HsaINT0038367 @ hg19
Intron Retention
Gene
ENSG00000108821 | COL1A1
Description
collagen, type I, alpha 1 [Source:HGNC Symbol;Acc:2197]
Coordinates
chr17:48277114-48279000:-
Coord C1 exon
chr17:48278772-48279000
Coord A exon
chr17:48277309-48278771
Coord C2 exon
chr17:48277114-48277308
Length
1463 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
CCCTCTTCCGCCTGTCCCAGTCC
3' ss Score
8.45
Exon sequences
Seq C1 exon
TCGTCGGAGCAGACGGGAGTTTCTCCTCGGGGTCGGAGCAGGAGGCACGCGGAGTGTGAGGCCACGCATGAGCGGACGCTAACCCCCTCCCCAGCCACAAAGAGTCTACATGTCTAGGGTCTAGACATGTTCAGCTTTGTGGACCTCCGGCTCCTGCTCCTCTTAGCGGCCACCGCCCTCCTGACGCACGGCCAAGAGGAAGGCCAAGTCGAGGGCCAAGACGAAGACA
Seq A exon
GTAAGTCCCAAACTTTTGGGAGTGCAAGGATACTCTATATCGCGCCTTGCGCTTGGTCCCGGGGGCCGCGGCTTAAAACGAGACGTGGATGATCCGGAGACTCGGGAATGGAAGGGAGATGATGAGGGCTCTTCCTCGGCGCCCTGAGACAGGAGGGAGCTCACCCTGGGGCGAGGTTGGGGTTGAACGCGCCCCGGGAGCGGGAGGTGAGGGTGGAGCGCGGCGTGAGTTGGTGCAAGAGAGAATCCCGAGCGCGCAACCGGGGAAGTGGGGATCTGGGTGCAGAGTGAGGAAAGCACGTCGAAGATGGGATGGGGGCGCCGAGCGGGGCATTTGAAGCCCAAGATGTAGAAGCAATCAGGAAGGCCGTGGGATGATTCATAAGGAAAGATTGCCCTCTCTGCGGGCTAGAGTGTTGCTGGGGCCGTGGGGGTGCTGGGCAGCCGCGGAGGGGGTGCGGAGCGTGGGCGGGTGGAGGATGAGAAACTTTGGCGCGGACTCGGCGGGGCGGGGTCCTTGCGCCCCCTGCTGACCGATGCTGAGCACTGCGTCTCCCGGTCCAACGCTTACTGGGGCAGGAGCCGGAGCGGGAAGACCCGGGTTATTGCTGGGTGCGGACCCCCACCTCTAGATCTGGAAAGTAAAGCCAGGGATGGGGCAGCCCAAGCCTCTTAAAGAGGTAGTCGGGCCGGTGAGGTCGGCCCCGCCCCGGCCCCATTGCTTAGCGTTGCCCGACACCTAGTGGCCGTCTGGGGAGCCGCTAGCGCGGTGGGAGTGGTTAGCTAACTTCTGGACTATTTGCGGACTTTTTGGTTCTTTGGCTAAAAGTGACCTGGAGGCATTGGCTGGCTTTGGGGGACTGGGGATGGCCCCGAGAGCGGGCTTTTAAGATGTCTAGGTGCTGGAGGTTAGGGTGTCTCCTAATTTTGAGGTACATTTCAAGTCTTGGGGGGGCCTCCCTTCCAATCAGCCGCTCCCATTCTCCTAGCCCCGCCCCCGCCACCCCACCTGCCCAGGGAATGGGGGCGGGATGAGGGCTGGACCTCCCTTCTCTCCTCCCTCGCCCTCCTCCTGTCTCTACCACGCAAGCCACTCCCCACGAGCCTGCCCTCCCGATGGGGCCCCTCCTATTCTCCCCCCGCCCTCCCCCTCTCACCCTGTGGTTTTTATTTCACTTGGCTTCAGCGCCAATGGGCTGAGGTTGGAGTTGGAAGCCACCGCGGACTAAAGCTTTGTTTAAATTCCTGAGAACTGGAAAGAGTTACAGCCTCCCTGGCCAGGCGCCTCGGCGCTGTCACCCGCGCTGATGAGGAGCAGGCGAGCTTTTAAGGATTTGAGGAAAGAAGAACGGGGGGAGGGGCGGGAAGTGAAAAATCCAAGTGTGCCTCTTAGACCCGGGGGAAAGGTGGTTAAGCTGGGGGTTGCAGTCACTACTGACAACGCCCCTCTTCCGCCTGTCCCAG
Seq C2 exon
TCCCACCAATCACCTGCGTACAGAACGGCCTCAGGTACCATGACCGAGACGTGTGGAAACCCGAGCCCTGCCGGATCTGCGTCTGCGACAACGGCAAGGTGTTGTGCGATGACGTGATCTGTGACGAGACCAAGAACTGCCCCGGCGCCGAAGTCCCCGAGGGCGAGTGCTGTCCCGTCTGCCCCGACGGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108821-COL1A1:NM_000088:1
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=0.400 A=NA C2=0.197
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009313=VWC=WD(100=47.5),PF0139113=Collagen=PU(33.9=16.1)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTTCTCCTCGGGGTCGGAG
R:
TGGTCTCGTCACAGATCACGT
Band lengths:
343-1806
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)