DreINT0132825 @ danRer10
Intron Retention
Gene
ENSDARG00000036626 | sema6ba
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6Ba [Source:ZFIN;Acc:ZDB-GENE-131024-1]
Coordinates
chr2:49571360-49573607:+
Coord C1 exon
chr2:49571360-49571491
Coord A exon
chr2:49571492-49573457
Coord C2 exon
chr2:49573458-49573607
Length
1966 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACT
5' ss Score
8.63
3' ss Seq
TGGATTTGTTACTCTCTAAGGCC
3' ss Score
3.89
Exon sequences
Seq C1 exon
CATCCCCGGCTCTGCGGTGTGTGCGTTTGACATGCAGCAGCTGGCACGTGTGTTTGAGGGCAGATTCAAAGAGCAGAAATCACCAGAATCCATATGGACACCAGTACCTGATGAACTGGTGCCAAGACCCAG
Seq A exon
GTAACTGTCTGTCCATCTACACATGTCCGTCTTCCATCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTTTTTCTTCCTTCCTTTTTTCTTTCTTCCTTCCTTTTTCTTTCTTTCTTTCTTTCATGCTTCCTTCCTTACTTTTTGCTGACTTCCATCCATCCATCCATGCATCCATCCTTCCTTCCTTCCTTCCTTCATTTTTTCTTTCTTTCTTTCATCCATGCTTCCTTCCTTCCTTTTTTCTGACTTCTATCCATCCATTGTTCCTTCCTTCCTTTTTTCTTTCATCCATGCTTCCTTCCTTCCCTTTTTCTGCTTTTGATACATCCATCATCTAACCATCAATCCATCCATCCATTCATCATTCCTTCCTTCCTTCCTTCCTTCTTTCTTTCATCCATGCTTCCTTCCTTTTTTCTGACTTCCGTCCGTCCGTTCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCACCCATCCATGCTTCCTTCCTTCCTACCTTTGTTTTTCTTTCTTACTTCCATCTATGCTTTTTTCCTTCCTTTCTTTCTGTCCTTCATACATCCATCCATTCATCCATGCTTCCTTCCTTCCTTTCTTTCTGTCTTTCATCCATCCATTATTTCATCCATGCTTCCTTCCTTTCTTTCTGTCCTTCATACATCCATCCATTCATCCATGCTTCCTTCCTTCCTTTCTTTCTGTCTTTCATCCATCCATTATTTCATCCATGCTTCCTTCCTTTCTTTCTGTCTTTCATCCATCCATCCATTCATCCATGCTTCATTCCTTTCTTTGTGTTTGTCATACATGCATCCATTCATCCATGCTTCCTTCCTTTCTTTCGGTTCTTCATCCATCCATCCATCCATGCTTCCTTCCTTTCTGTCTTTTACCCACTCATCCATCCATCAATTGATCCACTATTTTTGTCAATCCATTAATGTATCCATCCATGATTTTATCCATCCATCAATTCCTCCATTAATATATTATTTCATCTATAAACCCATCCATTCATGCATACATTTGTCCATCAATCCATCATGTTATGATTGATCGGTTTCATTCATCCACCAGTTTATACATTTATTCATTAATTTATGCATAATTTGTTATGCATTCATCCATCCATTAATCCACCAGAAAATCAGTTCATCAATTATTTTAGACATAAATCCATTCATCCGCTTATCATTTTTCATCCCTACAGTCTTCTATCAATAATTTAATCCATCCATCTATTTATCCATCAATCATTTTTATCCATCTAACATCCATCCACTCATTTGCCCTTCCTTTCATCCATCAATTGATGTATTTATCCATCAGTCCCTTCATAAACATTTTTTAACAATTCATCCCTCCTTGAATAATTTTCCATCTGTCTTTCCATCCATCCACCATTTAATCTGTTCATCAATTCATGTATCCACCAATCATTTTCATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTCATTTTCTTTCTTTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCGTTCCATCTATCCATCCATCCATCCATCCATCCATTTATCCATCCATTCATCCATCTATCCATCTATCTATTGTTCCATCTATCCATCCATCATCCATCCATCCATTTATTCATCCATCCATCCATCCATCCATCCATCTATCCATCTATCTGTCTGTCTGTCTGTCTGTCTGGATTTTTGTACAGCACATAAAGAAGCATTGCGTTTAGAAATGTTTAAATTTTATATGTGGATTTGTTACTCTCTAAG
Seq C2 exon
GCCTGGAGGATGTGCTGTCCAGGGCTCCAGATTCAGCACCTCCAACACCCTCCCTGACGAAGTGCTTAATTTCATCAAAATCCATCCTCTGATGGACGAAGCGGTTCCTTTGTTAGGACACAGACCCTGGATAGTCAAGACCATGGTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000036626:ENSDART00000154285:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.178 A=NA C2=0.137
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(10.3=100)
A:
NA
C2:
PF0140314=Sema=FE(11.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTGCGGTGTGTGCGTTT
R:
CGGACCATGGTCTTGACTATCC
Band lengths:
273-2239
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]