DreINT0132528 @ danRer10
Intron Retention
Gene
ENSDARG00000011672 | sema3b
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [Source:ZFIN;Acc:ZDB-GENE-081105-78]
Coordinates
chr8:26572190-26574242:-
Coord C1 exon
chr8:26574098-26574242
Coord A exon
chr8:26572410-26574097
Coord C2 exon
chr8:26572190-26572409
Length
1688 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGA
5' ss Score
6.56
3' ss Seq
TGTCTCTCCCTCTTCCTCAGTGT
3' ss Score
10.05
Exon sequences
Seq C1 exon
TAGTGTATTTCAAGGTTCTGCAGTGTGTCTCTATACTATGAACGACATTCGCCGAGCATTTTTAGGACCTTTTGCCCATAAAGAGGGACCCAATTACCAGTGGATTCCATTCCAGGGTAAAGTGCCTTACCCACGGCCAGGCATG
Seq A exon
GTATGATAAGATGCTCTAGATCTCACATCATACACACCTGTAAAAAGTTTTTAAAATCTTTAATACACACTACCTGACAAAAGTCTTGTTGTCGATCCCAGTGGTAAGAGTAACAAAGAATAACTTGACTTCTAGTGGATCATTTGGAAAAGTGACAGAAGATATATTTTAATAATGTCTAATAAATCTGTTAAACTGCATCAATCATCACAAATACAGCAGAAGACCTATTGGAACCAGCATGGACTCAAGATTCTCACAGAAATCAGTCAAGTTTTGTGAAGGAAAAATCATGGTTTGGGGTTACATTCAGTATGTGGGCGTGTGAGAGGGTGGATGGCAACATCAACAGCCTGAGGTATCAAGACATTTGTGCTGCTCATTAAATTACAAACCACAAGAGAGGGCAAATTCTTTAGCAGGACAGAGCTCCTTCTTATACTTCAGCCTCCACATCAAAGTTCCTGAAAGCAAAGAAGGTCAAGGTCACAAAATGAATTCTGCTTCCACTGCACCATGAATTTATATTCAATACTGTATATTTATTTAATAATATAAGTGGCAAAACATTTGTCTAAGCAAAGTTAGACCTTATTATCCTAATTAACCAAAAACCAGGATGTGATTATAATTTATTTTGTTAAAATAAGCGTAATCTAGAAGCCTTTGCCTTTTAAATAACCCACTTCTGATACCAACTAGAAGTCAAGTTATTATTTGTTGTTCCTACAAACTTAAACTTTTACAACAAGAATTTTACCAGGTTGTGTACAGTTAAAAAAAAAATACATATACATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATACAGTTGAAGTCAGAATTATTAGCCCCCCTGTTTATTTTTTTCCCCGTTTTCTGTTTAACAGAGGGCAGATTTTTTTTTTCAGCACATTTCTAAACAGTTTTAATACTCATTTCTAATAACTGATTTATTTTATCTTTGCCATGATGACAGTAAATAATATTTGACTAAATATTTTTCAAGACACTTCTATACAGTTAAAAGTGACATTTAAAGACTTAACTAAGTTAATTTGGTTAACTGGGCAGGTAAGGGTAATTAGGCAAGTTATTGTATAATGATGGTTTGTTCTGTAGACCATCAAATAAAAATTTACCTTAAAGGGGCTAATAATTTTGTCCTTAAAATGGTGTTTAAAAAATTAATAACTGCTTTTATTTTAGCCGAAATAAAACAAATAAGACTTTCTCCAGAAGAAAAAAATATGATCAGACGTACTGTGAAAATTTCCTTGCTCTTTTAAACATCATTTAGCAAATATTTTAAAAAGAGAAAAAAATCAAAGGGGGGCTAATAATTCTGACTTCAACTGTATATATTTTTAAAATAATTATTAATAATAAGTGTGTTGTAATATTTATAATTATTGGTTCATTATGGGAAAAACCCTGTGTAAGTGGTAGTCTAACATATTAAAGCATCAAAGTCATCAGTGCGTTTTCACACAGTTTGAATGTTAAAGTAAAAGTGCATTTAGATTCAATATTAACTGGTTAAATGTTTGAACTTGCTGACCTGTGTCACATGTTGATATCATGAGCGGATTATGTTTCCGGAATCTACAGATACAGTATCTCTCTCTCTCTGTCTCTCCCTCTTCCTCAG
Seq C2 exon
TGTCCCAGTAAGACCTTCGGCAGTTTCGAGTCCACCAAAGGTTTTCCTGATAACGTAATCCAGTTTGCACGGCACCATCCGCTAATGTTTAATCCAGTGACTCCTCTGGGTGGCCGACCGCTGTTCCTGCGCACCGGTATCCCATACACCTTCACTCAGATTACTGTAGACAGAGTCAATGCAGCCGACGGACACTATGATGTCATGTTCATCGGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011672:ENSDART00000027301:10
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(10.9=100)
A:
NA
C2:
PF0140314=Sema=FE(16.5=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:
TTTCAAGGTTCTGCAGTGTGTCT
R:
GACATCATAGTGTCCGTCGGC
Band lengths:
342-2030
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]