HsaINT0144947 @ hg19
Intron Retention
Gene
ENSG00000123453 | SARDH
Description
sarcosine dehydrogenase [Source:HGNC Symbol;Acc:10536]
Coordinates
chr9:136597545-136599325:-
Coord C1 exon
chr9:136598965-136599325
Coord A exon
chr9:136597724-136598964
Coord C2 exon
chr9:136597545-136597723
Length
1241 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
GCACCCACCCTCCCGGGCAGGCC
3' ss Score
5.91
Exon sequences
Seq C1 exon
CTCCCTGTTTCGCTGAGGCCTGGAGCCCCCATGGCCTCACTGAGCCGAGCCCTACGTGTGGCTGCTGCCCACCCTCGCCAGAGCCCTACCCGGGGCATGGGGCCATGCAACCTGTCCAGCGCAGCTGGCCCCACAGCCGAGAAGAGTGTGCCATATCAGCGGACCCTGAAGGAGGGACAGGGCACCTCGGTGGTGGCCCAAGGCCCAAGCCGGCCCCTGCCCAGCACGGCCAACGTGGTGGTCATTGGTGGAGGCAGCTTGGGCTGCCAGACCCTGTACCACCTGGCCAAGCTGGGCATGAGTGGGGCGGTGCTGCTGGAGCGGGAGCGGCTGACCTCCGGGACCACCTGGCACACGGCAG
Seq A exon
GTAGGGACCGGGGGCCAGGTAGGGGCAGGGAAGGATAGGACATAGCGAGGGGCCACAGCCCATTGCTAGCTGGGACAGTTCTTGGTTCACAACAACCAGCCTGGGGAAGAGACCCTGGGGAAGGGTGCATGGCCAGTTTGCAGGTGGGCGGAGCTGGGGGCACTGCTTGCCCTCCCAGTCGCTGAAGAGCTGTGGTGGGAGGAGGGAGCAGATGCTGCTTGTGTGGCCTGGAGAGTGAAGCTGGGGCCAGAGCTGGAAACTCCAGGCAGCTGTCCAGAGGGCAGAAGCCCCTTTCCTGGACAGAGCCACCAGGACTGAGGGCATTCCAGGGAGTGGAGAAGGACGGACGGGGACCATTGAGGGTGAAGCAGACCTGTGTCCTCCATGAGCACCAGAGGCTTCTACAGTTCTCATTCTCCTAACTAACCAGGGGGCATATATTAAGCACCTATGGTGTGCATGTCCCAGGACAGCCAACCTTCTGCCTTCACCATTTCAGCCATGGGTGTCCTGGCAAACTGGATCTCCTGACCTGCAGTGTTGGCCAGTTCCTGTGGTGTGAACACTCCCACCCTGGCCAATAGCAAAAGCCACCAGTGTGAGGTCACTGACTGTGGAGTTGGGAAGAGGTTTATCCCTGGGCTCCTGAGAGCTGATGCGAGCCGGCTCCCACAAGCCACTGCTCCAACTCTTGCTCTTGCCTTCTCACTGGCCCCCTAGCTGGGCTGTCATAGCCTCTTCCCTGACGTTTCGCCAGCCACACCCCTGGCCTGCCACCTCTCACATTCAGCTGCTGGAGGGCATCCTTTGTTGGGGAGAGTGCAGATTTAAGCTTCATTCAGTAGTGGGTTGGTGTCTCGGCGCCCCCTCCACTCACCTGCTCTGTGATCTTGGCCACAGAACTGTTGGTGCCACTTGAACTTGATCTATAAGAGAATCACGCCCTCCTCATAGGGCATGACAGGCTTAGCACGGGGCTTGGCACACAGTAGGTGCTCCAAAAATGGGGGCCTTTGCTATGTCACTCTCTGAGCTGCCCAAGGGCGGGACCTCCCTCACATTCATCTTGGTCCAGTTATTTTCTGCTCAACAACCTCTCCAGGCCCCCCAGGTCCTGCAGAGAAAGACCTTGCAGAGAAAGACACCCATGGTTGAATATCAGGGTATCCCCTGATATTCGTCTGGGGGAAGGAGGTGCAGTCCACTCCCTGGGGAGTGATGGCACCCACCCTCCCGGGCAG
Seq C2 exon
GCCTGCTGTGGCAGCTGCGGCCCAGTGACGTGGAGGTGGAGCTTCTGGCCCACACTCGGCGGGTGGTGAGCCGGGAGCTGGAGGAGGAGACGGGACTACACACGGGCTGGATCCAGAATGGGGGCCTCTTCATCGCGTCCAACCGGCAGCGCCTGGACGAGTACAAGAGGCTCATGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000123453-SARDH:NM_007101:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.457 A=NA C2=0.013
Domain overlap (PFAM):
C1:
PF0126619=DAO=PU(15.2=38.7)
A:
NA
C2:
PF0126619=DAO=FE(20.8=100),PF043038=PrpF=PU(4.6=10.0)
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:
TATCAGCGGACCCTGAAGGAG
R:
GATGAAGAGGCCCCCATTCTG
Band lengths:
342-1583
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)