HsaINT0038102 @ hg19
Intron Retention
Gene
ENSG00000187955 | COL14A1
Description
collagen, type XIV, alpha 1 [Source:HGNC Symbol;Acc:2191]
Coordinates
chr8:121381569-121384273:+
Coord C1 exon
chr8:121381569-121381724
Coord A exon
chr8:121381725-121383390
Coord C2 exon
chr8:121383391-121384273
Length
1666 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
CCCCCACTTTTCCTCTTTAGCTC
3' ss Score
10.22
Exon sequences
Seq C1 exon
GACCTTCAGGGGAGAGTCGGCCTGGCAGCCCTGGGCCCCCTGGCTCTCCTGGACCAAGAGGCCCACCAGGTCATCTGGGGGTTCCTGGACCCCAAGGTCCTTCTGGCCAGCCTGGATATTGTGACCCCTCATCATGTTCTGCCTATGGTGTGAGAG
Seq A exon
GTAAGTGTCACAAAAAGCCCCGCTTGTGGGCTTTGATCAATGTTTTAGTATGCTTAGTACCAAAATGGGAAGATAGTGCTATGAAAAAAGTTAAATTGGTTATGAATGGGAAGCAGAGCTTGAATGCCTCACTTCCTTAAATTATCCCGAGACATTTTCTATAAAGTGCAAATTGCTATAGAGGCTACTCCCTTAAAAACCTTAAGAGCAAATTCAAAATAACAGCACATCTAAGTCTTCCTTGCTTCCCAGTGATGACCTACATAGACTTGGCCTCTGACTTTGTATTTAGCACATTTGGAGGACATGGTTGAACATTCTTTTGGAGTCTCCATTCTTATGTGACAGCTGTGATGTGGCCAAGACGTCCCATAAAATTTTACTCTTGGTTTGGGGAAATGTCAAACTTAGAACTTCTCCCGTAATTAAGAGGGCTCCTTAGATTATTTTCAATGAAATCATGCATACCACTTGCATTTAGGTGCATTTAAGCACCACATTTTAGGTGACCAAGAATAGTTGTGAGAGGAAACAAAAATCATGCTGTCCTTGTCTTATCACTAGCTACTGGACTAAAAGAATATGCTTCCTAAAACATCTGCAGTGTGCATGCTGGCGTGCTGTGCAATGGCCCCTTTTCTGACATAGTCACTCTTGGAAGCATCAAGGGAGAGGCTGAGGGACTGCTGTGGGGCCATGAACTTACTAGTTAATGGGTTTAAAATTTTCTGCTTCAGTAGAAATTTAACCTTAGTTATCACAGGAATTGGTCAACAAAGTTTTGCTGATGTGTTTTTCTCTGTTCATCTTTTCCCTCCCTGTTCTCTCAAATACTCCTATCCTTATTAAGATCTGATCCCCTACAATGATTACCAGCACTGAAGTGGAAATCCTCCACTCTGGTTCCATTGGCCCCAGACATTTAGCTGTGGATACAGAACTGTCCTGTCAACCACCACCACCACCAAGCCCCTGCCCCTAACAATGGACACTCTGCTTCCCTGCTTCTTCTGCATCCCTGCCTTCCCACTTTCAAACCTCTTGCCCACTCTGCTCCAAACATGATGGAGTGATAACATCGGAACTTAACCAAATCATATATGTCTATTTTAATAGACACTGACTGCTCCATGTCAGCCTGGATAGAGGTATATGATCGTGTGCCAAGAATTTATCCCAGACTCCCCTGTGTGACAGCTTCATAATAAAGTTACTTAACTGTGCCTCTTCCTCCTTCCTCTCCCCACACAGGATGGATGGGCATCTTTCTCCTTGACCACCCTACTCTCCCTTCCTCCCCTGATCACCTCCCCTCCCTGCTCTTCCCTGGTGATGGACTTCTAACATGAGATTTTTTAAAAAAATTTCTATTTCTTTTATAATTTTGCTGAGTTTTCAGGGTTTCTTCTGTAAATAAAACATAATATTTAAATGGTTGGTTATGATTCTAGTTTTCTAACAATTTCTGTAATGTATCTTTCCCTTCGTCTATTTACTAACTGTCTGAAACCTTATGGGGAAGGTACAAGGGGCGTGGTGGATTAAGACATCCACTGCTTTTTACCCAGCAGGATATCTCTGTGTCTCTAAGGACCCAGGTGAGGGGAGAATATCAATTTATGATTCCTGGGTGCAGCAAGTCCCCACCCCCACTTTTCCTCTTTAG
Seq C2 exon
CTCCCCATCCAGATCAGCCAGAGTTCACCCCTGTCCAAGATGAGCTGGAAGCCATGGAACTGTGGGGCCCTGGAGTCTGATAGCCTCAGGAGAAATTTGAAGACCAACTGCAAGAACTCTTAAGGAATCTTGTTTGAGAAAATGTTGTTATGTGGTTTGTATGCTACTTTTGGGGGGCAGGGCTCATTTCAGCAGCCTAAATCTCCTCCTTGGATAATGTTAATATTATTATTATTATTAACAAAAAATATATATTTTTAAAAAGTTCCCTTAATCTATGACATGGTAGCAATGATTTCCCTTTGGTGTCTTAATGGCATGTCAGATAATTTGTTTTTCCAGAGAAGAGAGCTCAAAGAGGAATTGGGAAAAATAAATTGAACTCTGGAATCTTCTCTCTCAAGTCCTAAAATGAACAAACAGATATGATTGTGTTTGAGGGAAATATGTCCCTAGCAGGAAAAGAATTCAAAGAGGTTCAAAGAATATGTCACTTACTCCTACTTGCTGTAGGAATAACCTTGCTGATAAGAAAAAAAGGGACAATATTGGAGAAACTACCTCTTGTTTAATTGATCTGTCCAACTCTGAGATCACTTGGTAACTGGTTTCATGTGTATCCAAAAATCAGCATTTGGATTTAAGCTTTCTGAATTTGGTAGTTTAAGAAACAGATTTAGTTTTTCAGTGGTTTTAACTCATGTGAAATAATGATTTTCCACCAGCTCTGATGCAAAGAGATATAATTTTAATGAACGATTTATCCAGCAGTGTGTTCCAGGGGTTGCCTCTCCTTATCTACGGGGATTACTTTGTACATGCAGATAAGTTTTCGCAAACCTATTTCCATTTTCTTTTGTAAGCAAATAAAACTTTAAAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000187955-COL14A1:NM_021110:47
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.975 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(75.0=79.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCTTCAGGGGAGAGTCGG
R:
TTAGGCTGCTGAAATGAGCCC
Band lengths:
356-2022
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)