GgaINT0067163 @ galGal3
Intron Retention
Gene
ENSGALG00000010697 | SEMA4D
Description
NA
Coordinates
chrZ:42893003-42894962:-
Coord C1 exon
chrZ:42894864-42894962
Coord A exon
chrZ:42893097-42894863
Coord C2 exon
chrZ:42893003-42893096
Length
1767 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
TTCAACTTAATTTTTTGCAGAAT
3' ss Score
8.44
Exon sequences
Seq C1 exon
ACTGAGTGCCGTAATTATGTGCGTGTGCTGCAACAGCTAAATGACACTTTTCTCTACGTGTGTGGTACTAATGCATTTCAGCCAACTTGTGATTACCTG
Seq A exon
GTAAGATTATGTAGATTTTGTGACCCAGTAAAAACTTCAACAAAAAAACAGCTCATCTAAACAATGAGTTAATCTTTTTTTCCCAAATAGCATTGCAATTTCAGTGCTTGTCATAGCTTCTGAAATATTCATGATACTCTCTCACAGTGATGATTAGAGTACAGAAATAAACTGTACTGTTCCCTTTTCAAAACACTGAATTATTGATTCAGCTTGGTTATCAGCAGATTTACTCTTTCGTTGCTTTTTGTAGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCTCTGCTTGTCTTGTCTCTGCTTCTGGCAATGCCATAGCTTCATAACTCTGAGTGCTTCAAAATGAAGTCTTGGCTTAAAATCAAAACTCCCTTTTTTCATTGCTTACTCTTTCTCTTGTTCTCCTCACTGTGTCTCTTAACGATTCTGAAATTCAGAGATGTTGTAATTATGTTCAACTTAGTTCTTTTTTGTTTTCCCTGCCTGTAAGTTTGTCTGCCGTTAACCCTGGAACATTGCCAGAAGTCACTGCCCTTAGCCTCCAGTGTCTTCATTACACAATATAAGTGATTATTTTCCCAGTATTGTTGATTCAGCTCTCAATCATCTTTCTGATCCTTATTCCCTTGATTTTTAAGGGCTATAAAGCTATAAAGTATTAGTCATTCTGTTGTTTTTGAAAAATACAGCTAGATTATACCCCATCTAACAAATTTAAGTCTCAAAAATTGCTAAGTCCACTTCAGAAAGCTTTCTTAGTTTGTAAAACTGACGATTTTTGTGCAAGCTAATTTAATAATTGCAAGTTCTTGCCTTTCATCATCTAATTTCTCTGCCTTTCATATTGTGTGGTTTTTTGGCAGATCTCTTCCCTATCTTTCTCCTTCTATGCCTGGATTTAACTTTTTGTCTATTCTTTATTGCTACTTCCCTCAGTTTCCTCTCTCTGTTATACTTGATCACATTTTCTGAAAGCTTATATGTATTTTATAATCTTTGAAAAACAGTCACTTTGAAAGTTACTGGTCCATTGGTTTTTAGTTACCTTTGCATGATTCAGTTGCTTGAAAGAAAGAGTACAAATGGTTGGCTTGTGGTTTTCAACTTAATTTTTTGCAG
Seq C2 exon
AATTTAATTTCGTTTGAGCTCGAAGGTAAGAATGAAGATGGTAAAGGCAGATGCCCATTTGATCCTGCTCAAAGTTACACATCTGTAATGGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010697:ENSGALT00000017396:4
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=0.031
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(19.6=100),PF0086713=XPG_I=PD(23.7=66.7)
A:
NA
C2:
PF0140314=Sema=FE(19.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGTGCCGTAATTATGTGCGT
R:
ACAGATGTGTAACTTTGAGCAGGA
Band lengths:
183-1950
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]