DreINT0132862 @ danRer10
Intron Retention
Gene
ENSDARG00000002748 | sema6d
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:ZFIN;Acc:ZDB-GENE-040426-1933]
Coordinates
chr19:406581-407721:+
Coord C1 exon
chr19:406581-406710
Coord A exon
chr19:406711-407606
Coord C2 exon
chr19:407607-407721
Length
896 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
GTTTGTGTGTTTCTCTGCAGACT
3' ss Score
11.29
Exon sequences
Seq C1 exon
TTGACGGAAAGAACATGGTGTTGCTCTGTCATCATGGCGATGGTCTTATTAGCCTGGCTCCTCCCACTCATTACTTCTGCCACGCCTTTTCCTAGAGATCTGCAGCCAATTAGTGTGGTGGGATTGGACG
Seq A exon
GTGAGTCACATGACTGACATGGTCCCTCCTCCATTCCAACAGATTCTCTGTGCAATATACTTTATATTGAAATATTTATGTTTAATTATTATTTATTTTATATTTCTACGTAATCAAACAAATAAAGAAATCAAATAGAGATATATGATCACATAAGTACGTTACTGTCTGTAGACTTTAATATGTAAAAAATAAATAGTCAGTGTATATATAATGAGGTCAGTATAAACATATTAAATTAATTAATTAATATGTTAAAATAAATTTATTGAATTTGCATAAATGGATCTATATCTTCATATATGACATATATTGTGATAAATGTAGGACTTATAGCCCTACCGCTGCGATTAAAAATGCTGTTTTGTTGTAAGAGTTTTAATTAATGTTTTAATTATTTTAATGTTTTCTTTGCTCATAATTGGCTTTTTCTGCACTCACATTCACAGGCATAATGGATTTTCCATTAGCCATCACAATATATTATTGTCGACCAGAGCTTTAATAGAACTGATGTCATATTAGACAGATTTTACTCCGCTATTTCCAAACCCATCAGGCCTAAAAACATTAGGAACAGTAAATTTCATTTACTTTAATTGTCTAAATGTGTCATTAATTCAGAAATTAAACATATGTTAATGTTAGCATTACACCATGTACTTTTCTACCACTGCTGCATCATAATAACAGCATAAACTACAATGACACAGATCTCCTCAGGCACAGATTATGTGCTTTATTCAGTGTAAACTACTCCCAGTGTGAGTTTAAATGTCACATCTATTGCCTGAAAGCAGCAGCAGATAGTTCAGCTCAGATCTAACTAGCAGACGAAATGAAAGTCAGAGCTGTGAAAGACTGATAGACGGAGGCGTTTGTGTGTTTCTCTGCAG
Seq C2 exon
ACTCGTACCTGTACCCCAGTTTTCAGGGTCTGGTGTCCAGCAATGAGACGGAGCGTCTGGGTCTGGACTATCAGCGCATGATGAGGATCCAGCACATGCTGTACATCGCCGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002748:ENSDART00000136361:2
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:
NO
A:
NA
C2:
PF0140314=Sema=PU(4.0=43.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGGAAAGAACATGGTGTTGCT
R:
GCGGCGATGTACAGCATGT
Band lengths:
239-1135
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]