HsaINT0039123 @ hg38
Intron Retention
Gene
ENSG00000081052 | COL4A4
Description
collagen type IV alpha 4 chain [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr2:227002711-227008304:-
Coord C1 exon
chr2:227008018-227008304
Coord A exon
chr2:227007589-227008017
Coord C2 exon
chr2:227002711-227007588
Length
429 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
CTCTCTTGTTTTCTGGGTAGCAC
3' ss Score
6.96
Exon sequences
Seq C1 exon
GTCTGGCAGGGTCTTGCCTTCCCGTATTTAGCACGCTGCCCTTTGCCTACTGCAACATCCACCAGGTGTGCCACTATGCCCAGAGAAACGACAGATCCTACTGGCTGGCCAGCGCTGCGCCCCTCCCCATGATGCCACTCTCTGAAGAGGCGATCCGCCCCTATGTCAGCCGCTGTGCGGTATGCGAGGCCCCGGCCCAGGCGGTGGCGGTGCACAGCCAGGACCAGTCCATCCCCCCATGTCCGCAGACCTGGAGGAGCCTCTGGATCGGGTATTCATTCCTGATG
Seq A exon
GTGAGTCCCGTGCCCTTGAAAACCCTGGCTCATTCACCATTTCCTAACACCTTCTCCCGCCATTTCTCTCTGGATTGGACAGTAATTCTGAGCACTCTGCGCTTAGGACATAAGGTTACGGGGACTGTTGCAAACCATAGCCTGTTGGGATGCAGGGCCATTATCTTTTAAAAACACTTGTGATTGATTTTGATCACATTGGTAGAATTTAGAAGATGAGTTTGCTTCAGCCATCGGTGAAACTGGAGCCAATTTGTGTGCATACTTACCATGCTGAGTACGACTCCTTTTCAGCGCTTGTATTTTGTTCTTTATGGAATAATCTAAGGAAAAATGTTAAGATCAGACCCAAACCTGGGTGTGTCCCTGATTGGGTCTGGGGTTGTCTGTGTGTGTCTGAGCCCTAATTCTCTCTTGTTTTCTGGGTAG
Seq C2 exon
CACACAGGAGCTGGGGACCAAGGAGGAGGGCAGGCCCTTATGTCACCTGGCAGCTGCCTGGAAGATTTCAGAGCAGCACCATTCCTTGAATGCCAGGGCCGGCAGGGAACTTGCCACTTTTTCGCAAATAAGTATAGCTTCTGGCTCACAACGGTGAAAGCAGACTTGCAGTTTTCCTCTGCTCCAGCACCAGACACCTTAAAAGAAAGCCAGGCCCAACGCCAGAAAATCAGCCGGTGCCAGGTCTGCGTGAAGTATAGCTAGAGAATGCGAAATTCACCAACACGTGGCCAAGAGAAACTTCCTAGGGGGCTAAGACTTCCTAGACTGTGCTAAGAGATGTCATGGTGCTCATTTTGGACTCCCTTTCAGTGGTTCCTTCTGTTTTGTCGTGGTTATTCCCAGAGTCCTCTGGTTCCTTACACATTAAGCAAATGCTGCACAGATGGATTTGTTTGGACCTCCCAATCTAGGGAGCCTAGATACTCTTATTTTACTGAGGATGATCGAAGAACTGGCTTTACTTAAAAATATGCTAATTCTCAGAAAGGCAAGTAGATGATAAAGGCCAGATTACAAATTACATTACTGAAAACTTCATTCTTGGGTTAACAGTATCTCAAACAATTGAAGTCAATTACTCTATAATACAGTGGGCTTCTGGATGGATTTTATAGGAAAAAATAAACAGGTCAATGAATGAAACTAGAAAGCAGAGATTTTCAACATTTCAAAATGATTTCCTCTGTAATCTATTTTTCCATATACTTTAAATAATGGTAAAACCATGACGCAAAGAGAGATTTTTTTTTAAAGAAGAAAAAAAAAAATTCACACTGCCAGCGTTAACAGTTCCTTTCAAAGGAGAATGAATCATGATGGCAGGAAGGCCCACAGTCGCCGTATTCCAGAGATGCGACATTAGCATAAACACATCACAGATGAATATAAAACATTATGTTCTCTTCTGCATTTTTCAGAGAATAGAAATGCCTACTTTGGCAACCCTTTTGAAAAGTAGCAATTATGGAAAAAAAATATTCAATAAGAGATTAGGAGCCTAAAAGCTATTAGTGAATATTAAGGTAGTTATTCACAAAAATTGACTCCCCATTGCAGTGAACTTCCAGACAGACTGCTTTTCCCCAGTCGGGGTCCGGCGTGTCACAGGTGCGTGCGTGCTAATGGGACTGACGCTACATGGGGCTCACTCAGGCAGGCACGCGCTTCATACAAAGCATCTCACTCCCCTCCCCAGGAGAGCCTGCACAGCTTCTTGCACTCACAACGGACACTTTGCTCCACACACATAATGGCAGCTCACACAGGGACGTGACAGAGCTATCATTATGCACTTGGGAGAAAATTAAGGGCCGATTTAATTAAACTTAGGTAAGAAGATTCATTTAAGTCAGGGTTACCCCATCAGGAGGACATGGCACTATCTTTAAACGAAACAAAGACAATTTATAATTTGAATTTTATGCTCCCGTGGTTGGCTGTTACAGGAGCATCCCATTTTGCCAATTTTAAAGACATTCTTATATTTCATATCAGTCTTGTACCAAGGCAACAGTTTGACATTTGGCATTAGTATTTTCTAAAAAAGTTTAGAATGTGTGTCAATTTATAATGATTATTTTTTTCTGTAAAGCAAAAGATCCCTTTTTCTGTTTTGCTAGGAATTTGGTGATCTAATCCTAAATTTAAAAGATTTGTTGGAAAAAATTTTTAGGAAACTCACCTTCCTCATCTAAAAGAAAAAGGCATTTTAGAGAAAACTAAAGAAATTTCTCATGAGCGTGACACTCATTTTAGTGCTTTGTTTCCGTGCACTTAAAAATAATTGAGAAGAAAAACTCAATTAAAATTTTGTTTATAAGAAATGTTTTCCTTGCCAAACCTTGATTTGTAATGAGCTCTTATATGCAGAACACATTTCAAATGAGTTTTGCTATGGGCTGCCCCCAGGGTGGCAATTTATTTTAAGAGTATTTTCTGGTAAAAAGAAAAATGTGTATTTTAAGATGAAATATTTTCTTGATGTAGCAGAATATTTCCTAGTTCATTTGACCCATTTGATATTTTTTAAACCATGCTCTGGCATGTTGAATATTTTTGTGCACCTAAAACTTAAGCCAATTTCAATCTTATTTGTGATTACCTTTCTCCTTCCCAAAAAGCTTTATCTATTACCAAAAGTCAACCCTCCTAAAAGTTCAACCTGTTCATCTTGAACTTGGCCTGAGAACATTTTCTGGGAAGAGGTAAGGGTGACAAATGGAACATCAGAAACGTATCTTGCTTGCTAATTATTTTAAACACTTTAATGTTGGTATTAGAATATTATCTTCATAAGTTAATAAATAAGTAAAAAAAAAAAACCCACACAAAGACAGGCTAAATTATGTAGACAGTTTACTCCACAGTGAGCTTGGGAAGGTATCAGACTGTTCAAAATGTTAGTATTACAAGAGCTGTCTCTAAATGCAGCATTAACACTGCCCTCTAATTTTACAAAAGTATTTTAAAGGATCAAAAGGGCGGAAAAATAACTTCTTGGAATAGAAGATCCTGTTACCTTAAACCATTATTTTCTTCACCTGGTTATATATCAATGTGCCTTCAATTACCCTTTCTCTGTGGAGGTGATGAACAAAGCTTTTAAGTTGTTCTCCTAACCCATTATTGGAGATGATCCTTATCAAACCCTTCTCTCCCTGCCTCCCCACCAACCTTGTAGACTGGAACGTGCCTAGATTGCCCTAATGGGAACTGTTCTGTTCTGTGCCCGTGCTGGAAATCTGGGATGCTTCCTTCTGGGTTCTGATTCTCAGTGAGTGGAGCCCATTCATCCAGGCAGGTTTCCATGCTATGAGTGGCCCTTTCGTTCTGCTCTCACACTCCCCACATTGAAAGCTGAGTCATCGCTGCTTTGGATGGCTACCTCCTCTTTAGCCCCGTGCCCGTCTCACACAGCCTTTGTTTTCCACCTCCACCCTTGCAGTAGGCATCTCCCAGTTGGTGCCTTAGTTTCAAATCCCAGTTGCCATCTAAGATCCACCCAAACTTGATTTTGTCACCCTCTGGATTAGAATCCTTCTGTGACTCCGCTGCCCATGAAGTCCAAATGACTTCCTATGGGGTGAAAGGTCCAGTGGGGACTGTTCGAGGGTTCCCTCTAGGAGTATTTCCTGTCATGATGAACTGTGTGCAGCTCTGCAGACACTCCCAGCACCTCTTCGACTTTGCTCCTGCTTCACCAGTGATGTCCTCCCTGGGGTCAGTTTACCCTGCGTGGGAGGTGAATTCCCTGGGGGAAACTTAGGCTCCCTTCTGCTGCTCTTGTGCAGTGCACGGGGCTGTCCTCATTTTCTCCGTTCCCCATTGCTTCTTTAATGTCTCAGTGCACTTCCTTCATTCCATTGCCAAAATGCAAGCCCCTTGAGGGCAGGGACCATGCTTGACTCGTTTTTGTATGCCTAATGCCTAGCACAGAGTTGAACACATTACTGCCAATTCATTTTTTTCAATGACAATTCCATAAACATCATTAGGCATTAGGTGTTCAGCTCTGCATATAAGGTCTTCATCAGCAAGACGGTTACAAGTATAAACCATTTCCTATTTCAGAATATTTTAATATTCAACATATTTGTATACCCACATTCTCTTGTTACAATTATTGCCAGAAAGCCAATTGATAAGCTTTCAAAATGGGCTTATCACACCCCTCCAAAAATAGATTTTTGTTTTTTCTATAAACAGAAATTTCAGAAATGAGATTTGAGAGATCCGACTGAGAAGACCCTTCAGTAAAATGTGACATGACTTACCTTATGCTGTAATCTGTATTCCCTCAGGATTTAAGAGCTTCCTAGCATAAAATCTTTGCTAAACGTTTGTGTACATGTTATTGGTGCTCCGAAAAATAGTCAATGGAATGGTGCACTACAATTGGGCTTTATCATCTTATTTTGAACCTCGTGTAGATTACAGTAAAGCAAACCATTCAGTGTGTTCCAGGAAATTATATTAGATCTGTGTTTCTATCAGCTCACTGGAATAATCTGATAATTGTTACTTTTACTTGGTATGGCTGCAAGAATAGTGGAAAGAAGAGGACTTGAGAGTTGGTCGAACCCAGGTTTGAAATCTGGCTTAGTCATTTTTCAGCTGTTATCCTGGGTGAGTTTTGCCAACTTTCTTAGCTTCATTTCCCTCATTAATACGGTGGGACATAACAGCTACTCTTGCATTGAAAATTAAGTTAGATTACCTGTCTAGCATACCCATCATCATACACTTACTATGGTCACATTTTGTATTTAAAATAAACTAATACGAAAAATATTTCTTTTTTTTTACACAGAATTATGATTCTCACAGGGTATATAAATTACTGATTAGAATTATTTATATGTGGCCAATTCTTAATGTCATTGGGAATGCTGTTTCATTTCAATCCTCAAAGTTACTGTAGCACAGAAAATATCACAATTTCCTGCAGGGACATTATCAGTAAGTTCTGCAGGGAACAAACAATTGACATTAAAAATCAGTACTCTGCAATTGTCACTGTTATCATCTGCTAGAAACTCTGCATAATGCATTTTAAACCACCAAGGCTGGCTGCCACATCCATGTGAAATGCTTGAATTTTATGGTGCTTAAATATTTAATGATTCATGGGAAAAATGTGAAATGTGTCTAATAAATTGCATCCCTTTCTCTAACCTCTGGTTGTAAAGTTAAAGACTTTCAGCATGTAACTTTTGCAAGATGCCTGGTCTGCCATTGGCACTTAAATATTTGTTGTATTACGATTTATAATATGGTTCATTATATATAAAATTCTGTGATGACTTCCAAAAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000081052:ENST00000396625:47
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.034
Domain overlap (PFAM):
C1:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.6=31.2)
A:
NA
C2:
PF0141314=C4=PD(72.6=96.6)
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:
ATCCACCAGGTGTGCCACTAT
R:
GCGAAAAAGTGGCAAGTTCCC
Band lengths:
356-785
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