HsaINT0039647 @ hg19
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:2214]
Coordinates
chr3:48630970-48631981:-
Coord C1 exon
chr3:48631801-48631981
Coord A exon
chr3:48631130-48631800
Coord C2 exon
chr3:48630970-48631129
Length
671 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
CCACCCCTACCCTCCAACAGGAC
3' ss Score
9.2
Exon sequences
Seq C1 exon
TGACCTGCACGCGCCTTTACGCCGCTGACATTGTGTTCTTACTGGATGGCTCCTCATCCATTGGCCGCAGCAATTTCCGCGAGGTCCGCAGCTTTCTCGAAGGGCTGGTGCTGCCTTTCTCTGGAGCAGCCAGTGCACAGGGTGTGCGCTTTGCCACAGTGCAGTACAGCGATGACCCACG
Seq A exon
GTGAGTAGGGGCCCTGGGGGCTGGGGACCACGAGATCCCCACCAAGACTCCTTCCCCAGAGAGGGAGGAGACCCTGGAAACCCCAGGCCAGGTCTTTGCAGAAACAAGTTTTGGGGAACCTAGAGACCCCCTAGCCAGGACCTCCTTTGGAGACAGAGGTAAGGATTCCCTAGGTAGAACCTTCGTGCCCTGAGGCACCTCCAGGCTACTGCAAGACAGGAAGGTGCAAGACAGTGAGGCTGTGTTTTCTGATCTGGAGATGGGGAGCCCAGGAGGGGGCCCCCACGCCTGTTGGATTCTCCACGTTCTAGCCCTCTAACCCTTGCAGCCGTTCACCAGAGGTGCTCCATCTGGCCAGCATCCACTTTCCTACATCTGGACCCCTCCTCCTGCAATTATTTAATTAAGCAGCATCTTGTTCCCCACAGACTGTGAGCCCCTAAGGGCTCCTTCAGGTCTGCCCAGGCCCACCTGCAGATGGTGCACAAAGGAGCCCCTGGGGAGTTTGTTAACCTGGGGGTTCCAGAGGCAAGTGGGTGTGGAGAATGACAGAACGAAGGGACCCCTCAAGAGAGCCTGATACCCGTAACCCTCACCCTAGAGGCCTCCTCAAGGCCAGGGCCAGAAGAGATCCTGAGTCCTAGCCTGTTGCCACCCCTACCCTCCAACAG
Seq C2 exon
GACAGAGTTCGGCCTGGATGCACTTGGCTCTGGGGGTGATGTGATCCGCGCCATCCGTGAGCTTAGCTACAAGGGGGGCAACACTCGCACAGGGGCTGCAATTCTCCATGTGGCTGACCATGTCTTCCTGCCCCAGCTGGCCCGACCTGGTGTCCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270-COL7A1:NM_000094:2
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:
PF0009223=VWA=PU(29.5=83.6)
A:
NA
C2:
PF0009223=VWA=FE(30.6=100)
Main Inclusion Isoform:
NA
Other Inclusion 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:
GACCTGCACGCGCCTTTAC
R:
GACACCAGGTCGGGCCAG
Band lengths:
334-1005
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)