RnoINT0130709 @ rn6
Intron Retention
Gene
ENSRNOG00000006916 | Sardh
Description
sarcosine dehydrogenase [Source:RGD Symbol;Acc:621125]
Coordinates
chr3:5796138-5797927:-
Coord C1 exon
chr3:5797573-5797927
Coord A exon
chr3:5796317-5797572
Coord C2 exon
chr3:5796138-5796316
Length
1256 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
GTTGTCCTTTTCTGGCCCAGGCC
3' ss Score
8.07
Exon sequences
Seq C1 exon
GTACAGGAGCCCTAAGTCCCCATGGCTTCACTGAGCCGGGTCCTCCGTGTAGCTGCCACCTGTCCTCGAGGGAGATCTGCTCGCAACCTGGGGCTACAGCCCCTAGCCAGGGAGGCCAGGCCCACCACTGAGAAGAGTGTTCCATACCAGTGCACCCTGAAGGAGGAGGCCCAAGGTGCCTCTGTGGTGCCCCAAGGACCAAGCCAGCCCCTGCCTAGCACAGCCAATGTTGTGGTCATTGGTGGGGGCAGTTTGGGCTGCCAGACTCTGTACCACTTGGCCAAGCTGGGTGTAGGTGGAGTTGTGCTGCTGGAGAGAGAGCGACTGACCTCTGGGACCACCTGGCACACAGCAG
Seq A exon
GTAGGAGCCTGGGTGCAGGCAGGTAGGGGGGGACACAGCCGGGGGTCAGTCTGAGTGAGGAGTAGAGTTGGAGAGGGAAGACGTATGATGGATGTGGAAGGCCAGCCGGACTTTCCTCTCTGAAGAGCTGTGCTGGGGAGAGGCTGCCCCCTGGGTAGGGGTGAAGCTGCACCCAGGAGTTGTCTGTACTAAGAGCAGAGTCCCTGTTCCCAGACGAAGCCACTAGGTAGAGGCACATCTCCTGGAGGATGGATGGCCCTGTGTAGGAGGGGCTGTACCTTCTGTGGTACTCTCCTGACTCATCCCGTGCATGCCCATTAAGCACCCACAGTTCCATGTCCTCACCGCTTTTACCAGTGGTCCCCTGGAGAGCAGCTGCCGGTCTGATGTGGTGTAAACACTTGCACCTTGGTGACTGTCAAGAGGCCAACATGAGGCGCTCGACTTGGACCCTGGAGAGCTGATACCTAGAGTACACTGCCTCTAAGCTGGAGGTTCTCAACCTGTAGGTTGAGGGCTGGGGATTTGGCTCAGCGGTAGAGCGCTTGCCTAGCAAGCACAAGGCCCTGGGTTCGGTCCCCAGCTCCGGAAAAAAAAAAAAAAATCAACCTGTAGGTTGGAACCTTTTATGGGGCTGAGTATCAGATTTTTTGCATATCGGATATTTATATTATGATTAATAATAGTAGAAAATTACAGTTATAAAGTATCAATGAAATAATTTTGTCATCACAACATGAGGAACTATATTGAAAGGGCTTGTCATTAGGAAGGTTGAGAACCACTGCTTTAAGCCCATCTCCCAAGGTCAGGCCGGCTGGGCTGTCAGGCCTTGCCCCTCCATGACACAGCAGCCTCACTGCTGGCCACTATCCCTCGGCCTCTGCTGTCTTAGGAAGACAGGGATTTCTGGGTCCAGTCAGTTTTCAGTTTCACCATTCACCTGCTCTGTGACTTTGAATTCAACTAGTTGGGGTTTCCCTATGAAATAACTTTTAAAGCCAGGCAGGGTGGCCTAGGCCTAGCACTTGGGAGGCGGAGATTGGAAGATGAAGAATTCAAGTTCATTCTTGGCTACCTAGCAAGTTTGAGGCTAGCCAGGGCACTAGGAGCTGCCCCGGCATAGCCCTAACTCCACCTGTGGCAGGCCGTGTCCCACCTAACCTCCCTGGGCTCCCCACTGTTCCTCACTATTTGCCTGGAAGAGGGGTATGATGCCACCCTGCAGGGACCGATGTTGTCCTTTTCTGGCCCAG
Seq C2 exon
GCCTACTGTGGCAGCTGCGGCCCAGCGATGTGGAAGTAGAGCTTCTGGCTCACACACGGCAAGTGGTGAGCCATGATCTGGAAGAGGAGACTGGGCTTCACACAGGCTGGATCCAGAATGGTGGCCTCTTCATCGCCTCCAACCAGCAGCGCCTGGATGAATACAAGAGGCTCATGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006916:ENSRNOT00000009555:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.295 A=NA C2=0.017
Domain overlap (PFAM):
C1:
PF0126619=DAO=PU(11.9=38.4)
A:
NA
C2:
PF0126619=DAO=FE(16.4=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:
GTTCCATACCAGTGCACCCTG
R:
TGAAGAGGCCACCATTCTGGA
Band lengths:
349-1605
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]