HsaINT0039122 @ hg38
Intron Retention
Gene
ENSG00000081052 | COL4A4
Description
collagen type IV alpha 4 chain [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr2:227008018-227010501:-
Coord C1 exon
chr2:227010313-227010501
Coord A exon
chr2:227008305-227010312
Coord C2 exon
chr2:227008018-227008304
Length
2008 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGG
5' ss Score
5.53
3' ss Seq
TCTCTTCTTCCCTTCCCAAGGTC
3' ss Score
10.39
Exon sequences
Seq C1 exon
GGCCTCCTGGTCCCATTGGGGATCCTGGGCCCAAAGGGTTTGGCCCTGGATACCTCGGTGGCTTCCTCCTGGTTCTCCACAGTCAGACGGACCAGGAGCCCACCTGCCCCCTGGGCATGCCCAGGCTCTGGACTGGGTATAGTCTGTTATACCTGGAAGGGCAAGAGAAAGCTCACAATCAAGACCTTG
Seq A exon
GTATGGATACAGGATCGCCCATCTCCATTGCCTGAAGAGTAAAATTTGGGGTTAATTTTACTGATTCATCAGCACCTTAAATGATCACTAACCTTATATGGGATTATTCTTACTTTTAAAACAAAAACACTAGCATGGTCATTCTCAGCTAATCCTTTAAACTTATGATCCTATGAAGTGTCAAAGAAGCTCATTCTGGCTATAATTATTATCTGGCTATAATAAGTATATTATTATTATCTGGCTAATAATAAGTATATTATTAGTTTTATAAAAATGATTCTTCCTCAGTAAGTTAAATGTAACTCTGTTATGAAATGTACTTTTTGCTTCCAAATGTAAATTAACCAGAATGTGGTCAGTTCCTGTACTTACATGTAAAATGGTGCAGCCACAGCACGCTGATGGTTGTGTTACGGCACTTGCCAGCATCAACTCCCTACCCTACTCCAATTTAAATTACAGAACTTTATTTTGAGGGTCATCTTTTGGTGCTCCTTGTCACTTCTCCGCTCTCCGCTCTTCCCCTCCCCTACCTTCCCCTCCCCTCCCCTCTTCTCTTCTCTCTTCTCTTCTCTTTTCTCTTCTCTTCTCTTTTCCTCTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCACAACCTTGGCTCACTGCAACCTCCACCTCCAGGGTTCGAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGAGACTACAGACTTGTGCCACCATGCCTGGATAATTTTTGTATTTTTAGTAGAGCTGGGGTCTTGCGGCCAGGTAGGTCTCGAATATCTGACCTCAGGTGATCTTCCCGCCTTGGCCTCCCATAGTGCTGGGATTACAGGTGTGAGCCACCGTGCCCAGCCCTTGCCAATTTTCAATAGTAGATTTGCAAGCTGCGGGACTGATTTCAAGTCAAAGGCTTAAGTACCTGGCTGCCGGGAAACACTGTCTTTCCAAGAAAATCATGGTTAGAATGGAAGGTGCAGGAAGGATATGCTGACGGGGACAGTTGACGGTGAGGTGCTTGCCATTGCTCTCACTAGGCAGTGACCCCAGCTGTTAAAAAGGGTAGTCAAAGAGTGCAAGCCTGGGCTGGCAACTACTTGTACATCCCCTGCATTTCTCCCTTGGGTTTGGCCATGGCCTTTCCCATCACAAGGGGCTAGTTTCTTTGAGCACAGGAGAAAGGAGGAAGTGATGTTTAATATCCTGAATCTGTTTCCTTCTCTCCTTCTCTCCCTCTGCCATCAATTTCTTTCCTGCCTGGTCTTTGTACCATCATCCGTCTTGCTTCTCCCACCTTGGTCTAACCAGAGCACACATCTTAAAACTCTGCAGAACTCTTGGGATAAAGTCCAAACTCCTTAACGAGATTGACAAAGGCCACATCCAATGGTCTGATTTATCACTGGACACTCCTGAGACAGACAGTGCAGACACCCTCTCCTCATAGTCCCTGCACTGAACATGTCTGAGTTCTCTGAGCTCCACGATCCCTTATCTCCAACCCCCTCTGACGGTATATCTCTTTTGAGTAGTCACTACCACCATCTCCAAGCCTGGCTAAATCCTCTTCATATTTCAAGTCCTAACTTAAAATCACATATTCCAGTTATCCTTCCTTGAGGTCCCGGATCCCCACACTTCTCATTCTTAGGGCTTGTTGTGCTGTATTTTCATTGCTTGTTTGCTCATCCAGTTCCCTGCTAGGCCATGAGCTTCCTGAACACAGAGATGTGCTTGGTGCCCACCTCCAGCACCTGGCCCCCTGCTTGGCTCGAGTGAGGGATGAGGGGATGAGGGCTGGCCCACAGGACCAGGGAGGTGTCAGAAATGGCTTCCTCACCACAGAAGCAGGCTTTGGCGAGGGCCTCCAGATTTCAGAACACGTATCTGCAAAGGCCAGATGGAGGAAGGAAGGGTCTGGGAACACCTACATGGGGTGCTTGGACACCAGCTGTCTCTTCTTCCCTTCCCAAG
Seq C2 exon
GTCTGGCAGGGTCTTGCCTTCCCGTATTTAGCACGCTGCCCTTTGCCTACTGCAACATCCACCAGGTGTGCCACTATGCCCAGAGAAACGACAGATCCTACTGGCTGGCCAGCGCTGCGCCCCTCCCCATGATGCCACTCTCTGAAGAGGCGATCCGCCCCTATGTCAGCCGCTGTGCGGTATGCGAGGCCCCGGCCCAGGCGGTGGCGGTGCACAGCCAGGACCAGTCCATCCCCCCATGTCCGCAGACCTGGAGGAGCCTCTGGATCGGGTATTCATTCCTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000081052:ENST00000396625:46
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.281 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(31.7=29.7),PF0141314=C4=PU(39.8=67.2)
A:
NA
C2:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.6=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:
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
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development