HsaINT0039638 @ hg19
Intron Retention
Gene
ENSG00000114270 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:2214]
Coordinates
chr3:48601506-48602413:-
Coord C1 exon
chr3:48602216-48602413
Coord A exon
chr3:48601856-48602215
Coord C2 exon
chr3:48601506-48601855
Length
360 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
TTCCAACCTGTCCTCACCAGGTA
3' ss Score
7.98
Exon sequences
Seq C1 exon
ACCCCTGTTCCCTGCCACTGGATGAGGGCTCCTGCACTGCCTACACCCTGCGCTGGTACCATCGGGCTGTGACAGGCAGCACAGAGGCCTGTCACCCTTTTGTCTATGGTGGCTGTGGAGGGAATGCCAACCGTTTTGGGACCCGTGAGGCCTGCGAGCGCCGCTGCCCACCCCGGGTGGTCCAGAGCCAGGGGACAG
Seq A exon
GTATGGGCTGAGCCCCCACCGTGGGGAACTGGGCACTGAGCCTGCCTGGATCGGGTTCTGGGGGAGGAGTCCTTGGGCCAGGGTTCCAGGTCAGGGTCCTGGAGGAGACGCTCCCTCGCAGTAGGGGACCTGGGGCAGACGCCCAGACCAAAGAGCTGAATATAGAGCCCCAGCCGTGGAGCCCCCAGTAGGGTCCCCTTCCATGTTCCCTCCTTTAAAGACCTAAGTATGGACCCCTCTGAGGTCAGAGCCCCCACTTCCTGTTGTAGCCTCCGCTCCCTCCCCTTGGCGGTGCCTCTGCCTGAGCGTCTCCGGGGAAGGTCAGATGGCTGACGACCGTTTCCAACCTGTCCTCACCAG
Seq C2 exon
GTACTGCCCAGGACTGAGGCCCAGATAATGAGCTGAGATTCAGCATCCCCTGGAGGAGTCGGGGTCTCAGCAGAACCCCACTGTCCCTCCCCTTGGTGCTAGAGGCTTGTGTGCACGTGAGCGTGCGTGTGCACGTCCGTTATTTCAGTGACTTGGTCCCGTGGGTCTAGCCTTCCCCCCTGTGGACAAACCCCCATTGTGGCTCCTGCCACCCTGGCAGATGACTCACTGTGGGGGGGTGGCTGTGGGCAGTGAGCGGATGTGACTGGCGTCTGACCCGCCCCTTGACCCAAGCCTGTGATGACATGGTGCTGATTCTGGGGGGCATTAAAGCTGCTGTTTTAAAAGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000114270-COL7A1:NM_000094:117
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.209 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0001418=Kunitz_BPTI=WD(100=83.6)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGCCTGTCACCCTTTTGTC
R:
CACAGTGAGTCATCTGCCAGG
Band lengths:
348-708
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)