HsaINT0039006 @ hg19
Intron Retention
Gene
ENSG00000134871 | COL4A2
Description
collagen, type IV, alpha 2 [Source:HGNC Symbol;Acc:2203]
Coordinates
chr13:111158762-111160568:+
Coord C1 exon
chr13:111158762-111158953
Coord A exon
chr13:111158954-111160281
Coord C2 exon
chr13:111160282-111160568
Length
1328 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGT
5' ss Score
6.86
3' ss Seq
CATGACCCCTCCTTCCACAGGGC
3' ss Score
11.32
Exon sequences
Seq C1 exon
GTGCACCAGGCCGTCCAGGGAGCCCGGGCCTGCCGGGTATGCCAGGCCGCAGCGTCAGCATCGGCTACCTCCTGGTGAAGCACAGCCAGACGGACCAGGAGCCCATGTGCCCAGTGGGCATGAACAAACTCTGGAGTGGATACAGCCTGCTGTACTTCGAGGGCCAGGAGAAGGCGCACAACCAGGACCTGG
Seq A exon
GTAGGTACCTCCCACCCGGCCCCCGTTGCCTGCTCAGGGCTGGCCCGGAAGTGGCCAAGATCAAAGGGCCACAGCGAGACTCCCAAACCCTCCACGGCTGGTAAGTTCCCCTGACGGAAGGGTCCATCTACATTCCTCGAGTGCAGAAAGATTAAAACGGCCTTTGAAGCAGAAGCCTTACAAAGCCCTTAAACCTCAGGACCTTAACACAGGGACCTGCCTTTTAACCTGGTATTGACTTCCGCAGGCTCCCATGTGACCCGTCTGACCCCCGACCCCTCTCCAGTGGAGACCACCAATTACTTCACCTCCTTCTTGTTTTTGACCCAAGTTCTGTAGACTTGGAGTCAGGCAGGGGCCATGAGGGGCTGGGGTTCATGTAAGACTCTCCCATACAGCCCCCCGAGGAAAATGGACCCATGGACACGTGTGCATGCTCTTATTTAAGGAAGCCTTTGAAAGGCATTAACGCGACTTCGAATACAGAAAATGCAATACACACAAATTACAAGTGGAGGTAGCTTAGTCTGAGGTCCTCTTTGAGGGGGTGACGGGAAGGGTCTCTGGGATACTGGCTGTGTTCTGCCTCCTCGGTGCAGGTTACATCAGGCGTTCTGCCCCCGGGAAGCATGTTGCTGGCTCATGGTGCCTTCACATTCCTGCCTGTGCGCCCCGCCTCCACAATGAGTTTCTAAAGAACAACGGGGCAAAGGCCGCCAAGGATAAGGGCCAAAAATAGATCTAGGAACAGGGCCAAGGAGGCAGCCTAGCACCGGGCATGTTTGCTAAAGGTGGCTGCACTTCTGGGTCTGAGCTTTTCAGCAATCCATGTGAAGAGGGAAACCTGCTTAGCTGCAGCATTCGTTGTGGCCAGGAGATAAAGGCTATCTTAGTCTCCAGAAGCAATAAAGCTACATGGAAGGGAGAAGGGCCAGGACTCCTTCTGGGGTGGCTCCTTGGGGTCAAAGAGCGACCCCTTGGAGGCCATCAGAGTTTTCTTGGGGCCAGTGCTGTTAAGACCCCACTAAGGTAAGGCTCACCCAAAATGCTATTCCATGAAGACGCCACTCCCTGGTGATCCAACTTGGCCCAGTATGTGTGAGAACTTGTAGAAGAACAGAGCTGTTCCAAAATGCCAGTGGAGTCTGATCAAAAAGAGAAAAAGAAAGAAATTGGGAAGCCTTAGCCTGGCCCTCCAGTAGGTGGCTAAACTCCACCAGGTGCCCTGGGGCGAGTCCGTGACACACAGCCTCCTGGGCCTGGCTGGGGCTGGCAGGTGCGTCTTCTAGCCACACTGCACTGTGATCTCATGACCCCTCCTTCCACAG
Seq C2 exon
GGCTGGCGGGCTCCTGCCTGGCGCGGTTCAGCACCATGCCCTTCCTGTACTGCAACCCTGGTGATGTCTGCTACTATGCCAGCCGGAACGACAAGTCCTACTGGCTCTCTACCACTGCGCCGCTGCCCATGATGCCCGTGGCCGAGGACGAGATCAAGCCCTACATCAGCCGCTGTTCTGTGTGTGAGGCCCCGGCCATCGCCATCGCGGTCCACAGTCAGGATGTCTCCATCCCACACTGCCCAGCTGGGTGGCGGAGTTTGTGGATCGGATATTCCTTCCTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000134871-COL4A2:NM_001846:46
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.292 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(36.2=32.3),PF0141314=C4=PU(39.8=66.2)
A:
NA
C2:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(26.1=31.2)
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:
CCCAGTGGGCATGAACAAACT
R:
TATCCGATCCACAAACTCCGC
Band lengths:
357-1685
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)