DreINT0132621 @ 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
chr6:42893227-42895988:+
Coord C1 exon
chr6:42893227-42893346
Coord A exon
chr6:42893347-42895848
Coord C2 exon
chr6:42895849-42895988
Length
2502 bp
Sequences
Splice sites
5' ss Seq
ACGGTATGC
5' ss Score
8.56
3' ss Seq
TTTTTGTCTGTCTCTTTCAGATC
3' ss Score
13.99
Exon sequences
Seq C1 exon
ATGGCCAGCTTTATGCCGGCGTCTACATCGATTTTATGGGAACAGACTCTGCCATCTTTCGCACGTTGGGCAAACACACGGCAATGAGGACCGACCAGTATAACTCCCGCTGGCTCCACG
Seq A exon
GTATGCCCAAAATGTTTGAACCGTGGCACACTACCAAGACAAATGTCTTTGTTTAGTTGTAAAACTGCCAGAAATGAATATTCGGCACAGACCCCTTGTCTTACTAACATCATATTTCATTCACTTCTGCAAAAACCATTTCCCTCAAGCAACTGCTTGCTTAGCTGTGCTTAATCCCTGACAGTATTATTACTGTAAAAATTCCAATGTTTAGTGTTTGTAGTTAAGTTAATTTAATTTAATTTAATTAAAAAAAACAAGTAATTGTTTAATATTTATGCCCTCTATACACATTAGCAATATTACATGAGTAGCAGTGTGATATGGCTGTATATTGGCACTGGTGGGAGGCGTGCGTTAACACAAGGCTGCAGGCCAAGTGCCTTAGTGTCCCACCAGTGATGATTAGGGATGCGTACCAAAACTCGGTACTTTATCGGTATCGGTGCTACAATATAAAAGACAGAAGTATCGATAAGCTCTGACGTTAACGGTTCTGCTATCAGTACTGGAGAATTATTGCTGAATAAACATTACTAACAGTAGCACAATTTAACTGACCAACCTTTTTTAATTTGCAAAATTTTATATTCGTCTGCAAAGTTAGCAATCTCACATGCGAAATGCTTGTGTTCCCGGTGAGCACGTCAAGTATAAAAGGCTTCACAGTTCTTGCTGTGCACAGGCACTCGGCGGAGACTCGCGCTAAGCGCACACACATGGCTCGCGGCACAGACTCACACACACATATATCTCGTAAGCTTGCGGAGTGAACCAATTGAGTTGTATTTCCCGAATGGAAAGTGGCAATGTCCGTTGCAACAAGTCTATTTCTTGTATAAGTGGAAACGCAAACAATCTAGCTAAGTGAAAATATCTTCAAAAGTGCATTAACTGCAATGAAAAGTAATGAAAGGTTTTTGACTGCCTAGCTACTAACGGTAATGTTAATCATCCATATCGTCATGCAAGCAGTCAATCACCTAAATTAGTGTAAAATTAATAGTTAAATAAACACACATTCTGTTACAATGAAATCAGTATTTTTTTGCAGAAGCCAAAATAAATATTAAAAATTAAAAATACTTTTACATCAGCTGTATTTACAAATATAGCCCATGAAAAGCCTAATAATAAACAATGCTTATAAAAAAAATATTTAAAAACTGCTTATTTTTACATTGCAAGATGCTCCAAAACTGTAATAAAAACACAGTTAACTTCCAAAACTCTGTTAACTCATTTATGTGAATGCGTTAATAAAAAATACTAAACATTATCTCATTTAACTGCATTTTGCAACTCAAAAAGAGTATTTTCAACTACAGGGAGCACAGTAAACCAAGAAAGATCCCAACTTCTGCCAGAAAAGGCAATTGTTAAAACCTGAGAGTCATTTTCCTTTAAACCATTATACATTCTTTTACAAAAAAAAAAAAAAGATTTATTTGATGTAGAATTATTGCTTTCATTTTATTTTATATTAAAAACATAACAATAAAATAATGTGTTGTTAACTCTGTTCAACTAGTTTGTTTTTTTTTTCATAAAAAAACAAACACTACAAAAAGTATTGTTAAAGTACCAAACCGATAAGTGGTATCAATAAAAATACCGTTAAAACCTTAACAATACCCAACCCTAGTGACGATATTCAACCATATCGCACTGCTACAAGTGTGATATTGCATTTATACAACAGTTTGTCACATAATCATATAAATAAAAAATAAAATCAAACAAAAAGAGTCTAAAAACCCTTTTGTATGAGGAACTGCATAATAAATAATAAAATAAATAAATAAACTGCATAGTTGTAATCAAACAACTACATCCTCGCCTAAAAAAAGCTTCAAAAGTACATTAAGTTGTTCAACAGCTGCAATAATTGTCAAACTGTAGTTAGTTTATCTGCTGCTACTCTGTGTGGGTGGAATAATACAGAAGTTAATACAGAACTTTTGATATTGTGGAATATTGCATGGCTATCAGCCAGTCAGATTCGAGAACCAGACACAAATGTTGTATACATCTTCATTCGCAACACCCCAGATCTGTTAATAACATTACATTTTAAGTTTTGTCAAATTCACCACCACAGCTTGCTAAAGACAGTGTAATATGCAATAAATTTCATTTTTCTTTTGCAAACACTTGATTTGGTGAGACATGTTATTACACTTAAAACATTTTAAGACATGATTTGCTTTTGTATTGCGTGTGACTCCTTGACTCTTGATTCTGTGCTTTAGTCTTGCTTTTTGCATGAGTGTCCACTAGATAACATCACAGACTTCACACATATGCTTTGAGACTCCCCGCAGTGTAGTGACCATCCAGTGTAGTAAATAAGAATATAGGCTAACGCTTCACATTAGTTTCAGTGTTATTTAATATCATCCATTTGCTTTGCTTTTTTCTCTTAGCCTTTTTTGCTCCAACTGTGATTAATCTCCTTTCCTGCTTTTTTTTCCTTCCCTCTTTTTTGTCTGTCTCTTTCAG
Seq C2 exon
ATCCAACATTTGTCCATGCTCAGCTCATCCCTGATAGTGCAGAAAAGAATGACGACAAGCTGTATTTCTTCTTCCGTGAGAAGGCCTCTGAGATGGGTCAGACTCCCATGGCTCAATCTAGGATTGGCAGAATTTGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011163:ENSDART00000046498:8
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=0.011
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(8.5=100)
A:
NA
C2:
PF0140314=Sema=FE(9.7=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]