HsaINT0038464 @ hg38
Intron Retention
Gene
ENSG00000164692 | COL1A2
Description
collagen type I alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2198]
Coordinates
chr7:94401567-94404600:+
Coord C1 exon
chr7:94401567-94401620
Coord A exon
chr7:94401621-94404555
Coord C2 exon
chr7:94404556-94404600
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:ENST00000297268:6
Average complexity
IR
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