DreINT0018782 @ danRer10
Intron Retention
Gene
ENSDARG00000067801 | SEMA4D
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D [Source:HGNC Symbol;Acc:HGNC:10732]
Coordinates
chr21:2779618-2781796:-
Coord C1 exon
chr21:2781698-2781796
Coord A exon
chr21:2779712-2781697
Coord C2 exon
chr21:2779618-2779711
Length
1986 bp
Sequences
Splice sites
5' ss Seq
CTGGTGTGT
5' ss Score
4.96
3' ss Seq
GTAAATTTCTATTTCTTTAGTCT
3' ss Score
4.91
Exon sequences
Seq C1 exon
ACGGACTGTCGAAACTACATTCGAGTTTTGCAAGTGCTGGATGAAGAACATCTGTATGTTTGCGGGACTCACGCGTTTCAGCCTCTCTGTGATTATCTG
Seq A exon
GTGTGTACATCTCATCATATTCACTTCTGTGCATCTCTTCAACTGTCAGACAAGCTATAGACTGTAAATGTAAAGCAGATTTTCTTTCAGTAAAGAAGTTTAATATATTAAGGTGAACCAAACTAACCAGCTCACAGATTAATCACGTTACAACAGTGCAAACGCCATTATGCTGGAAAGAAATATTCATTCATTCATTTTCCTTCAGCTTAGTTCCTTATTTGTCAGGGGTCGCCACAGCGGAATGAACCGCCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAATGTCCCGAAAGATAGTTCTGGTGGATTAAGGCACTGGTTATTGTGCTGAAATAGGTGCAGATCTTCATTTTTGTAAACAGTTTGTTTTTAGCAGTAATTTAATGCTGGGCGTGTCATCGTGATTGACAGCTGTGATTGACAGTTTCTCAAAGCAGCGCGTCTGAGCTTCGGCAGAAGACTGAAGTGTTATTATTCGATTTCTGTGTTATTTTACCATGATAAAATGAGTTCAGCAGTAAACTATAGTTTCTGACATACATGATCCTGGTGGAACACTGTTTATACGCTAAGGTCAGGGCTTTTTTGGGGCTTTATTAGTTTGCTGATACATGCCTAGCCACCCAGATAGCAAAATACACTCGGGCCAGTTCCGGCTAGATTCTCGCCTGCCGGAGACTTACCCCTCAGACTGACTACCTCTGCTGGACCTACTCCGGATGCCTGGACTCACTGCCCGATTCCAGCCTGAGTTAATCGAGCCAGATGCGGCGGCCGAGCGAGCAGGCGCTGCCGCATGCGAGCTGGAATCAGCCCGCGACGCCGCGAGTAGGTTATGTGCAGCGGCCCGGAGCTGGCGCGATTAAATATATAAAACCCTCATATTTGTTAACGTTATTACATCCATTTGTGTTGATATGACAGCAAACGCATGCTGAGCAGTTCGGGGGGCGTGGTTTATTTTACATAAAGCGTTTGGTTGGAAGCTTGACTCCGCTCATTTTCGCGGCTCCTCCTCTGGCTCCATCAGACAGTCCTTCTGCGCATGTCAAGGCTCCAATTTCAGCAGTCTTTTGTGACAGTTTGTGCCCGTCAAGCAGGCGTTTTGCCCTCAAGGCGTTCAATGGGAAAAGGGGCTGTCGCGTTGTCCATATTTTTTACAGTCATTGGTAAATACATAGTAAATTAGTCATTTATAAACTTAACCTTAAGTTAATTTTCAAGGCGATACACTTTTTACTGGTATTTCAAGTCAAGTCAGGCTTTATTGTCATACCGCTACATGTATGGACATACAGAGGAACTAAGTGTCATGTCTCGCAGGACAACGGTGCTACATAAATCATAAATACAAACACAACACTGGACATAGCTATTTTTAAAAACCCTATGCATAACTAACATATACTATATGATATAAGACTATACAAGGCTATGCTAGTACTTTTACATGAGACTGAACAATGAAGGTGTTAACATGAAAATTGTGCAAAAGAGGTATTTAAGGTTGAATTAAGCAGTGCAACATGATGTGGTTCATTTATAGTAAACATCCAAAAGTTGTACTTAGTGTTGTATTAAATTTGTACTTAGTGGCTGCATTTTTTGTTTGACATTAGTTACTTTTGGGGAACTTTATTCTTCTGCTTAATAGTTTTTAACAAAAGCATGATCCATTTCAATCTCTGTGACATTTTACCTTGTCACTGTTTTCCTCGTAACTTCCCAGAAATTCATATAACAATGTCTCTGTTCCTACATTTGAATACAATAGTTTCCTCTTTCAGTCACCATAAAGACAGACAGACAGACAGACAGCATGATCACATGACACTGCAATCTGTGTGTTGTTATTTTGCTTTAACATGCATCCTCCTGAATCTCTTCCCGTGTAAATTTCTATTTCTTTAG
Seq C2 exon
TCTCTGCAAGATTTCCGGCTGCTCGAGAAAGCAGAGGACGGAAGAGGGAAATGTTCCTATGATCCGTCTCAAAGCTTCACCACTGTGATGGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000067801:ENSDART00000097664:4
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=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(7.4=100)
A:
NA
C2:
PF0140314=Sema=FE(7.1=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:
ACGGACTGTCGAAACTACATTC
R:
AGTGGTGAAGCTTTGAGACGG
Band lengths:
183-2169
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]