HsaINT0039006 @ hg38
Intron Retention
Gene
ENSG00000134871 | COL4A2
Description
collagen type IV alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2203]
Coordinates
chr13:110506415-110508221:+
Coord C1 exon
chr13:110506415-110506606
Coord A exon
chr13:110506607-110507934
Coord C2 exon
chr13:110507935-110508221
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:ENST00000360467:46
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.489 A=NA C2=0.068
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
Other Skipping 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