HsaINT0039098 @ hg38
Intron Retention
Gene
ENSG00000081052 | COL4A4
Description
collagen type IV alpha 4 chain [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr2:227077894-227080549:-
Coord C1 exon
chr2:227080443-227080549
Coord A exon
chr2:227078078-227080442
Coord C2 exon
chr2:227077894-227078077
Length
2365 bp
Sequences
Splice sites
5' ss Seq
CCAGTATGT
5' ss Score
5.8
3' ss Seq
TCATGACATAACATTCCCAGGGG
3' ss Score
2.71
Exon sequences
Seq C1 exon
GGCACAAAGGAGAAAGAGGTCCTGATGGGCCCCCAGGATTTCCAGGGCAGCCAGGATCACATGGTCGGGATGGACATGCTGGAGAAAAAGGGGATCCAGGACCTCCA
Seq A exon
GTATGTAGAATTCTTCTCTTGCTATAGAATTTCACTTTCTTATATGGTCATACAAACAACTATTTCCCCTTTCTCTATTTGCCAAGCTGAAATTCAGTAAAATATCAACATACTATAAATCAGAGTCACTTTTGGCACCCTGACATGGAAAGATGATTGTTTTAAGAGGTATAGCATCATTGGACATGGTCTAAAATCCTCTTGGCAGTTCAGTCCTAGCAGGACTTTCGGTCCTTGGTCTTTATATCATTCTCGTGGTGTTCATTTTCTTCTGAGAAACTTGTATCCTAGAAGGGCCCCACTGATTTTAGGTGTATTCAGTTGACTCTGTGGGGTGGAGGATGGAGCTCGGGTCCCGATGTTTAGCATCAATTCTGTTTCCTGGAGAAGATGCACATGGGGGAAGTAGTGAGCATGAAAGGGTGAACTCGTGCAAACCCACAGAGTCAAGGCGTTGGCTGATGGAAAATCTCACTGATAAAGGATGTTGCTGCATTTTTCAGACATGCGTTGGGTGGATACCATGTGTAGGTAATGGTAATTAAGGTCATAAAAGAAGAGGATGAGATGATCCGATGCTTAGGAACTTAAAATATCTTAAATATGTGCAGTATTTCTGAATGCTTACAATATCACAGAAACCAGACTAGATGGTTTCCTCAAAACAGTCTTCTGAAAAGCAATACCTTTCCAATTTTACAGTAAGAAAATGGAGGCTTAGCATCTGATATTCAAGGCTACCCATCTGTCAAATAGGCAAAATAGGAGTGAAAACTTGTCTGTCTTATTTCAAAGTGCATGCTATTTCTACCAACCTGTGCTGCCTGCCATATATAATGGGAAGCCACTGAGAGTGTTGCAACAGGGAAAGACCATGTCCTGATTCTACAGGAAACCCTTCAGACAGAATCCAAGTGAACAAGAGAGAGAAGCCTGGAAATTGGCTTAGATGGTGTTTATAGCTTTCTGACCTTTCTCCTGATCACAAGTATGTGAATGATCTCTGCTTTAGGCTTGGTAATCTCTGCTTAATTCATTCTTCCTCTCAAGGAACTACTTAGAAATCACTGTCACTGAGTGGATATTGTCATAATGTACTCATCTAATTGTGAAAAAGCAGCGTCTATATAGATCAAACTAGGAGACGAATTTCAACGTTCGCTGAGGTCTTCCTAGATTCGTTGAAACAATCCAGATCCATAAGACTGTTGTAGACCACATTTGAGACCAGGCCATGTAGAAGGATAAAAGGTCACTCAAAATGCCAGCAGGACAGTGTCAGATATTCCTTGCATTTGAGAGTGCTTGCAGCTGTTCAGTCAGGTGGGGTGCAAGAAGGGATGAGACCCACATATGGTGGGCATGGAGGCAGCCCTGACTTGAAAGCCTCATTCCCCATGGGAGCTGTTATCCACTGCACAGCTTTTGAGAACCCCACCAGGGATTGCCAGTGAGGGAATCCTTGATGCAGGCTCCCCACAGTTCTTCCAGACCAGATGCAAATTTTGCAACTGGGGATTGATTTTACTATAAGCAGTACTGCCTAGGAAGGTAGTTGACAATCTAATTTTTATCAGAGGAACAGAACCAGACAGTTAACCAAAAGTCAAATTGTCATGCAAGAGGAGAAAGGACTTGCTAGGCTTTTACCCACAGGGGTGGAGGATGATGGAGTCTAGCTATGTATCTTGTCAAGAGAATACATAAGAATGTATTTGATTTGTAATCCCACCACCTCCCTTGATCTACTTATTTCTATATTCTATGACATATGATATTAGAGAATGGTTTGACATAAATCTCTTATTCTGTATTTAAGGCATATCACACACATTGTTTCCAGTATTTGAGGCTTAACACACATGCTTATATTATATGTATGTATATAAATTGTAAAATGTGTATATTGGCCAGGCGCGGTGGCTGACGCCTGTAATCCCTGCACTTTGGGAGGCTGAGGCAGGTGGAGGTCAGGGGTTTGAGACCAGCCTGGCCAACATGGCGAAACTCAGTCTCTACTAAAAATACAAAAATTAGCCAGGTGAGCTGGTGGGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGTGGAGGCTGCAGTGAACCGAGATAGCACCACTGCACACCAGCCTGGGTGACAGAGAGAGACTCCATTTCTATATATATATATTTAAAATATTAAAAAGTATCTAAGTTATTTATTTTAAACTTACATTTGCTTAAGAGTAACTGTCTCCTGAAATTATGGACTTTTGCGTGTGTTTCTGTAACCTACAATGACTGCTTTGAGTTCATGGACATTCAGTGGTTGGTAATTGACTCATGACATAACATTCCCAG
Seq C2 exon
GGGGATCATGAAGATGCGACCCCAGGTGGTAAAGGATTTCCTGGACCTCTGGGCCCCCCAGGCAAAGCAGGACCTGTGGGGCCCCCAGGACTGGGATTTCCTGGTCCACCAGGAGAGCGAGGCCACCCAGGAGTTCCAGGCCACCCAGGTGTGAGGGGCCCTGATGGCTTGAAGGGTCAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000081052:ENST00000396625:24
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=FE(56.5=100)
A:
NA
C2:
PF0139113=Collagen=PD(11.3=11.3),PF0139113=Collagen=PU(93.3=90.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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