DreINT0132766 @ danRer10
Intron Retention
Gene
ENSDARG00000088143 | sema4gb
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Gb [Source:ZFIN;Acc:ZDB-GENE-111117-1]
Coordinates
chr12:33734033-33736253:-
Coord C1 exon
chr12:33736031-33736253
Coord A exon
chr12:33734149-33736030
Coord C2 exon
chr12:33734033-33734148
Length
1882 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCCG
5' ss Score
6.46
3' ss Seq
GCTTGTGTGCTTCTCTCCAGATG
3' ss Score
10.2
Exon sequences
Seq C1 exon
TGTATAACTGATGAGCATCGTGGCAAGCTCATAAATTCCTCTCGGGATCTGCCTGACAACACTCTGAATTTTGTTCGGAGACACCCTTTAATGTCCACCCAGATCCAGCCGGTGGAAGGACGTCCACTTTTGCTCCAGAAAGCTGCAGATTACACTAAAATCATTGTTCAACAGGTTGAGGGTTTGGACGGACGGACCTATGACATGCTCTTCATTGGAACAG
Seq A exon
GTGCCGAAGGATTGGCTTTTTTATTAGAAATCCAACCATCCTTTGGTTTTCTTAATTTTTTTACTGTAATTTACTCTTGGGGGATTAGTATGACTGTTTAATGATTTTGGGATGGGTGCATTGATTCTGCAGTATCCTTATATTGATACACACAAGTACTTTAAAATGCAATTTCTTGTCAGGTATAATGCAGTTTTCAGTCTCACAATATCTTTTAGAAATTGTTTTAATATGCTAACTTGGTACTCAATAATCTTTTATTATTATCAGTGTTGAATGCAGTTGCACTGGCCACATTTTTTATGGAATATGGATATTATATTTATTTATTTAAAGTTAAAAAAAGATTACATTCATGCAATCTTAAAAATTTACCAAAATATACAAAATGGCAAATTAGCATGAAAGTACATTATTATAAAAGTGTAGATGGGAGATTGGCACCAATAGCCTATTTGTTAAGTGTACCTACATATACTCAACAACCACTTTATTGGGTACACCTGTCCAAATGCTCGTTAACACAAATTTCCAATCACAGGGCATAAACTCAATGCATTTAGGTGATTTAAGTGACTTTAAACATGGCATGGTTGTTGGTGCCAGACGGGCTTTTCTGAGTATTTTAGAATCTGTGGATCTACTGGGATTTTCACACAGAACTATCGCTAGGGTTTACAGAGAATTGTCCTGAATTGTTGATGACAAAGGTCAGAGGAGAATGGCTAGACTGGTTCGAGCTGATAGAAACGCAACAGTAACTCAAATAACCACTCGTTACAACCAAATTATGCAGAAGAGCATCTTTGAACACACAACATGTCCAACCTTGAGGCGGATGGGCTACAGTGGCAGAAGACCACAACGGGTGACACCAAAATTGGACATTAGAAGATTGGAAAAACATTGCCTGGTCTGATGAGTCTTGATTTCTGCTGCGACATTCGGATGGTAGGGTCAGAATTTGAAGTCGACAACAAGAAAGCATGGATCCATCCTGCCTTGTATCAACGATTCAGGCTGCTGGTGGTGGTGTAATGGTGTGGGGTATATTTTCTTAGTACACTTTGGGCTCATTAGTACCAATTGAGCTTCATGTCAACACAACAGCCTACCTGAGTATTGTTGCTGATCTCTTTATGACCACAGTGTGTCCATCTTCTGATGGCTACTTCCCGCAGGATAACACCGCTTGTCCTAAAGCGTGAATCATCTCAGACCTGTTTCTTGAACACGACACTTGTACTTGAACAGATCACTGTACTCAAATGGCCTCCACAGTCACCAGGTGTCAATCCAATAGAATACCTTGGGGTGTGGTGGAACGGGAGATTCTCATCATGGATGTGCAGGTGAAATAAATCTGCAGCAACTGCGTGATGCTATCATGTCAACATGGACCAAAATCTCTGAGGAATATTTCTTGTATCTTGTTGAATCTATGCCACGAAGGATTAAGGCAGTTCTAAAAGCAAAAGGAGGTCCAACTAAGTACTAGTAAGGTGTACCTAATAAAGTGGCCAGTGAGTGTGTAGTCCTAGCTCAAGGTCCTTTGCCAATCCTTCCTTTGGGCCTTAAATAATGATAATAAAGTGACCAGTGATGGAACAAATGATAGAGCAGTACCAAAAAACAGTTTTGCATCTGAAAGGTAAACTCCTAGAAATGCATATGTAAAAAGGTCAGTTGCAAATATATGTGTCTGTGCATTTTCACCGTTTTTCTTTCTTTAATAAATCCTGACAGTACTTTGTTTTTAGTACCAAAGAAAAAAGATTTTCACTGCCTCGAGCTGTTAGGAAATTTGGCCCTTAATTTGTTGTGAACAGCAGTGTATATTTGCTTTCTTTTCTTGACTCGTGGCTTGTGTGCTTCTCTCCAG
Seq C2 exon
ATGAGGGCTGGTTACAAAGAGCTGTGAAGATTATAGACCGTGTGCACATCATTGAGGAGCTTCAGCTGTTCCAAGAGAAACAGCCCATCATTAACATGGTGATATCACAAAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000088143:ENSDART00000131181:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.053 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(18.9=100)
A:
NA
C2:
PF0140314=Sema=FE(12.5=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:
AACTGATGAGCATCGTGGCAA
R:
GTGATATCACCATGTTAATGATGGGC
Band lengths:
326-2208
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]