DreINT0132716 @ danRer10
Intron Retention
Gene
ENSDARG00000079611 | sema4c
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C [Source:ZFIN;Acc:ZDB-GENE-080303-16]
Coordinates
chr5:14060997-14064661:-
Coord C1 exon
chr5:14064554-14064661
Coord A exon
chr5:14061060-14064553
Coord C2 exon
chr5:14060997-14061059
Length
3494 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
CATGTCTCTTTCTCTCTTAGATT
3' ss Score
11.95
Exon sequences
Seq C1 exon
TACACCATGTTGACCCTGGCAGAACACGAGAGGGTTTTGTATGTGGGCGCCAGAGAGAACATCTTCGCCCTGGATCCCAACGACATCAGCAGACAGCTCCGACCACAG
Seq A exon
GTATGTTCAGACAAGAAAAGGCCTTTTTTCTAGTATTGACATTCAAATGGCTTCCATTTATGGGTTCCGCCATATAACGGTATTGACGATAATCGTGAAATGTAAGAAATTAAACATTAATATTTATTTAGGATGTTATAATATATTGATAAGGCAGCACATGGCTCAGTGGTTAGCACTGTCACCTAACAACACTGACATTCGAGTCCCAGCTGGGCCAGTTAGCATTTCTGTGTGGAGTTTGCATGTTCCCCCTGTGTTCGCATGGGTATCCTCTGGGTGCTCCGGTTTCCCCCACAGTCCAAAGACATGCGCTATAGATGAACTGGATGAAATGATTTGGCCATAGTGCATAAGTTTGTGAGTGAATGAGTGTTTCCCAGTACTAAGTTGTGGCTTGAAGTGCATCTGCTGCGTAAAACATTTGTCAGAATAGTTAGCAGTTCATTCCGGTGTGGCGACCCCTGATAAATAAGACACTAAGCTAAAGGAAAATTAATGAATGATAAATATATTGATATTGGAGGACACCATGATGTTTAAAAAGTAATAGTTCACATAATATGATGCATAAATAAATCCAGAGGGGTATGTTTAATTCCTACTCCACACCAGAGGGCGCCCTCACACAGAAAGTTCACAAGCAAGTATCAAATCTCATAGAGTAATAAAACTGGTTCCTGGTAGTCTTCGAAATGGACGGATGTATCAAGCTATTGTAGTTAGGGATGGGAAGTTCGGATCATTTTACTGACTCAGACCTTTGAGTCTTGTTCAGCAAGGTGAACGAATCTTCGAAACGAAGTGAAAAAAATCTTAAGTCATTTCGTTTAATTTACCAAAATATTATTCAAATGTTACGAGTTGCTCCCAAACTCATCTACAACTAAACTAAACGTTGATCACACTACAAACAAGTCATAACTAGAATGCTATAGGAAAGAGTAAATAATGATGTATTGTTTACCTGGTCTTTTATCTATGATTATGTCCGCTCACCTCTTCTGGCAAGTCTTCAAATTTGAGTTCGTTCACATCACACTAACAGTCCCATATAAGCTTAACCAATGCACACAGTCTGAGCCAAAAGGAACCATGATTAGTTCACCATTCGAGTCTTCTGGTTTTTGAGTCGCTAGCTCATCACGTGACAGCATTTAAAGAGATGCCTCAAACCCAAGGACTCGAGAGATGAACGGAACAAATCTTTTTCTGGCTATAAATGCATATGATTGGCTACTGTTTTTGACTCAAGCAAAGTCAAACGAATGACTCGAACTTGATAAAAGATTTGAAAAAGGAACTAGTCTTTTACTCCACCTGCTCAAATGTACGCATGCACAAATGAACGAATCACTCCCTGAGAGGACTCATTGTTCTCGAATCATACAAAAGATTCGTTTAAAATGAACGAAAAGTTCAAGAGCGACCCATCACTAATTGTAGTATTGATGAATAAAAAGCAGATACAAATGTTTTAGCTTAAAGATAATCAAACATTTTCAACAGTATTATTTCATTTATTTGTATTCTTTAAATAATTTCAGGGATTTTCACAACATCGATGTTTATTTAAAATCCAATACTAATCGATATTATTACTATGTATTACTCGTTCATTCATTTTCTTTTCGGCTTAGTTCCTTTATTAATCTGGGGTCGCCACAGCTAAATGAACCGCCAACTTATCCAGCATATGATTTACACAGCGAATGCCTCTCCAGCTGCAGCCCATCACTTGGAAACACCCATGCACTCTTTCACACACATACACTACGGACAATGTAGCTTATTCAATTTACCTGTACCACATGTCTATGGACTTGTGGGGGAAACCGGAGCACCTGGAGGAAACCCACGCAAACACGGGGAGAACATGCAAACTCCACACAGAAATGCCAACTGACCAAGCCGGGGCCTGAACCAGCAACCTTCTTGCTGTAAGGCGATTGTGCTACATGTTAAAAAAATGTTTAACGTCCACCTCGTTTTGTGATAAAAAATCACTTTCAATTTTGAGTATACGTAAACTGTAATGACATTTTCATGATTGTTTTACTTTGATGCTGTGCTAAGCTCAACTTATATCATTTTAGTTTAAATTTAGTTTACCCTGTTACGTTTAATTAATATTTTTGTATTCAATGTTGTGATTTATTAGCCAAGCAAACAAATTAGTTCTCTGGATTTGCTGTTAATATGTGCAATTTGAGCGAAATGTTTGTGTTTTATTTTATAAATGACTCGTCTTTTAAATTTCAAACGAGAATATTATGATTTCATGCAGATATTATGATGTAAATATAAAATATGCCAGATTTCCAGAATTGTTTTTCTTGTATTCAACTTCTGAACAAAAAAGAAAATATTTTGTATTAAAATACTGACATTTTCTATAGAGAAATTTTCTAAATGATAGTATTCCTATGATTTTAGGACATAAAAATAATTCATTTATTTTTCTTCAGCTTAGTCTCGATTTATCAGAGGTCGCCACAGCAGAATAAACCGCCAATTATTCCAGCATATGTTTTACACAGCAGATGCCCTTCCAGCTGCAATCCAGTATTGGGAAACACCCACACTACATTCTCACATGCGTGCACGCACACACACACACTTTGACCAATTTAGTTCATCCAGTTCACTCATAAAGCCTGTCTTTGATTATGAGAAACCGCAGCACCTGCTGGAAACCCACACGAGCATGAGAAGAACATGCAAACTCCACACAGAAATGCCAACTGACCCAGCCAGGATTCGAAACAGCAACCTTGCTGTAAGATGACAGTGCTAACCACTGTGCTGCCTTATAATATAAGTAGTTTATAAAATGAATTGAAAATTCATTCATTCATTTTCTTGTCGGCTAAGTCCCTTTATTAATTCGGGGTCGCCACAGCGGAATGAACCGCCAACTTATCCAGCAAGTTTTTACGCAGCGGATGCCCTTTCAGCCGCAACCTATCTCTGGGAAACATACACACACACATTCACACACTATGGACAGTTTAGCTTACCCAATTCACCTGTACCACATGTCTTTGGACTGTGGGGGAAACCGGAGCACCCTGAGGAAACACACGCGAACGCAGGGAGAACATGCAAACTCCACACAGAAACGCCAACTGAGCCGAGGATCGAACCAGTGACCCAGTGTCAGTTTTTTAAGTTTTGACTGTCAGTTTTTTAAGGATTTCAGTAGTTATAGCAGTATATCCTTATCTTGAATTCCTTTGGCTCAACAATGGGGGAAAATCTGATATTGTGACAGGCCTACTCCCACGCAACCAATAAATACTAAACCGCAAGCCATCAAGCAAAAAGGCCATTAGCATTTTATCATTCAAAAATATCAGCATTTAAAAATGACTCACTTTTTCAATGCCACAGCCATTTGTAGTAAATTGCCAGTTGCGGCAGTCAATAGCGAGTGCATGTTTTACATGCAGAGTGCTGTTTGCTCGTAAAAGTCATGTCTCTTTCTCTCTTAG
Seq C2 exon
ATTGAGTGGTCTGCTCCTGCAGAAAAGAAAAAAGAGTGTGCAGCGAAGGGGAAGAATAACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079611:ENSDART00000160511:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.014 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(8.1=67.3)
A:
NA
C2:
PF0140314=Sema=FE(4.7=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:
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]