HsaINT0156822 @ hg19
Intron Retention
Gene
ENSG00000137642 | SORL1
Description
sortilin-related receptor, L(DLR class) A repeats containing [Source:HGNC Symbol;Acc:11185]
Coordinates
chr11:121428023-121429546:+
Coord C1 exon
chr11:121428023-121428114
Coord A exon
chr11:121428115-121429299
Coord C2 exon
chr11:121429300-121429546
Length
1185 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGT
5' ss Score
9.65
3' ss Seq
TCTGTCCCCATTTTCGCTAGGGT
3' ss Score
8.27
Exon sequences
Seq C1 exon
GTAGCTAATCCAGATGGCGACTTCCGACTCACAATCGTCAATTCCTCTGTGCTTGATCGTCCCAGGGCTCTGGTCCTCGTGCCCCAAGAGGG
Seq A exon
GTAAGTGTTGCCCCAAAAGGAAATCAGTCTTGCGTCCAATGCTACACTAATAGATTCTCATGGAAACACAGACTGCGGGACAAAAACTCTGTTTCTCATGATGGTGGTTGAAATGGTCTATTAACTGAGAAGTTTGAGACCACAGCTTAGTCATCGTGGTCAGGTAACTCCGTTCGCTTTTTGTTAGCCAGTGTCAGAGTCTCTTTAGGCATCCAGATGTCTTGCATCTGTGGGTTGTTTCTCTAGAAAAGTTGATGTTAAAAGAGAGCTTCTGTAGACATAGACAGGCCTGCTTGGATATTGTGAGAACTTTCTCTTGAGTTTCATGCATGGTACAAACATTTAATTCATTCCATCTTTCCCCTGCCTTCCCAGCATGTGTAGGTTTTCTTACGTACAATCAGTGTGCACTTGGGGAAGGCAAAGGTGCTTTTTATTAACTCATTAACTGAAGGAAACATAATTAAGAGGGAAATTCTGGATTTGACATTCTGGCTTTTCCTCTCTCGTAGCATTTATGATAGAGAATTGGCACAATTTTTTTCAAGGAAAATTCTAAGAGTAATGTATGTACTTGGTTGACAATATTTAGAGAGAACAGCACTTTATGAAAAAAATTTGCATTCTTCCTTTTCATTCTTAACCCTTTACCCTCACACTTCCTAGTGGTAATCATTGTTAATAATGTCTTGTGTATCTTTCATGATTGCTTTTACTTATGTACAAGTATTATCTTTAAAACACACACATATACACACACATGCACGCCAAATAGGATTGTAGTGTAGTTACTATTCTGTACCTTTTTAAACAAACTTAATATGTATTGAAAATAGTTCTGTGTGAGCATATATAGATTTTTAGGTTTCACAGTATTCTATTATATGTACCATAATGTGTCACTTCCTCTGCTGATTAACATTTAGTTTAATATACATACATATACATTTCTTTGTATATTATCTTTGCATAATTTGATTTTATCTATAGATAAATTCTAGTAAAGGAATTTCCAGGTGAAGGAATTTAAGTAGTTTCAGGTGTTGTCATTACATATTGTTATAATAATGCTGAAATAACCAGCCGGATCATTCGAAAGGAGTTTCTGACCTTTTCTGGAGTAGTATTTGAGCTCCCATTTCTCTAGTATTGATGAGGTATGTGTTCTGTCCCCATTTTCGCTAG
Seq C2 exon
GGTGATGTTCTGGACAGACTGGGGAGACCTGAAGCCTGGGATTTATCGGAGCAATATGGATGGTTCTGCTGCCTATCACCTGGTGTCTGAGGATGTGAAGTGGCCCAATGGCATCTCTGTGGACGACCAGTGGATTTACTGGACGGATGCCTACCTGGAGTGCATAGAGCGGATCACGTTCAGTGGCCAGCAGCGCTCTGTCATTCTGGACAACCTCCCGCACCCCTATGCCATTGCTGTCTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000137642-SORL1:NM_003105:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=PD(63.4=83.9),PF0005812=Ldl_recept_b=PU(0.1=0.0)
A:
NA
C2:
PF0005812=Ldl_recept_b=WD(100=50.6),PF0005812=Ldl_recept_b=WD(100=48.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTAATCCAGATGGCGACTT
R:
AAAGACAGCAATGGCATAGGGG
Band lengths:
334-1519
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
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)