTGTGCAGGTTGATATCAATTGTTTTCTCTCTCTCTCTTTCTCCAG
Seq C2 exon
GCCAGGGTCGTGTGCTGGTGATGGCCCTGCTGCTGGTTACAAGTCCTCCACAAATTTCCCTGATGAGACTCTTACCTTCATTAAGTCTTATCCACTAATGGACGAGGCTGTGCCGTCTGTCAACAACCGACCCTGCTTCACACGAACCACCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000000189:ENSDART00000135723:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.333 A=NA C2=0.189
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(10.5=100)
A:
NA
C2:
PF0140314=Sema=FE(12.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCACTGGTTCTGCTGTATGTGC
R:
CTGCTGGTGGTTCGTGTGAAG
Band lengths:
286-1707
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]