DreINT0132712 @ danRer10
Intron Retention
Gene
ENSDARG00000074414 | sema4ba
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Ba [Source:ZFIN;Acc:ZDB-GENE-070705-31]
Coordinates
chr18:25824689-25825919:-
Coord C1 exon
chr18:25825808-25825919
Coord A exon
chr18:25824806-25825807
Coord C2 exon
chr18:25824689-25824805
Length
1002 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGT
5' ss Score
8.14
3' ss Seq
TCTGTTTTTTTTTCCTTCAGATG
3' ss Score
12.38
Exon sequences
Seq C1 exon
AACACATCAAACTTTTCCCTGGTGCGCAATGAAGTGGGAGAAATAATGACTGAAGATGGTCGAAGCCGATGCCCCTATAACCCTGAATACAAGTCCACGGCCATCATGGCTG
Seq A exon
GTATGTGCTAGAAAAACATTGGTGTTTACAACGGATGCATGCATGAATGTATTAACCTAAGATGTATTCAGATGCATTCTTTTATTTATTTATTTATTTTTATAAATAAGATATTGCTGTAATTCAGTAACTATTGATATCCATAAAATAAAAATACTATGGTAGTCAGTGGTTACTGTTTTCCAACTTTCTTCAAAATATATTTTTGTGTGTGTGTGTGTGTGTGTGTGAGTTCAACAGAAGTATAAATCTCAGATAGGTTTGGAATAAGTGGAGTTATTAAATGATCACAGAATTGGAATTCAGAATTTTATTCTGAACTGTCTCTTTAAACTTGTTTCTGGAGGGCCAGTGTAAACGTGTTCTTGTTTTTACTTGCGTTCACATCTACCCAAGTAGAGTTCAAATGCCTAGATGTGTTATTGCTTTGCCTCTTTTATCAAGGATACACCAAAAGGTGACTTGTGTGAACTTGCAATGTACAGCAGGTATCCCAGAATGTATCTTGAACCACCAATGGCAGAAAGAAATGTGAAAAACAGTACCTTTATTGACACAAAATGTAAATTTTAGATCTTTTAGTGTGAGAATGTGGTTTAAAACTCAAAGCTGCTTTTTATTTATAAAGATTTTGAAAAGATTATTTGCAAATGTAAAGATATGACATCTAGATAGAAAGTGGTCATTCAGTGCTTATGTACTCCACTAAGAACAGCTTTACCTTGGCCAATAGCCAATGTTTGGTTTAATGAATCTATTATTTGTTCCCAGGTTTATTGTTGTGACAAAAAAAAAAAAAAAACAGTTAAGGTTTGCTATTAAGCAGGTCAAGTAAGGAGTTATAGTAACTTATAGCCAACAATACAAAGTGTTACTATTGAATAGTTTTAGTTAATAGCACTAGAATATATTTTTTTAAACCTATCTGTGCTAAAACGTTATGTAAAATGTAAAGTATATTTGCTAATTTGCTTTATTAATGTCTGTTTTTTTTTCCTTCAG
Seq C2 exon
ATGGAGAACTGTATGCTGGCACTGTCAGTAATTTCCAAGGAAACGATCCCATCATTTACAAAAGTCTTGGCCAGGGCACAGCACTAAAGACTGAAAACTCACTGAACTGGCTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074414:ENSDART00000143899:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.026 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(8.4=100)
A:
NA
C2:
PF0140314=Sema=FE(8.8=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:
TCAAACTTTTCCCTGGTGCGC
R:
CTTGAAGCCAGTTCAGTGAGT
Band lengths:
223-1225
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]