DreINT0132750 @ danRer10
Intron Retention
Gene
ENSDARG00000076595 | sema4ga
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Ga [Source:ZFIN;Acc:ZDB-GENE-060503-381]
Coordinates
chr13:9394170-9395895:+
Coord C1 exon
chr13:9394170-9394268
Coord A exon
chr13:9394269-9395801
Coord C2 exon
chr13:9395802-9395895
Length
1533 bp
Sequences
Splice sites
5' ss Seq
ATTGTAAGT
5' ss Score
8.54
3' ss Seq
TATTTTTTGCATTTTTCCAGGAT
3' ss Score
9.56
Exon sequences
Seq C1 exon
ACGGAGTGTTTCAACCACATTCGCTTCCTGCAGAGGTTCAACAGCACACACTTGTACACGTGCGGCACACATGCTTTCAGCCCTCTGTGTGCATACATT
Seq A exon
GTAAGTCACTACCATTTTTGCACATTGTAGGTTGAATTTACACTGACACCATTTTCAATCAAAAATGCAAAGAAGTTGTTATATTATTTTATGGATTTTGGCTCTTCATTTACATGACAACAGCAAAAATCCTTGCTTATTTTTAGTACAATGTTTTCATATTCAGATGGGCAGTTTACAAGACAACGTTTTAAGCTTAAAACATTACGTTTTTTTATATGTTTTGCCTGTTCATTCATACGACAATGCCACTTTTTTGACTCAAAACCATACATTTCAAAGCAGGTTCAATGCCACAATAGATGCGACCGTGTAAACATCTGAAAACAAAGGTATTTGAAAATGAAGACAAAGGGGGAGTATAGATTAAATCCCGGTCAGATCACACAAATTTGTCATGATTTTCTTTGACATAGGGTGTTGTGGGGATTTATAAACAACAAATAGGTGTCGTGACTCTAGGGATGCAACGATTAATCTGTTTCACTATTAACCACGGTCCGTGACGTCATTGACATTCGCTTTAAGATTTAAAGGGCTAGCGTTGCACCAGACCCCCTTAAGTGGTGTCGTTGGAAAGTGTAGAATCTATATTTTATGCACATATGCATCACTTCGGTTTTTATTCTACTGTATAAAAGTTATTTACACTTTAATACACAGTATTTTAGAGACCCGAGCTAGGTTCATTTTCATATTTTTTCATATGACACATGTACAAGTTATAGCTCAAATGAAAGCTCTTTCCGGTGCTCATACAGTTCTAGCATTTTTTTACTGAATTATATTCATATGCCAAACAGTTGTTGAATGAATTGTGGTGTTTCCATGGCGCAGAAATGTAAACAATACATTCATGATCAATAAGCAGCCCCAGATAGCACAGACAGCTGTCATCTCTTACCTTATGCTGTGCGCTTCAGGGCCATTCTCCTCTGTTTTAGAGGTGATGTGCATAAGCAATCCTTTTATATGTCTGATTTGGTCTAAACACAGTGAATTATGTTTGATCAAACAAAAGAATAGTGAAATATGTAAACAAGGATCGGTCTCTGTGGCTTGTATAGCACCTCTCATCAGTTGGAATGCAATAACTTTTGCATAGATTATGGTAGAGACATTTTTCTTTTTTCCTATGATTACAGACATGTGCAGGAAACACCAAAATTAATTACAGCACGCTAGACCACACAGAACCTAAAAGGTGCACTTTCAAATTTGAGTTTATAAAAAAAAAATACAAAAAGCGCCTTTTTTAAGTGTTTATTATAACACAGACAACATATACAGTTATTTTAAACACTTTTAATAGTGTTTTATGAAAATTTAAAGAGTTTTCTTTAAAATGATACCACATTTTTGCATTTACACCTCTGCATGTGGATTTGGGAAGCTTTTAAATTTGGGTAGGCAAAATCTAGGCGGAAATTCCAAAATAACAGCAGAGTTTAAGTGGTTGAACGCGCTTTCGATCATCACAGTTACTTAATTGCAAAGGCTTCTCAACATCATGTATTTTTTGCATTTTTCCAG
Seq C2 exon
GATGGAAGGGAGTTTAAAATCTCATCAGTCTTTGAAGAGGGTCGAGAGAAATGTCCATATGACCCCTCAAAAGGCTACACTGGCCTGCTAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000076595:ENSDART00000111365:4
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(7.1=100)
A:
NA
C2:
PF0140314=Sema=FE(6.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGTGTTTCAACCACATTCGC
R:
CAATTAGCAGGCCAGTGTAGC
Band lengths:
191-1724
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]