DreINT0132609 @ danRer10
Intron Retention
Gene
ENSDARG00000011163 | sema3fa
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Fa [Source:ZFIN;Acc:ZDB-GENE-050513-1]
Coordinates
chr6:42911153-42912044:+
Coord C1 exon
chr6:42911153-42911375
Coord A exon
chr6:42911376-42911955
Coord C2 exon
chr6:42911956-42912044
Length
580 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAC
5' ss Score
5.56
3' ss Seq
GACTTTTGATTATTTTACAGACA
3' ss Score
7.32
Exon sequences
Seq C1 exon
TGTCCAGGAGGGACGTTTACCCCCAACATGAAGTCTACTAAAGATTACCCAGATGAGGTGATCAACTTCATGCGCACACATCCCACCATGTTCAATGCAGTTTATCCAGTCCACAAGCGCCCCCTGGTGGTACGAACCAACGTGGATTATGAGTTCACCACCATCACTGTGGACCAAGTGGCTGCAGCTGATGGCAACTATGAAGTTCTGTTCTTAGGAACAG
Seq A exon
GTGAACTTACTACACATCTACATACATGGGTTGTTTTGAGATATATGTAGGCTACTGTGAGATGTATATACAGTCAAGCCTAACATTATTCATGCCCCTGACAAATTCTGACCTAAAGTTTTTCTTCAAATGTAAATAAAATCTGAGAAATATTTGATGCCACTTGTACATCTTCTTGTTATGTTTTAGGAAAAGATAATAATAATTAATTAAATAAATAAATACAATAAGTGCAATAAAATACAATTAAAAACTTGCTGGGTAAATAAAAGATTAAGTGAGAATTTGCCACCAAGGGTATGCATAATTTCAGGCTTGTCTGTTTGTGATGTATATTCATTTGTTTTATAGACATACTCTAGTCAAATGTCTTCATTTTATTTCTTTATTTCTTTAATTCTTTATTTGTTTATTTATTTATTTATTTAGTGCTGTGAATTCCTCAATTTCTAAACCATAACCATAACAGAATGGGTGGCACAACAAAGCAAATAATTTGCCCTTTTTTTTTTTTTTTTCAGAAAATAAAATTGTATACATTTGAAATATTTCTGACTCCTGACTTTTGATTATTTTACAG
Seq C2 exon
ACAGGGGAACAGTTCAGAAAGTGATTGTCCTGCCCAGAGATGATCTACAGACTGAAGAGCTGGTTTTGGAGGAGGTGGAGGTCTTCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011163:ENSDART00000046498:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.120 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(15.7=100)
A:
NA
C2:
PF0140314=Sema=FE(6.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCAGGAGGGACGTTTACCC
R:
TCTGAAGACCTCCACCTCCTC
Band lengths:
310-890
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]