DreINT0132858 @ 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
chr19:413066-414565:+
Coord C1 exon
chr19:413066-413194
Coord A exon
chr19:413195-414487
Coord C2 exon
chr19:414488-414565
Length
1293 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGA
5' ss Score
5.24
3' ss Seq
CTGAGTGTGTTTCTCCACAGACG
3' ss Score
10.01
Exon sequences
Seq C1 exon
GTGTGTTGGTGAGCGTGCAGTGTTGGGTCTGGAGCTGGATAAGGAGCATCACGCTCTGTTTGTGGCCTTCTCCAGCTGTGTGATCAGAGTTCCTCTCAGCCGCTGCGCTCAGCACGCCACCTGCAGGAG
Seq A exon
GTCAGACCGCACTGCACACGATACACACTGCACACACAGCAGCTGGAGCAACCTTTCCCATCATCTGCTTTCCCATCATCAATTTTTGATTGAATTTTGATGGTTTAAATTATAAGAATGATAATGCAGATCTGTTCATCTGAATTCATAAAACTCTTAACAGGTTAATAATTTATTGACATTTTATATCAGGAAATGTCTGTGCATTTGTTTGTTTTTTAAAGAAATCTTTTTACCAGATTTTGTCATGATGAATGCTGGTTATCAAATTAAGGGATGAACATCAAAAGTGTCATTCTCCTTCTAAAATCTAAACTAATGAAAAAAGTAAGTTTAATTTTGGCACACAGTGCTGCACATCAAAGGGTTTTAGTTCAAATGAAAGCATCGCAGAAATATTAGAGTGTACTTATAAAGTCTTTATAAGTATTATTATTCATCTTTATTATTATTATTATTATTATTTATATTGTTTATTCATTCAATTTCCTTCGACTTAATCCCTTTATTCATCAGGGGCCACCAACTTATCCAGCATATGTTTTACACAGCAGATGCCCTCCCAGCTGCAACCCAGTATTGGAAAACACCCACACTCACTCATTCACACTCTCACACACACACACAGAAACACAAACTGACCCAGCCGGGACTCAAACCAGTGACCTTCTTGCTGTGAGGCCACAATGCAACACCACTGAGCCACTCTGTCGCCTTATTATTATTATTATTATTATTATTTATTATTGTTATTTGTATATTATTATTATTATTTTATTATTAGTAATTGTATATTATTATTATTATTATTTTATTATTATTATTATTAATTTTATTATTATTATTTATTATTATTTTATTATAATAAATTTTATTATTATTATTAATTTTATTGTTATTATTTTATTATTTATTATTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATTTATTATTAGGGTATTATTATTATAGAAGAAGCAAGTTCTACTCTACAGTAGTAATACATTTCTTTCACCATCATGTAGAGTGATATATAAAATAAATAAATGTTCAGCTCGTAATTTATATTCAGTAACTCTTCTTATGAATTTAGGGATTTTTACTATTTTCTTTTCGTTGTTGGATTGATTCGTCAGAACTCTACTTGATTCATTTACAGCATAGGTTTATTACAGTGCAGCCAGATGTCAACAGAAAGTCTTCAGACTCCTTACTGAGTGTGTTTCTCCACAG
Seq C2 exon
ACGCTGCCTCTACACACATGACCCATACTGCATCTGGCTGCGGACGGGACGCTGTGCTGACATGGCCCCGGGGTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002748:ENSDART00000136361:14
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:
PF0140314=Sema=PD(1.9=18.2),PF0143720=PSI=PU(16.4=20.5)
A:
NA
C2:
PF0143720=PSI=FE(47.3=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:
TGTGTTGGTGAGCGTGCAG
R:
TTGAACCCCGGGGCCATG
Band lengths:
206-1499
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]