DreINT0132547 @ danRer10
Intron Retention
Gene
ENSDARG00000007560 | sema3bl
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3bl [Source:ZFIN;Acc:ZDB-GENE-030131-2956]
Coordinates
chr8:26550570-26552159:+
Coord C1 exon
chr8:26550570-26550795
Coord A exon
chr8:26550796-26552025
Coord C2 exon
chr8:26552026-26552159
Length
1230 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGA
5' ss Score
9.63
3' ss Seq
TAAAGTGTTTCTCTGTTCAGTGG
3' ss Score
6.26
Exon sequences
Seq C1 exon
CAAACTCTGTTTGTTGGATCACAGACAGCTGTTGTCCAGGTGCCGCTGCACCGCTGCAGTATGTACGGTAAAGCTTGTGCCGAGTGCTGTTTGGCTCGAGATCCGTATTGCGCCTGGGACGGACAAACCTGCACACGATACCTGCCAAACACCAAACGGCGCTACCGCAGACAGGACATCAAACATGCAAACCCAGCAGTGCAGTGCATGGACCAAAACCTCAGCG
Seq A exon
GTAAGAAATGACAGCCTCCTTAACTGAGTGCAGCCATGCAGCATGAATGTTAATGTAGCAGCAGGTTCCTCTGACAACTTCAATTGGGTTTATATGTTAAAGAGCTCACTGATGTGAGAGTGCAATTTCTTCAGAGATTTGTTCAATCAGTGGAGTTAGAAACTTCAATACACTTTTGAGCTTGTCTAATAGAAAGATTAATAGGGTTTGAAGGGCAATCTCCTAACTCTGCTGGGACAAACTGTCTGTGAAAGACAGGAACTGATAGAGTGAGAGGTGAACAGGCAGATCACTCTCCATCGCTCATCACAGAGGAGAGAGAGAATGAGAGGAAAGAACAAAAGAGGTGTGAGTGAAGAGCACATGAGTGTTTGCATGCCAAAGGTGAGGATGTTGGTGATGAAAAGGGATTACATATGTATGTGTGAACACATACAAACGCATACGCAGTGGAAAATCCCTGAATGACCCTACACTGAACCACGTTGTGTGACTGCTGAAGTGTCACTTTAAAGCTTTTTTTAAAATTACATTAAATGCATATAGTGCAGTGTGTATTGAAATGTGATTGTGAATGTAAAGGTTCTAAGTTTTAAAGATCAAAGTGTATAATAAATACAGACTGTTTTTAACACACACACACACACGCAAATTAAACTCTGAACCACTGAATCAAGTCATCAGAAATTCCAATTGCAAACATGGAAACCCCTAAAATTCTCACATATGCAAGTCTTCACTTAAACATGTTGTACACACACACACACACACACCTATTATTCAGCTAAAGTAGGCTATGACGAACCACAAAACTTTTTTGAGTGGAAACATTCTACTTTTGTTGTGCTTGTGATGGAGATTCTGGATGATCCACTAGTTTTTCCAGTGTTTCACCATTGGAAAAGCTTAAATGTATGCAGGTAAATCCTCTCTCAGTTATTTCTACTGTATATACAGTATTTATGAGGGCTGAGCTAAGGAAGCCTCCAGACCAGATAAAGTAATGGCCATTTTGTTTCAAATACATATTGTCAGCAGTAGACCAATCTCAAGAGATTATCATATGACCAATCAAAGCAAACCAGGATCTCAGAAAGGATGTTTTACATCTCAAACAAATCACTTCAGATTTTTACACCCCCGATGTTAACCTATTGTAGAAAAAGGTAAAATAACACAACAAGGCAGTTTAAAGAGTCTGTATTAAGAGTAAAGTGTTTCTCTGTTCAG
Seq C2 exon
TGGAGGATGTGGATCTGAGTGAAGAACGGGTTGTTTACGGCACTGAGAACAACAGCACCTTCCTGGAGTGCGTCCCTCGGTCGCCGCAGGCCACTGTCACATGGCACATTCAGAGAGATGACTACTTAGGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000007560:ENSDART00000046863:13
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=PD(4.9=30.3),PF0143720=PSI=WD(100=69.7),PF0248011=Herpes_gE=PU(11.4=25.0)
A:
NA
C2:
PF0248011=Herpes_gE=FE(26.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTTTGTTGGATCACAGACAGCT
R:
AGTCATCTCTCTGAATGTGCCA
Band lengths:
342-1572
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]