HsaINT0038464 @ hg19
Intron Retention
Gene
ENSG00000164692 | COL1A2
Description
collagen, type I, alpha 2 [Source:HGNC Symbol;Acc:2198]
Coordinates
chr7:94030879-94033912:+
Coord C1 exon
chr7:94030879-94030932
Coord A exon
chr7:94030933-94033867
Coord C2 exon
chr7:94033868-94033912
Length
2935 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGC
5' ss Score
7.14
3' ss Seq
TATATCTGCTTTCTTTACAGGGC
3' ss Score
11.13
Exon sequences
Seq C1 exon
AACTTTGCTGCTCAGTATGATGGAAAAGGAGTTGGACTTGGCCCTGGACCAATG
Seq A exon
GTATGCTTATCTGTTTATCTTAGCCAAAAAAATTGCTAAATAAATCATTCATTTTATGTCACATTTTACCACGCCATTTATTTAGCTACCTAAGTTAACACTCAATACTTAGATTATATAAAAACAACTCTTTTTGTTTTCAAATTTATGAAAACATAAGTTAAGGAGTTCACTTTTCTTTACAAAAGAAAGATTAATTGATCTTTTATGATTATATGATCTTTTTGATTATATGATCCTCATTAAGATAGATCATATACTTATGTCCAAGAAATAATCTTTGGACATAGTAACCATAACTTGGGCAAATCAATTTAATTTAAAACAGTAATCACTCTGATTAATTTTTTAATATTCTTTAACATTGCTTAGAATTTTAAGCAACACTTAGAGGCATAGAACTATTTATTAAGTTCTCTGAACTTGTTGGAAAGGATCAACAAGTTCTATCTAGTCCAGCTAACTCATTTTAAAATGGGAGAGTTTAAGCCCTTTTCTCAAAGTCATCCAGGTAACTAATGACATAACTAGAACTAGATGCCAGGCAAGATGTCTAATATTTGCTTACATCATGGTTTATGTACCTAGTCCTTGAATAAACCACTCATTTAGTCAACAGATATTAATCAGATGCCTTCAATGGGCCCTAAACTGTATTAGGAACTGGGGAAATTACAAGGAATATGACAGATTCTGATCCTTCCTCAAGGAGTTAACAATATAGGAAATGTTTCTTTTTCTGAATTTTGACCAAAAAAATCCTTTTTTAGTCTATTGATTGTAAATCTATATAGAAGAGAGTATGAGTAAAAATCTAGCATTTATGTCACTCAGTACAAATATTCAGCACCATACCCTATCAGTGGAGCACCGCTTAGAAACATTCCCTATATGATGATGATGATGATGATGACTATTAACAAATGAAGCTTCTAACAAGCATTAGAGAGAAGTTTGAAGGGAAAAATGCTAATACGAGCATGCAAAATGTATACTAGCATATATGAAATAGAGGGGAAAACTGCCAGAAGTCAAAGTGTTAGGTTGATTAAGCACTACAGAATTTAATGTATACACACACACGCAATTTAGTGATTTTAATTAATTGTTTCAAAACAAAGGTATTTATCTGCCCAAAGTCAACAAGGTCTTTAAAATGTAAATTTTACCTGGGCAGTGCACTTAGTGCTCTATCTTCAAAAGAAGATGTTCTGCTGGAGCTAATGGCCCACAGTAAGCTAATATACTCTAAGGGTGAGATAATATTTTCTGTAAATTAAAACTCCCACTTGAGAAATAATGTACCTTTAATTGACGACTTCTAATTCCCTAATTTTTTCTGGTAGTTTAAAATGTTCATATCTGAAATGAAAAAGTAGAGTGTTTCTTTTGGCTTTGTTTATATTGGATTTTTGAAATTAGCTGTTTCAGCTAATGCTGGACATTAGTCAGTTTTAAAGCAGTACCTACATCTCAAGAAGAAGCAAGGGGGCGGAAAGTAAAGAGCTACTAAATGTCATTTTTAAAAAGCCCACTAAGCTGGGAAAATTAATATGGATTTCAGATACCCCTGTTTTCGGAACATCTGTCTTGGCATAAAGCAGAGTATTTTACTTTGAAATATCAGTGAAATATAATTTAAGCTTGCACATCCACACACATGCACAGACATATGTAATCAACAGATATCTGTTTCACAAATAGGGAAGATAGGCAGCAATAAAGTATTAAAATAATTTCCATGTTGGAAAATCAATAACTATAAAACCCCACAGGGTTCTTCTCTGAATTAATGAGTAATCACAGCCTCCATGAAATACACTACATTTTATGTAAATGAAATTGTTGCAAATACATGAAAAAATAAATATAATTAGAAATTCATGATGTCAAAGAAAATTATTTTTTAATGTATGCCTAAAAAGCTATTGTGATGGAAAAGTGACAGTTTCTTTTAATGTCAGAGCAATTTCTAAAACCAAATGAATAATTCTTATAATTAAAATGACATACATTTTAGATAAAATCCATGTTATTTCACTCTAGGCATTAATACAGTAAGGTAGGTTTGACTGCAGAGTCCCCACAGCTGATGTCATGAACAAATTACTTGAGACTGGTACATGAAATATTTTCAGCATTATGAGGAACAGACCCTACGGATGAGCTTACACAGGCACTGATTACTGCAAAGAGGAGTCAAGAAAGTGTATTTAGCTTACAAACTATTAACAGCCTGTTTTACCCTACTTTTGTGCTATGGAAACAACAAAGGGGAAAACAATCTTCCATCATTTGGGCCATATTTTCAACAATAATATCATATAATAGACTCTTCCAGAAGGCTGTTTCAATAATGTTTTATTTTTCCTTCACCCCTCATTACATCCACTTTTGTTTGACATTTTCATCAGTCACCAATAACCCTTAGAGGAGCGATAAGGTTATAACAAACTTCTCTCTAATCATTAAGAAGGACTTTTGATTCTTTTCAATTTATGTCCTTTGTGGCAATAAAAATACCAATTTCTTAGCTAAATATGACATAGGAAGATGACATATGATCAAAGATATCCAAATGGACATGCTTCATCTGCTGTATAGAAGACAATTGTATATTCTGCACTTCTGCAAAGACTGATTCACTTCATTGCATCAGAACAATCTCAATATGCCCAATTGTGCACAACTTTAAGGAACCTATCTGCCCCGTCTAATTCTCATTGATTTCTGTTGATAAGGATTGGGAGAAAAGGAAAAGCAAAGGGAGAGAACTAGTGCAGGAAGTTTGAGTCCTTAAATTCTTCCTTGGGAGGAATAAAAACTATGGAATCAAACCACAACAATGGCACTGCTAAGTTGGTCATATCTGACCCCAGCCAACACCATGACAACTTATCAGTGCTAACTGTTGATATATCTGCTTTCTTTACAG
Seq C2 exon
GGCTTAATGGGACCTAGAGGCCCACCTGGTGCAGCTGGAGCCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000164692-COL1A2:NM_000089:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(11.1=33.3),PF0139113=Collagen=PU(7.9=27.8)
A:
NA
C2:
PF0139113=Collagen=FE(22.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)