DreINT0132707 @ 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
chr18:25796914-25798020:-
Coord C1 exon
chr18:25797947-25798020
Coord A exon
chr18:25797681-25797946
Coord C2 exon
chr18:25796914-25797680
Length
266 bp
Sequences
Splice sites
5' ss Seq
CACGTAAGT
5' ss Score
10.16
3' ss Seq
TAAAACCATCTAACCCACAGGTG
3' ss Score
7.99
Exon sequences
Seq C1 exon
TCAATGGCAACAAGATGTAGAAGATGCCAACACTGCCATTTGCAAAATGCCCAGTCCCCGTTCAGGAAGACCAC
Seq A exon
GTAAGTAACAGCCATGCTTTGAACACCTAAACTCAGCATGAATCAATATTTAAAGACTTTATCTTCAACCAACCACAAAGTAGCATCGAGTGCATGAGGCTTAGGCAAGCTCTGCCAGTTACAAAAGCACTATGGCATTTACATAACGCCTCCGGCAACAAGCTCTGTTAGTCTGCAAGTAATTGAAGCAGTTGCACGGTGGTTTGCAAATATGCAAGTTTAAATGTTTGATTTATTAGTAACTAATAAAACCATCTAACCCACAG
Seq C2 exon
GTGTTCCAGCATGCCATGTGGTAGAAATCCCAGCAAACACATTTACAGTTCTACCCTGCAAACTGCGATCCAATTTAGCTGCAAGACGATGGGAGTACAGTGATACCGCAGAGCGTTTTGTCTACCCAAGTCCTGATGGCGGCCTGGTGGTTGTAGCCCAAGTGGACAGGCAGGAAAACTACGCGTGTTGGTCCGAAGAAGGCAACTATCGGCAACTTCTGGCCAGTTACTGTGTTAAAGCGGAGCACGAAAGCACCACCCTGACTGGACGTTCCCGAACACAGCAGGTGACCCAAGGAGAGACTATTCTACCTGGCGAAACGTGGTCACCACAAAAAACCAAAACATACTGGAATGAGCTGATTGTTGTGTGTGCCTTACTCGTGTTCTCCCTAGTAGTACTGTCGCTTTTTGTGGCGTACAGGAATCGAGATAGGATGAAGTCCATGTTAAAGGAAGGCGAGTGTCCTAACATGCAACAGAAGAAGCCGCGAATTCCAGGGAAGCACACTGAAAGCCTTCCGTTAAATGGCAACAACATCCCGCCCTCAGTGTCCGACCACAAGGGCTACCAGACTCTTAATGACAACTACATCTGCAGCACTCCAACCCACGAATGTTCCTCTCCCGAAAACAGCAAGAGCTTCTCAGAGTCTGAAAAGAGACTGTTGACTGTTAACTTAAAGGAGAGCCATGTGGAGATCTCACCCACTTGCCCGCGGCCTCGGGTACGACTAGGCTCGGAGATTAAAGACTCCATTGTTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074414:ENSDART00000143899:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.192 A=NA C2=0.329
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(28.0=53.8)
A:
NA
C2:
NO
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:
GCCATTTGCAAAATGCCCAGT
R:
TGCTTTCGTGCTCCGCTTTAA
Band lengths:
295-561
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]