DreINT0132618 @ 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
chr6:42886679-42888598:+
Coord C1 exon
chr6:42886679-42886798
Coord A exon
chr6:42886799-42888508
Coord C2 exon
chr6:42888509-42888598
Length
1710 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAC
5' ss Score
7.82
3' ss Seq
GTACACACCTTGTTTTATAGGGT
3' ss Score
6.44
Exon sequences
Seq C1 exon
GGCGAATGTGGTAATTTCATCCGTCTAATCGAGCCGTGGAACCGGACTCACCTGTATGTGTGCGGGACGGGAGCTTACAACCCCATCTGCACCTATGTGGACAGAGGCCAAAGGGCACAG
Seq A exon
GTAAACCATCATTCACAGGTCACCTGCTACCACTTGCAGGTCAGGGGATCAAGCTGTTGGCTACCTTAGTCAAAAGGTATTATGTCATTAGAGAGGAATGTTTCCCCACCCTGGAACAAACAGGATAATCTTTGCCACCTGTATGTCTTTTTAACTCTGTTACTCTTCCTAGTGTTTAGGAGGGTAATTACATTTAAACACAGTCCCAATTTCACCTCCCTTCTTTCCCATGACCACGTCCCATCATTAAGCACTGTCCAGGAGAACATCATTTAGACGTTTTAATATATCAAATGTTGAGATCACTGAAGAAAATGTTATATGATTTAAAATAAAATCTCTCTGTAACTCAGTGGGCACTGTCATACACCTGGCACAATATGGCGCAAGACGTGTTTAGTATGATTTGTTGCTATTTTTAGACAAGCGCAACCCTAATTTTTACGTTTTGCACCACATTGTTTAGTAGCAAATCCATTCGCGCTACTTTGTGGACTCCTGGGCATACTGGTCTAAAGTAGAGATGTGTTAAGCGCGTTGCTATTTTGAGGAACTGAAATGGACTGCATAACTGACCAACTATAAGCTGGTCTAAAGTCCAGCGCAGAGCACGTTAATTGTGCACCTATGTGGATCCAAACACCTACACATTGCTTAATACACACAGAATGCACAGCAATACACAAATATATTTACATATGAAAAAATTAAGGATTAAAATGTTACAAAAATTATTATTTTCTACATAAATATAAAAAACACTGTCTGCATGCCTTCTTCATGTCGGGGGGCTTTTTTCAGTTCATTCATGACAATTTGCATGTACCCTGTCAGGTTTTGGAGATGTATGCATCACCATGGGCTTAAGAATAGGACGTGTGTTTGGATATACTGTTGTATACTCAGTTGTATATAACGCACTACGTTATTATTGTTCATTTATTTGTTTGCTGGAATTTAGAACTGAATTTAGAAATAGTTTTGAAACAAATTTTCCTTATTGTTTCCTTATCCACGAAAGTAAAGGAGTAAAAGTAAAGAGAAAGAGAAAGTCAAGAGGCCGAATGGAGGAGGCTCGTTCTTTACCATTGCACAGATCGTTTGTTTAAATGATTTCTTGCAAGTGAAGCATTCAGTTTTTCCACTTACAGAATCCGCTATGTAAATAGTAAAATGTGCCATGGCACGACGCAACTGACTCTTAAAAGAAAAGGGAGATGAGACTCTGATTTAATGCATATTATGCTCAAAACACACCCATAACTCATTTAGAAAATAAGCACAACCCTGTTAGTATATGCGCCAGGGTGCAAACCGTATTTTTTCTGTCCTTAAAATATCAAAAGTAGATTAAAAATAAAATGTGAAAAAGCAATGAAAAATCATATGAACAAAAAAAAACATTTTCAATGGTGGTCTCAGGTTTTGAAACCTAATATGTTTCTTTACTTTCATGTTTTTTTTTTTTTTTCTGACATGCATGTCTGTTTCTATTATATGCATGAAAAGGGAATTTTAATGTGCTAAAAAGGTTTTTCAGCATGTGCATGCTTTGAACACAACTTCTTTCTGTGGTTTCTTGACACAAACTGCAGCCATCTTTTTTGCATCTCAACCTTTTCCTTGGAGCATAGCCTGGGACGCTCTCTTGGGTCCTAACTGAATTCATAGAAACGGGTCTTTTATTGAGGTACACACCTTGTTTTATAG
Seq C2 exon
GGTTTTCTGCAAGATCAGATGCCTCGTGCAGGAGGCCGAACCAGTCGAGCTGCTGACCCTAGTGCCTCACCAGAACCATATGCACCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011163:ENSDART00000046498:5
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=0.667
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(8.3=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
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCGAATGTGGTAATTTCATCCG
R:
TGGGTGCATATGGTTCTGGTG
Band lengths:
208-1918
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]