GgaINT1024768 @ galGal4
Intron Retention
Gene
ENSGALG00000004844 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:9411613-9413660:+
Coord C1 exon
chr10:9411613-9411669
Coord A exon
chr10:9411670-9413492
Coord C2 exon
chr10:9413493-9413660
Length
1823 bp
Sequences
Splice sites
5' ss Seq
CTGGTTAGT
5' ss Score
6.32
3' ss Seq
AAATCTGTTTGCCACCACAGACA
3' ss Score
5.36
Exon sequences
Seq C1 exon
AAATTTTGCCTACTACAGCTACACCAGATTACAAAATATTTGGCGACCCAACATCTG
Seq A exon
GTTAGTTTTTTTTAATTTTTTGAATTAATGACCTTTACTTTCCTTCAGTTCAGCATTTTCAGCCCTTTTTTCCTTCCTTTTGCACAGTTGGCAATCCTTCATTTTTGTGCTTTTCCTCATGTTCCCACTGATGGTAAAGATAGTGAGACTCTTCTCACTCAGCACTTCACCCTGTGTAGTCGCATGTTAACAGCTCATTATTTATTGAGACATCTTTTATTAAAGAGCCTGATTAACATAGATGACATCTTCACTGCACGAAAGTCCACTAAGCTTTACTCTGTATCCCCAGCCATGCATTTGTGAATGCCCCTGTTGGTCATCTCTAGTAGATGAATGGCAGAATTTCATCATCTTCGTCCTTACCTCTCCTTTTCTCCTTCCTCCTTTCCCAGCAAGCTTTTGGCACAAATACACATTTCTAAAATGTGTATTTTCTATATTTTTAAAATGTTTTAAGTAGTTTGTGCTAATGGAAAAAAATGTAAGATCACAAACTGTCTAGCTTAATGAGGAGTTGTGTAGACAAAGGTGGCTTCTTAGAAAATTTTAGGCATTGTTGTCAAATGGACTTTCACATCCCTTCTACCTTCAGTGGTTTTTTCTAACAGTGTTTTCTCTGTCGGCCCTGGTGTGTTCCAGGAGTCAGGACCCAGTGCTGCTCTGTTGAACTCAAAAGCTGAACCCTGTTGTTGACTTCAACAGGAGCAAGACTGAGCCCTGATTTTCCAGTGCTTGCTCCTGAAACCTGGTCTCTGTTTTCAAACCAAGGGCACATTCCTGACTGGCAAATCTGAAGAGAATCTGTTTGTGTGTTTAATTTGTAAAAGAGGTGCAATAAATTATTTTGGTTTGTTTTAGTTTCTGATTATATTTCTGTAACTTGAAGTAATGTCTGAGACAAAATCTTCCATAGATATATATATACACACCCATAATGTAACTTAGAGATTCAATTAGGAAAGCAAAACAAAACTGTATTATTTGGAAGTGCTACTTTGCTTGCATTAGTGGTTATCAAGCAAATTTTCAACCTGGTATTTTATACTAGATGCAATTGAACCTGTTTTTCAAGTCCTGATTGAGCGTGCTGTTGGAGTACTGTCAGATTTCGAGCTGCAGCCATTTGTGCCTTGACCTACTGGGACAGTGAACACAAAATACTTGAGTGTGCAAAGTAGACTTTGGACCGTAAACCCAGTCTGTTTCCTCCTCGTGCATTTTCACATAGGTGATAGTGATTCTGTTCAGTAAGTGTACTACAAAGAAGCCAAGATCTATACAGTACTGTTCCTTAGGAGCCATTACAAAATAGAGGTTAAAAACATTCCTTTCATCGTCCCCTCAAGAAATGGCTTATTCAACAGTTCCTGGTGTACTGTAACAGCACTAATGGAGCCGATCTGGTTTCTCAGGAGTAACCTGTAGTAAGCATGTATCTTTCTAAGTAATTTTTTTTTTTTTTTGAGATGTGTAGAAGGTAATGGAATATGTTGTCTCCAGTGAACAATATAGCAATTAAGTAGAGTAAGTTCTGCTTTTCATCTCCACCAGTTGCTTACGTTAACTTTTGCATTGCTTTCATGTTTGACTTCTCTGGCTTTTTGGCTAGCAGCTGTTGATGTTTTAATGTATTTTTGTCATACTTAAAAGTTTTGAACCGATTGATTTTAATCAGCCCTCTGTACTTCCATGGGCTGCATTTTGCTCTGTCAAGTAACCTCCCGTTAAAAGCTGTCTGCAGCTATAGCTTAGATATACCGTGAAACAGTGAGGAAACCCTGACTGTAATACACATTAATAAAATCTGTTTGCCACCACAG
Seq C2 exon
ACATGAAGTTCTCCTCAGCTTCCATTACCACAATGGCAAGTATCCCAGTTATATCACCTAGAGTGATTGGTTCCTGGAAACCTAAAGTGACTGGCTCTCGGAAATTTGTAGTTCAAGATGACCCAAACACTTCTGATTATTCTGATCCATTATCAGGTGTCCCAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004844:ENSGALT00000007734:16
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=0.105
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(5.0=15.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTTGCCTACTACAGCTACACCA
R:
CCTTTGGGACACCTGATAATGGA
Band lengths:
222-2045
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]