DreINT0132719 @ 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
chr5:14028884-14033223:-
Coord C1 exon
chr5:14033128-14033223
Coord A exon
chr5:14030415-14033127
Coord C2 exon
chr5:14028884-14030414
Length
2713 bp
Sequences
Splice sites
5' ss Seq
TACGTCAGA
5' ss Score
-1.45
3' ss Seq
TTCTCCCCAGATCATTCAAGGTT
3' ss Score
-0.61
Exon sequences
Seq C1 exon
CTCCACATCCACACTCTCGCAGGACCTCATGCTGGAGAGGTTCAACCGAGGAAAAGCCAAGTTTGATAAGCCTTTCTCCATCCCCAGTCCTGGTAC
Seq A exon
GTCAGACTCGCGCTGCCCCCTGCAGGCACCCTTTTCACTTTAGGGGTCACACACACACACGCACTTTAAAAGCTTTATAAACTCTGTCTGGGCAAAAATATATATACAATATGCAGTTGAAGCCAGAATTATTATCCCCCCTGAATTATTATCCCAACAGTATATTTTTCACCCAATTTCTGTTTAACAGAGACAAGATTTTGTTTCTAAACATAATAGTTTCAATAACTTTAAATAACTGATTTCTTTTATTTTTGCCAGGATGACTGTACTTTTATTTTACTAGATATTTTTTAAGACACTAGTTTTGAGTGCAATTTAAAGACTCAACTAGGTTAATTATGTCAATTAGGCAAGTTGGGGTAATTAAGCAAATCAGTGATAATAATTCTGACTTTAACTGTATATGTATGGTTGAATTTTTATTGTAGTGATTAATATGTTTCTGGCTTGTTGCATATATTGGCGACTATGTAGCATATAGGTTTTTATTGCTTAAGCTGTGAGAAATAATGTTGAAACAAATGTTATAATGACTGCACACTGTAATCAAAATACAGTCAAAGTAAATTCACTGTCTGATTCTGAGAAGAACCACTCTGTAAAGTCTACACTAGCATAATCCAAAGATGTTCAATCTGTCACTGGATTAGTATCCCTTAGCAATACGATGAAATTAGCATTTACATTTAAAATAATATGATTAATGTGATGCACAATATTTATGATGCAAATGACCAAGAAAAATTGTAATCGAGATAAAATTTCAATAATATACACACACACACACACAAACACACACACACACAGGCCACTTTATCTATTTATCTATTCCACGAAAGATTAAGGCAGTTAGTTCTGAAGGTAAAAGAAGGTTCAACTTGGTACTGGGAAGGTGTACCTAATAAAGTGGCCGGTTAGTGTAGAAGTCAATAACGTCACTAAATTGAACAAATTGAGCTGTCTGTAAAAGTCTGTAAAAAAAAAACTAAATCTGACTATAGCCAAAAGGTTTACTATTATTATTTTAGTGATTTTTTTTATTTCATGATACTTTTTTATTTAATTATTTTGAAATCTGTACTTGCAAATGTATTAGAAATAATTTATTATACAGCATTTTCAGTCCCACACTTTCATCAAGGATGTACAAAAACTGTTCAGCAATGTTTCAATATACATCCAATAATTGTTATTAATAAAAACAATAGCAAAGGATTTTAGAGAGAGACTTTTGACTTAACAATCTCTTTATTTACAACCACTTTTTTTAACACGTTAATGAAAATTTTAAAAAGTTAAATAAATATATATTAGAGCCGGTTAACCCACAATTATTCACCATAGAGCCGGTTAACCCACAATCATTCACCAATCAAGCAAGTATTTCCAAACAACCATTATGACCAACTTCACAGAGACATTGATTAATACACCATTTAGATCTAAAAGTGTCCAGATCATCAATCAACTTATAATATGCATATTCTATTTTTTTATAAATATTTTTAAGGGGTTTTTCACCTTTATTATGACAGGACAGTTAAAAATTCAGACAGGAAAGCATTGGAAGCAGAGAGAGGGAAAGGATTGGCAAAGAACCTCGAGCCAGGAATCAAACTCGGGTCGACGTGAGCACGTTGGTGCTATATGTCAGCATGCAGTACAAATAGGCATAATATGCATATTTTATTTTAATATAGGATTTAATAAGTTCCCTAAAAAACCAAAAACCATTAGTCATCCCCAGACCAGTCAGTTTCCTTTTCCGTGACAACCAAAAAGCAAATTTTGCTTGTCCATAAATAAAATTGAATAAAACATAGACTTGCATCTTGTTCCTGTTGTATTTAGGCCCATAAATAAAAAGACTGGGCGTAAAAACCTCTTCCAACATTTGACTGTATCCATTCAGCTGATAAAGGAACATTTGTAATCTAGAGCAATTTAAAAATAAGTAAAACACTGTTTCCCCCACCTAGCAGAAAGAAAGAAAGAGAGCGACACATACACACACACACACACAACTAGATGATTATAAATGAATCATTGTAAATATACTGATTATTATTGTTTTTATTACTGTTTTATCCTAAAAATGTACAGTTTATTGTAATCTATTTTTGTATTGATTTGTATGAATAATTAATGTAGAATAATAATATAATATATTGAATATTAATGTGATATATTGAATAATATGATGTATTGTTGATATTTTATTTAATTATTATATATAAATATCATCTTTTTTGCTACTACTACTACTACTATTTACTGTGTGTACTGTTTTTTTTATTATATATGTATATTACTATTTATGCAAACTTTATTACTGCTTTGGCAATACATTTGTAACAATTGTCATGCCAATAAAGCAATTATTGAATTGAATTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCAAAAATAAGTAAAAACATTCTGTATAAACCCTCTACAGCAAAACCTGTTTTGTTTTGTACTGTGTGCTGTAACTGATTGCTTTTATATGCCTGATGAAAGTTCTGGAACTGAATCATACAAAAAATGTACTGGTTTTAAAATAGTGACAGTAATCAGGATTTATCCAGTTTTGTCAAAATAGTTATGCTGCACACCTCTTGATTACCTGCAGGTGTGTGAAGTCAATTGAAAAAAAGAAAAATGAATAATAATTTATCATTTGTTTTCTCCCCAGATCATTCAAG
Seq C2 exon
GTTAAGAAATGTGACAGTGGTCGTTGGCTCAGATCTGGTATTGCCCTGCAATCTTGTTTCTAACTTGGCCCAGCCTTTCTGGGAGCTCAACGAGCGAGAGCTTGCTTTGGTGGAAGGAGAAGCCATTGGGCCACGATTCGACCGGGCGCTCCGTGCCCTCGTCATCCCTCAAGCCGGATCTCTTCAAGCAGGCCGTTACATCTGCTACTCGGAGGAGCAGGGCGTGAAGTTCCAGACTGAAAGATACCAGGTCGCAGTGGTAGCCAGCGCACCTGTCTTCATGGAGGCTCGAGCTCCAGACGGCAGCATGGGTTTATTCTGGGTGCTGGTGATCACCTTAGGTGCTGCTTGTCTGTTGCTGCTAATTGCATCTTTGTACCTTCGAAGAAGATTGAAGTTGGCATTGGGCAAGGGGGCGGAAATGAAGCCACTGGAGAGCACTCTGGTATACCCCATTACCTTGCCCAAAGAGCCTCCCAGCAGGCCATCCTTTGTGCCAAGCAGGATGGCAAACGATGAGGATCGCTTCTGGGAAACGGGAGCTAATTACTACTGCTCAGACGGCTCCCTAAAAATCGTTCCTGGCCACGCAATGTGCACCACTGGAAGTTCAGCATCTCCAAGTGCCATTCCGGGTCAGCCAATTCACTCGCCGAGCAGGCTGAGCCTCACCAACATTCGAAACTCAAGCACTAATGGATACATTCGCTTGAATCTGAGCACGGCCGGAGAGGAGAGAGCGAGTACGGGAGCAGGAATGGGCATGGGAAGCGGACTCGGATTGGGCAGCCGAGAGAACGATTACTCCAGTCCGTTCAAAGAGGAGCTCCGGAGAACTCTGCAACAGAGGAGTGTGCTTCCTGATGCCAATCCCGAGGAGTCTTCTGTGTAGATCTCACAGGAACCACAGGAAACCTCACCTACCTCCCTCCTGCTTGGGGAACTCTCTTCATTTTACTCAACAAACCCGCTTCTACTCTGTCAACTCTTGGCGAACATCTCCCGTGCCATAAGGCCACCGTGCTTCAAAACATTCCCTTTGGATTATTCCGGTTCTCTTGTGTACTCAACCGAGACTGAACACAACTCGCGAAGCTTTTGTAAATGTCTGTATTTAAAAGGACCAGACCGACAGGGCCTTGTGTTGATCTTGGCTAACAGGCGAACACAGGTACATCTCTGAGAGGAACCCAAATAGCCGAATGTAGCTGTCAGTTTGATCTGCGTAAGGCGGACATCTGGCAACGGATACTTATCATTTGGCAAGCTGGAGGATACAGAACCTATTTTTGACGTCCAGAGGTTGCTTGCCTCGGTTAAAGCAGGTGTTTGGACATTTTTTTTGTATGGGTAAAACGCATGAGAGGAGATGAAGAGGACATGAACTTAAAATCGCAAGATGACAATCACGCTCTACTCTCATGAGGATCCCAGAGGGAAATTATTCAAGAGGCGAGAGAGGGGAAAAACAATTGTGAGCTGTAAAACCGAAACAGGACTTGAATAATGAACAAATGCTTTGCCTTTCTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079611:ENSDART00000160511:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.316
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(26.5=39.4),PF138951=Ig_2=PU(9.4=27.3)
A:
NA
C2:
PF138951=Ig_2=PD(89.6=28.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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]