HsaINT0039123 @ hg19
Intron Retention
Gene
ENSG00000081052 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:2206]
Coordinates
chr2:227867427-227873020:-
Coord C1 exon
chr2:227872734-227873020
Coord A exon
chr2:227872305-227872733
Coord C2 exon
chr2:227867427-227872304
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-COL4A4:NM_000092:47
Average complexity
IR-S
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
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
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)