DreINT0132622 @ 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
chr6:42895849-42898516:+
Coord C1 exon
chr6:42895849-42895988
Coord A exon
chr6:42895989-42898401
Coord C2 exon
chr6:42898402-42898516
Length
2413 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
TGAGCTCATTTCCTCTGCAGAAT
3' ss Score
8.92
Exon sequences
Seq C1 exon
ATCCAACATTTGTCCATGCTCAGCTCATCCCTGATAGTGCAGAAAAGAATGACGACAAGCTGTATTTCTTCTTCCGTGAGAAGGCCTCTGAGATGGGTCAGACTCCCATGGCTCAATCTAGGATTGGCAGAATTTGCCTG
Seq A exon
GTGAGATTTTTTTAAATCTTCGTCTTATATTCTAGTACAAACGAACTACACATAGTAGATTGCTTCTTTTAATTGATTTCATGTTGCTCCAAATATGCATGATTTTTTTCATGATAAGGAAAATTGCAAAAGAATGAGGACTTGCAGTTTTCTTTCAGGCTTTAAAATGAACTATAAACATCATAAAAGTGTCCAGCACAAAGTGTTATATTGCCACAATATGTGATAACTTGAAATAATAACTCTATTTTTGTATCAGTAATCATTCTCTCCACTGTTTATAGAGTAAGTTGCTTTACTGGAAGCAGCTTTTTGGTATTGAACATGGAAAAACATTGCCAGTGTTACTTTCAATTAGATTTGACATCAAAGAAGGCAGCGACACAGAGCAATGTGTACATAATCACAAAGGACCAATAGTTTACATGTGTTTATCCGCTGGAGGGAATTTTTCTTTAAAGTTTGCTTTGGGAAACTGCTTCAAACTCATGAACCGAACTCCAAATGACCTTTATTTTGGTCAGATTATGTTTAAATTTAGTTTGTTCTGTGATTCTCTACCAGCGGACACCTTAATGTCAAAATGACAACAAAATAACATGGCAAAATATAAAAATTGATTTAATGTTTATTGACTACCTTAATGTCAAACGACTGTCCTGTAATCGATTTTTCGGCTTGTTTTTTATGCCAATGTTAAATTTCAATTTGATGTCATTTGATGTATTTTTGAGACCAAGGTGGCCACTGGGGCTGTTTGGTATATCTAATATATGTAAGTTTTAATATGTAGTTTATGTATAGTTTTTAAAAGCTGCATCTAAATGATTAATGATGCACTGAACTTGACAACTGTTTAAAGTATGAATCAATTGTACTGTTTTAGTGAGCTGAATTATTGAAAAGAATGGTTCATTCACAAAACTAGGCAGTGCTTCTACTTGATTCAGGTTCGACTTCATTCTACTTACACACAAAAGAGATTTCCTTGCATTTACAGTAAATCTGTTCCTTACACAAAGTTATCATATATATCACGTATGTCTTTAAGGCCCCTTTTACACTAATACATTTTAGTTTTAATTTAAAATGCAGTTTTGCTACGGTTACGCCTTCTGTCAACACTACCCCAGAACTTTCGAGCCCCGAAAATGAAGCATTTTGAAAACGCTGGTTTTAAAACGCTGCTGCTCCATGTCAGTTTGGATGGGGGATTCCTCCTTTCATTTTCATTGAAAATACAAAACGTACCGTCTCTTTTGCTGAATATCAGTTTTAATCATCAATAATGGCCATGATAAAAGTATAACGTACATTAAGTTTATACATTATCTGGAATAAAGACAAGCAATCAGTCAAATGTGCAAAATCGGTGTACGTGGTTAAATTAATATATTAACTTATCTTTAGGCTCAATCAAAACACGTTACTTGAGAAAAGGTAATAGATTCAAAAGACCGAAAAATCGTTAGATATAGACGAGATGAATTAAATAGCGCATATAACAAATATAGTGGGATGAGATCCAGCGGCACATCCTTGGTGAACTGTCCAACGTGCTCTGCTCTCACCTGGGGAGGTGTGCTCAAAGCTCTGCCTGGAGCTCAGATGTGCGCATACGCTACAGCGCATGACAGATTGTGTTTGTGTGTGGTCATGTGATGTGTATTTATTCAGCTGTATGCTGAAACGCGAGGTAAAACACCAGTGTGGACATGGATCGTTTTCGTTCTACAATGCCGTTTTAAAACTAAAACGTGTAAGTGTAGACAGGGCCTAGAAGATCTGAATATAGTCTTGCGGACTTTTAATGCCACTTTTCCATCGTTTTTTGAGCTCAAACAAACTTAGTTTATATTTCACAGAAGAAAGTCATTTAGTTTGTAATGACTTCAGGGTGGGTAAATGGTATTCGTATTCATTGTTCTCATTAGCTCATTACAGATTTGTTTTTTAAACATTAGGTGCTCCTATGCTGAAAATGAAGCTATAATGTCCACAACAGGACTGAATTGCTGATTGACACATCCTCCATGTCCTCGGGTTCCGTCATTGTCCAATGCCTCCTACATGAGCAACCGCTTGTTTCTTGGTTATTTTTTGCTGTTTTAATGTGAATCAAAGAAGCATGTTTGTAATGTGTGGGTAGCTGCTGGCGGCTGGTCACTGGGCATCGCTGCGTCTCATTATTGAATTTGGCTGTCGTCCACAGCAGATGGGGCTGAGCAGTGCTCAAAGCCAATGTTTACAACCCAGTCACAGCCAGTTAATGCAAACCCACAGAAATAGCCTTGATACTGATGTAAAGCAATGTCTTCATTTCACAGATACAGGCTGTCGAGGTGTTCGTCAAATCAAACTTTGTGTCTGACAGTGAGTGTTTGTGTCTGACATGAGCTCATTTCCTCTGCAG
Seq C2 exon
AATGATGATGGAGGACACTGCTGTCTGGTGAACAAGTGGAGCACCTTCCTGAAGGCTCGGCTCATCTGCTCTGTCACCGGCTCTGATGGCATCGAGACGCATTTCGATGAGCTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011163:ENSDART00000046498:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.011 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(9.7=100)
A:
NA
C2:
PF0140314=Sema=FE(8.1=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:
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]