DreINT0132748 @ danRer10
Intron Retention
Gene
ENSDARG00000076595 | sema4ga
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Ga [Source:ZFIN;Acc:ZDB-GENE-060503-381]
Coordinates
chr13:9393306-9394096:+
Coord C1 exon
chr13:9393306-9393454
Coord A exon
chr13:9393455-9394033
Coord C2 exon
chr13:9394034-9394096
Length
579 bp
Sequences
Splice sites
5' ss Seq
ACCGTACGT
5' ss Score
8.98
3' ss Seq
TTAATCTTGTACTTGGCCAGATT
3' ss Score
5.26
Exon sequences
Seq C1 exon
GGCTGTTGGGTTGCAGGCGCTTCAGAGGCCTGACACTGAACTACAGTTTGCTGCTGTTGGAGGAGGACGCAGACCTGCTGTACGTGGGAGCTCGAGGGGCTTTATTCGCCCTGCAGGCCAGTGACGTCTCCAGCAGCTTAGCACAGACC
Seq A exon
GTACGTATCAACACATCATTATAGTGCGCAGTGGACTGCAACATGTTCATATTTCCAAAAGATACTAGTTTCATTCCTCCACTACACTTTTATTAAATAAAATCAGCTAAAAATGCACAAGATTTAGACTGCACTTTGACACTTTGAAGGCCCTGGTATCCTTTAAAGTTCTTCTTTTGTTTGAGTGCAAAAAGAAGCTTAAAGGCATTCTGACACCCCGCGATGCAGTAGGTGGGGTTGTAAATGTGTCAAGCTGCTCTATTGCCGTGTACCCCTAAACACAGCGATGGTGACTGAGAAAGAAGTAAGACACATGAACACATTTAACAAACAACCTTTTCCATGAAAATCACCATACACCACTTTTTAAAATAACTTGTATATACTTTACCTGCTTAGACTTTAGATTTCACTTTAGTTTTCAACTAGTGCGAATAGTAGGTTATTGCAAGAGTTGTTTACAAACAGCAGTTGGTACAACTTGGCTCTGCAAACTGAAGCAGGATCTTGTTTTGCCAGGAAAACCTTTTTACAAGTCTTGACAGTTGAAGAATTTTTGTTAATCTTGTACTTGGCCAG
Seq C2 exon
ATTGACTGGGAGGCATCAGACGATCAGATGCAACAATGCTGGAACAAAGGGAAAGATAACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000076595:ENSDART00000111365:2
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:
PF0140314=Sema=PU(7.7=70.0)
A:
NA
C2:
PF0140314=Sema=FE(4.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTGGGTTGCAGGCGCTTC
R:
GGTTATCTTTCCCTTTGTTCCAGC
Band lengths:
206-785
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]