DreINT0132726 @ danRer10
Intron Retention
Gene
ENSDARG00000079611 | sema4c
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C [Source:ZFIN;Acc:ZDB-GENE-080303-16]
Coordinates
chr5:14036162-14038684:-
Coord C1 exon
chr5:14038540-14038684
Coord A exon
chr5:14036376-14038539
Coord C2 exon
chr5:14036162-14036375
Length
2164 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGC
5' ss Score
8.02
3' ss Seq
TGTTCTCGCTTTTTCCCCAGTGC
3' ss Score
9.79
Exon sequences
Seq C1 exon
GGGGGACGTGGATGTGTCTGCTGTGTGTCAGTACCAGATCGGGGAGGTGAAAAATGTGTTCGACGGGCCGTATAAAGAATACAGGGAGTCGTCTCAGCGATGGGGCCGTTACACTGGCACTGTGCCCAGTCCACGACCTGGAGCG
Seq A exon
GTGAGCAGAGCGGCCGTTCAGATGGGAGGCCAGCCGAGAGGGCAGCCGTGACTAAGCAGAAGGCTAAAAATAGCTCAAGATTTTTGTATATACAGTAATATTTCACTTCTAAAGCAGAACTTTAGAAGAGTACGATTAATAAGTGTCCTGTTAGATTACAGTGTTCTGAATTAAGGATACAAGTAAGATTATATCTAAGATGTTTTCAGTAAATGTTTTGAAATATATTTTAAAAATATTTATTTTTGTGTCGTTTTGCACTCAAAAAATAACTTTTGCTGCTTGTTTAAAGTACTTATTTAAAATTTGAGTCAAAACAACACAGTTCTTTAAGCTTTTTGGGAAAATTTAATTTGTTTATGTTAAGTCCGCATAAATTAGCAAAAAATGATTGAGTTAACTTTGTGTTGAAGGAATTTTCACATTTTCTACAGTGTGAGAAATTATTTTAGTAATTACTTTGTGATGAAGAATGTATTGGGCAACTCAGAAGTGAATATAAAATGCATATCATTTTTTTATACTGTTAAAACATTTAGGGTTAGATTTACTTTTGAAGAAATTATTACTTATAATCATAAAGTATGCCTTAAAGGGTTAGTTTACCCAAAATAATCAATTCTGCTAATGATTACCGACCTGTTGCCATTCCGAGACTTTCGTTTATCTTCAGAACACATTCAAATATTTTAGATGAATTCTGAATTCTGAGAGCTGACATAGGAGAGAAGACATAGGCAAATAAAGGCATTCGTTTTTTTTTTTTTGGCTTAGTCCCTTTGTTGATCTTCAACTTATCCAGCATATGTTTTACGCAGCGGATGCCCTACCAGCCGCAACCCAGCACTGAGAAACGCCCATACACTCTTGCATTCACACACATACACAATTTAGCTAACCCAATTCACCTATACGCATGTCTTTGGACTGCGGGGGAAACCGGAGCACCCGGAGAAAACCCACGCAGACACGGGGAGAACATGCAAACTCCACGCAGAAATGCCAACTGGCCTAGCCTGGGCTTGAACCAGTGTCCTTCTTGCTGTGAGGCGATTATGCTACCCACTGCGCCAGAAAAAATTTTCTTGAAGCTTCGTACAATGACGAATTTGAACGTATGATTTTGACTTTGAACGTCTCGGGATTATTGCTATCTATTGAGGATGAGAGAGCTCTCAGACTGCATCTAAAATATCTTCATTAGTGTTTCGGAAGATAAACGAACGGTTATGTGATCGGACATCTCAGTTGTTACTAATTTCCAATTTAAATAATTGTCAAAATACATTTCAGTAAACATGTTTAGTTAATTAAAATTGAACAAAATTGTGTAATTATTCCCTTAAAAGTTCCTGTAAAGTGCTTTGAAATGTCTATTTTTATTCAATGTCATTATTGAGGGCCCACTACCCGCACCCTACAGCCCTCCCTGCCTTTTCGCCTTTATCCACAATGCCCCCCACCCCCCTGACTCTTCGCTTTTATCTGTGACATAAGTTGAAGTAATGAGGTATTTAATTAACTCATTGCCTTCAACATTGAGTTTGAAAACTCTTTTCAAATGAGTAGAAATAACTTTCAGTACATTCTGAGTTAACTACACTCATTTCATTTGATAAACTTGACTGTTTTTACAGTGTAATAATACTGATACTAATATCTTAAAAACATTTTCATTTCATGGAACCTTTAAAGTTATTGATGTTAATCATTTATTAAATGAATTCTATTGTACAATAATAATAATAATATTTATTGTTAAAAATTCCTAAAGTTAAAGCTAACTTTTATTTTGACAGGCTGTCACAAAGACACTTATGTTCTTGATATTATAAATTTTCATATATTTGTCTAAAAAATGCCCAAATTTCTACTAATGTAGTTTCTAACGAAGCACATTTTTTTTGTATTTTTAGTTCACATTTATTAGTACTATTTGATAAAATATCTCTTTTCTTCTGTAAATTAAAATTCACTCTTCATCCTAATATCCCAATTTTTTGATGATTTTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATTTTTTTTTTTTTTTTTCAAATACAAGTCAGAATCCCCAATCAAACTTTCTGTTCTCGCTTTTTCCCCAG
Seq C2 exon
TGCATCACCAATTTTGACAGGGAAAATGGCTACAACAGTTCTCTCCAGCTGCCTGACGCCACGCTCAACTTTGCCAAGAAGCACCCGCTGATGGAACTCAGGGCTGAAGCTCGCCCTCTGCTGCTGACTAAAGGCATCAACTTCACCCGATTGGCTGTGGACCGAGTGAGCTCACTGGACCAGAGATCCTACAACATGCTCTTCATAGGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079611:ENSDART00000160511:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.082 A=NA C2=0.014
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(11.2=100)
A:
NA
C2:
PF0140314=Sema=FE(16.5=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]