HsaINT0144949 @ hg19
Intron Retention
Gene
ENSG00000123453 | SARDH
Description
sarcosine dehydrogenase [Source:HGNC Symbol;Acc:10536]
Coordinates
chr9:136596427-136597723:-
Coord C1 exon
chr9:136597545-136597723
Coord A exon
chr9:136596607-136597544
Coord C2 exon
chr9:136596427-136596606
Length
938 bp
Sequences
Splice sites
5' ss Seq
TCGGTGTGT
5' ss Score
5.93
3' ss Seq
CCTCCCCTGGGTCCCCCTAGCTG
3' ss Score
7.92
Exon sequences
Seq C1 exon
GCCTGCTGTGGCAGCTGCGGCCCAGTGACGTGGAGGTGGAGCTTCTGGCCCACACTCGGCGGGTGGTGAGCCGGGAGCTGGAGGAGGAGACGGGACTACACACGGGCTGGATCCAGAATGGGGGCCTCTTCATCGCGTCCAACCGGCAGCGCCTGGACGAGTACAAGAGGCTCATGTCG
Seq A exon
GTGTGTGCTCCCCTGCGGGGGGCAAGGAGGGGGGCTTGGGTGGGTGGGTGCACTCCCTGGGGGGTCATATTGGTGGGTGCACCCCCTGTGGGGGGGTAGGGTGGGCTCCCTGTGAGGGTGGAGGTACGCTGGGGGTTCATGTCCGTGTGCGCATCCCCTGCGGGGGGCTGGGGTGGGGGGCTCGTGTGGATGAGTCTGCTTCCTGTGGGGTCGGGAGTGGGGCTCATGTCGGTGGGCACCCTTCTGCCGCGAGAGAAGGGGACACGCCACAGGGAAGGAGCCCCGGCAGGTGACAGATCTGGGTTCCAGCCCTTGCGCTGCCCCTTGCTGGCTGTGCCACCTGGAGAAAGCGACTTTGCCAGGCTTCATTCAGAATTCCCAGACAGAGAATCTGATTGGCCCAGCTTCTCCCTGTCCCAGTGGTCCACGCCTGAGGACACTGATTGGCTGTTCTTGGGCCAATCAAATGTGGGGGCGTGGTCTATCTGACAGTCTGAAACAGGATCTTGGCCTCTCTTGACAGCTGGTCTGACTGGGAAACCTCTCAGGCCCAAAGTATTAGACCTGTGGGGTTATTTATCTTATATAATAGACACTTTGTGCCAGGCACTGGTCTAAGTTCTTTGTCAATGACATACACTATTCTCACCCCCACTTCACCTGAGTGAGCCTGAAGCGACTTTGCCCCAGGTTGGTCACACAGCTGGCGAGGGTCGGATTGGCACAGGCGGCCTGGCCCCGGAGCCTGCCTCAGTGCCCTGCTCCTTAACTCTTATGCTGAAGCGGATTCAAGGGACAGGCTCCGGGGGCGTGGGGACCGGCTAAGGCTTCTGGGAGAAAGTGAGGCTGGGGTTTGCGGTGGATGCCCAGTTGGGGAGGGGAGTGGCCCAGGGGTCTGCTCCCCACGGACTCAGTTAACCTCCCCTGGGTCCCCCTAG
Seq C2 exon
CTGGGCAAGGCGTATGGTGTGGAATCCCATGTGCTGAGCCCGGCAGAGACCAAGACTCTGTACCCGCTGATGAATGTGGACGACCTCTACGGGACCCTGTATGTGCCGCACGACGGTACCATGGACCCCGCTGGCACCTGTACCACCCTCGCCAGGGCAGCTTCTGCCCGAGGAGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000123453-SARDH:NM_007101:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.013 A=NA C2=0.060
Domain overlap (PFAM):
C1:
PF0126619=DAO=FE(20.8=100),PF043038=PrpF=PU(4.6=10.0)
A:
NA
C2:
PF0126619=DAO=FE(20.8=100),PF043038=PrpF=FE(45.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGCCCAGTGACGTGGAG
R:
CTGTGCTCCTCGGGCAGAAG
Band lengths:
342-1280
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)