DreINT0130775 @ danRer10
Intron Retention
Gene
ENSDARG00000058102 | sardh
Description
sarcosine dehydrogenase [Source:ZFIN;Acc:ZDB-GENE-040426-996]
Coordinates
chr10:10430670-10432830:+
Coord C1 exon
chr10:10430670-10430996
Coord A exon
chr10:10430997-10432651
Coord C2 exon
chr10:10432652-10432830
Length
1655 bp
Sequences
Splice sites
5' ss Seq
CTGGTATTG
5' ss Score
3.14
3' ss Seq
ATCTTTTTACCTCATCGCAGGAC
3' ss Score
8.39
Exon sequences
Seq C1 exon
GGGCCATGGCCTTCTTAGGAACAGCAGCATGGAGGGCGATGGTGTGTCGGCAGCCCCTCTCGCCCCTCTGCCGTGCTACCACCCGCTGCTATAGCTCTCAGTCTACACACACCAAAGAGAAGAGTGTCCCGTATGAGAAGACCCTCAAACATGAGGATGGCCTCAGTGGGCCTACCAAACCCCTTCCCAAGTCTGCAGATGTTGTGGTGATTGGAGGAGGAAGCCTGGGTTGCCAGACCCTCTACCACCTGTGTAAATTAGGCATGACCAATGTGGTTCTCCTGGAGAGGGACAGACTGACTGCTGGCACCACCTGGCACACAGCTG
Seq A exon
GTATTGCATTATGTTTACTTTGTTGACATCTGTATGTTAACTTCTGAATGATTCAGTAATGTTGTTAACTTCTGAATGTTAACTTTAAATGAACAATGCTCCTGTGCAAAAGCAAAAAGCTGTTACTTAATTTTTGTCTGAAAAAACTTTCAATTTAATTAAATTACCCTTTATTTGTATAGCGATTTTACAATGTAGATTGTGTCAAAGCAGCTTCACATAGAAGGTCATAGTAAACTGTAACAGTGTAGCTCAGTTTCCAAACACTGAAGAGCAAATCCATCGATGCGCAGCTCTCCAGATCCCGAACCATGCAAACCAGTTGTGACAGCGGCGGGGAAAAAAACTTCATCGATTGGCGAAAGTAAAGAATTTAAAATCTTGAGAGAAACCAGGCTTAGTTGGGCACGACCATTTCGCCTATGGCCAAACTTGTGCAAATTTGCAGTCTAGGGGCTGGAGGCTGGTGAACGCTGGACCTCAGCAAAGTCTTGTCTGTCCCTGGAGCGTCACAGGAATCAGTCTCATGCTCTCCACTCCTCCATGACCACCACAGCAGCTGCTCAGGATAAGGCCTAGTCCAGGATTATGGAAACCTTGGGATTATCTCGTCGCTGGTCTTGGACCGAATCAGTGGCGCTGCATTGTCTCTGGGTGGCTTCAGGATGAGTATCCCCAGGTGGAAAAGGAGAATAAAGAGAAAAATTAGCGTAGCTGCTGTCCATAGTGTACATAAACGAGATGCAAAAACTTGCGTGAGGCACATTCATGTTTCATACCGCTAAGTGATGCACTGAGTGTATGCTTTACTAAAAAGATAGGTCTTTAATCTAGTTTTGAACTGTGAGAGTGTGTCTGAGCCTCAGACATTATCAGGAAGGCTGTTCCAGAGTTTAGGAGCCATAAATGAGAAGGCTCGACCTCCTTTACTCGACTTTGCTATTCAAGGTACTACCAGAAGCCCTGAGTTTTGAGATCTTAAAGAGCGAGTTGGATTGTAGTGAGACAGAAGGTTAGTTAGATAAACAGGAGCTAGACTATTTAAAGCTTCATAGGTGAGAAGCAATATTTTAGAATCAATATAAAAACTTAACAGGCAGCCAGTGTAAGGAGGATACAATTGGGGTGATATGATCATATTTTCTAGACCTGGCAAGAACTATGACAGCTGTATTTTAGCATACTTTGTAACTTAGCGATATTTCTCAGATGGAAGAAGGCAGTTTTTGTGACATAGAAATATGATTTTCAATATTTTTTATTAATATTTTTGAGTATCCTATCTGGTTACTATTTGATTAACCTAACCTGGTTTCATTGTTTTTTTTTATTGCCAAATTTCCAGGCTCCTTCCTATGATTATTTTGTCTGGACAACTAAAAATATTTCAAGTCATTTTTCTCAGTTCCACACTCTAGGAACTTTAGGTCTTTTGCCTTTGCAGGGCAAAAGTGTAAGAGAAAATTGAATCTGGGTATTAAATCAGATTTCATTTTCTACTTGTACAGCATTTACTCCATGAATAGGCTGACAGAACTGGTTGCATAAAAGCCAAATCCATGGGCGTTGCAGTTTGTCAGATACAAATGAATTCTTGATAGTCTGTTCAACTTTGTTTTCTTTGTTTTGAATGAGATCTTTTTACCTCATCGCAG
Seq C2 exon
GACTTTTGTGGCAGTTAAGACCAAGTGATACTGAGGTAGAGCTGTTGGCTCACACTCGCAATGTGGTCAGCTCAGAGCTGAAGGAGGAGACGGGCCTTGAGACGGGCTGGATCCAAAATGGAGGCCTGTTCATTGCGTCCAACAAGCAGCGATTGGACGAGTACAAGCGACTCATGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058102:ENSDART00000080904:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.185 A=NA C2=0.017
Domain overlap (PFAM):
C1:
PF0126619=DAO=PU(11.9=39.8)
A:
NA
C2:
PF0126619=DAO=FE(16.4=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:
TGCTACCACCCGCTGCTATAG
R:
TCTCCTCCTTCAGCTCTGAGC
Band lengths:
344-1999
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]