HsaINT0039118 @ hg19
Intron Retention
Gene
ENSG00000081052 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:2206]
Coordinates
chr2:227887221-227892725:-
Coord C1 exon
chr2:227892616-227892725
Coord A exon
chr2:227887228-227892615
Coord C2 exon
chr2:227887221-227887227
Length
5388 bp
Sequences
Splice sites
5' ss Seq
GGTGAGCTT
5' ss Score
-18
3' ss Seq
GCTACTCCAGTAAAAAATGGCCC
3' ss Score
-13.18
Exon sequences
Seq C1 exon
GACCAGTGGGATTCCCGGGACCGCAGGGACCACATGGATTTCCTGGGCCACCTGGAGAGAAGGGTTTACCTGGACCTCCAGGGAGAAAAGGGCCCACTGGTCTTCCGGGT
Seq A exon
GAGCTTCCAACCTACATACAGCATTTTGTTTAAACATTTACTAAAATGATCATCGTTCAGAAAGTAGTTAATATTCTGAATTACTAGCACATTCTTATTATTTAAGCCCTTTTCTTATATTAAGAGTATATTTCTTTCAGGCCGCACTACAAAGTCTCATGTTTGGTAAAGTAATAATTTATTGTCAAAATGAAAAAGTTTGAAAATTAGGAGTTGATTTTTTTTTACTTTATTTTTTAATTTTTTTCTATATATATATATTTTTTATTATACTTTAAGTTCTAGTGTACATGTGCACAACGTGCAGGTTTGTTACATATGTATACATGTGCCATGTTGGTGTGCTGCACCCATTAACTCGTCATTTACATTAGGTATATCTCCTAATGCTATCCCTCCCCCCTCCCCCCTCCTCCCACTCCACAACAGGCCCCAGTGTGTGATGTTCCCCTTCTTGTGTCCAAGTGTTCTCATTGTTCAGTTCCCACCTATGAGTGAGAACATGCGGTGTTTGGTTTTTTGTCCTTGTGATAGTTTGCTGAGAATGATGGTTTCCAGCTTCATCCATGTCCCTACAAAGGACATGAACTCAAAAAAAAAAAAGGAGTTCATTTTATATACACATTTTTTTTTCTATTTTTTTTTTTTTTGAGACAGTCTTGCTCTGTCATCCAGGCTGGAGTGCAGTGGTGTGATCTCAGCTCACTGCAGCCTCCGCCTCCTGGGTTCAAGTGATCCACCTGACTCAAACTCAAGTATCTAGGATTATAGGCGTGTGCCACTGCGCCTAGCTAATTTTTGTATTTTAATAGAGACAGAGTTTCACCATGTTGGCAAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCAGCCCACCTCAGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGTGCTTGGCCCACATAGACTGTTTCTAAGGGAAATAAATATGTGTTCCTTCATGCAAGAGGCAAAGACTGATTTGATTATTATTTGTTAGGATCGTATATTCAATTCCGATCCCTGAATTTTCATTGATTTTCCTAGATGTTTTATTTAATTTTTTTTCTGTAAATTCCATTCGTTCCTAGGAAGGGAGAAAGCTATTCAGTTTAACTCTATAGGCAACACTTTTTAACCATAGGGTCAAATTACGACAAGGAAGAGTTGGGGAGAGAAGGGGCAAACAGACATGTGTATTTGAGATGGGCAGAAGTAATATCTTTCAAGATCCTAAATCAATATTACGGTAATGTGGCGTCAGTTCAGAATATTTCGCAGTATCCTAAATTAGCACTCTAGTCCAAAGAATAAATAAATAGCACTGCTTTATGATGTATCATAGGACAGGAGGAACAAGGGCTTATATGTTGATTCTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTTTGTCACCCAGGCTGGAGTGCAGTGGTGCGATCTCGGCTCACTGCAAGCTCCACCTCCCGGGTTCACGCCCGTTCTCCTGCCTCAGCCTCCGGAGTAGCTGGGACTACAGGCGCCCGCCACCTCACGCAGCTAATTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCACCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGAGCCTGGCCTATATGTTGTTTCTTTTCATATTTCCTTTCTATGCATACCCTATACTTGGCAAATTAATATGAAATTTTCAGAAGCTTTTAAATGGATAGAATTCCTACATGCATTAAATTAGAGGATATTTGCCAGAAGAAATCAACTAGAATTTTATATTGCTCAAGAGAGTTTCAAGTCATTCTAGAGATGAAAACTCCGTTACTAAATCATAGCTGCTCCTGTCAGTCACATTGATGTGGACATTTTATGTAAATAAGGTGCTGCCATTCTGCTTGTCATTGATGCTGCCTCAAATTATTATGTATGTTCTTAATCTATTTCATTTTTGTCCTAATCCACAAATTTAAAATCTCTTTCCACCCTGTGAAAATCATGGACTGGCCTCGTTTGTTGTCTTTGGATCCCTCTAGGTCCCAGAGGTAAGCTTTGCTATAAAATTGGTAATTTCCCCTCACTCTGGTTTCTAGTCATTTCTGTACTTGTCCTTTTTCCTCTGTATGTGTGAGCTAAACTTTGTTACATTTTTATAGATGGGGTGCTGTAAGGATATTAAGCTGCAGTGTTTTGCTTCCTCGTTACAGATATAGTAACCTCATATTAGAGCATCCTAACATTCAGCCTCATTATAGGTTGTCAAGGCAGTGTAGAGCCTTTGCTTATATAGTTTCAATTTGGGCATGAAGTATGTGGGCTTTCTCTGTCAAAGGCTATATAGTACATAACCAATGTAAGTTCCTTTTTTAAATTCTACAATATAAATACCTAGAGCATCCCTAAAATAAATGGTATATACAACATTAAAAAATGGGGCCTCACCTCCCAGTAAGGGGCTGTGACAAGCCTTTCCTATCACACCCTCAAGTCCATTTTCAAGGAGCACATTTCTTTGTGTGTTAAAAGGAAAATGTTCACTTAATGCTCTGCAGTGCAAAAACAATGTGTTATTTTGTGCCTGGCATTTTCAAAGAAAATCAAAAGCATTTCTCAGAAGAGAAAAAGAAAAATTGTGAATGCCTGCATTTGTTCTTTCCAGGCCTCTGTTATTAGTCCTAATGAAAATTGCTGTGAATATAGACACCATGTATTATTTTTAAGGTCTTTAGAAGACAGGCCTCAGCTCCCCCTTTTTATTTTTCAGTTTCTGACTTATTAAAAAGTAAAGAAAAGCAAAATCAAAAATGTAAAAAGTCCTGGTATTTTCAATGTTTATATTTAAAAATTAAACTGTATTTGATGTTTTCATTTCAATCCTGTCTCTCTGTGATTGTATGTATAAAGTCATTTCAAGAGAGCATCAAAATTCTAAATAGGAAGCACCAAACACATGCTCCCACTTTCTGAACTCCGTTCCCACTGGGAAGGGCCAGACATTACTCATGGAAAATAGAAGATGCCTCTATGCATCTCTCTCAAGTCACCCATAGTAGAAAAGCCAAGTTTTACATTAAACTGTACTTATTATAAAAATACATTTGGCCCTGTGTGGCTTGTGGTTTTATACCATATTTTACACAGAGTTAAATTCCAAATAGCTCATAAGAATTCCAGGTCATTTTACACAGGCCCAGTAAGTATTAGGAGACTAAAACTTTGTTGTTATGCCACATTTTGTTAAGGATTTTCTTAGTGCTTTATGATTGATGTTCCTGAAATTATTTCACACTTTTGCATACATTTGAAGAACACCATAGCTAATCAGATGATATCTTTTATTTTTATTTAATTTTTTTGGAGACAGAGTCTTGCTCTGCTGCCCAGGCTGGCGATTCCACCACTGCACTCCCAGGTTCAAGCAGTTTTCCTACCTCAGCCTCCCAGGTAGCTGGGATTACAGGCATGTGCCACCACACCTGGCTAATTTCTTGTAATTTTAGTAGAGATGGGGCTTCGCCCTGTTGCCCAGGCTGGTCTTGAACTCCCAAACTCAGGCAGTCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAAACACCATGCCCGGCCAGATGATACCTTTTAAAATATGTTTCATTTCTTAGAATTTGTTACCCAGATATTGAGAGTTCCTGATGCAGTCTGATGAGGTGGTTAAGAACATGGGTTTGGAGCCAGAATGCCCTGGATTGCAATCCAGACTCTGCTGTGTGTAAGCTGTGTCACCACAGAAGTGTCACTTATTTGCCTGAGCCTGAGTGGTTTTTTTTGTTTGTTTTTTGTTTTTTTTTTTTGAGACAGAGTCTTGCTCTGTCACCAGGCTGGAGTTTAATGGTGTGATCTTGGCTCACTGCAATCTCCGCCTCCCGGGTTCAAGCGATTCTCCTCCCTCAGCCTCCTGAGTAGCTGGGACTGTGCACCACCACACCCGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGCTAGGATGGTCTCAATCTCTTGACCTCGTGATCTGTCCATCTTGGCCTCCCAAAGTGCTGGAATTACAGGCATGAGCCACCGCGCCTGGCGAAGCCTGAGTGTTCTTGTTCATACCCTTCTCATAACAGTAGCACATACACAGTCTTCTCGGGAGGATTTAATAGTAAAAGCATTCAGCACAGGGCCTGATACATGATAAAGCATTCAGTGAGCCTTAGCTGTTGTCATTATTGTTCAGTGTTATTATTTCTTATCCCTCTGTGATGTTTGCAGGATGACTGAATGAAGCTTTAGAAAAGATGTCTTAATGATGTGAAAGTAAAAGAAAAAAATCTCACATCTTTAGTATAGTGGTTTTCTTTTTTCTTTTTTTTTTTTTTGAGATGGAATCTTGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACGATCTCAGCTCATGCAACCTCTGTCTCCTGGGTTCCAGGGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGAACTACAGGCACTTGCCACTACACCCAGCTATTTTTTTTTTTTTTTAAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGATCTCAAGTGATCCACCCGCCTCGGCTTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGTGCCCAGCCTGTGTTTTTCAAAGTGAGATTCCCAGATCAACGCCATCAGCCTCCCTGGGAACATGTTAGAGATGTACATGGCCCCCTCTTCAGACCTTCTGACTCAGGAACTCTGGTTTCTAACAAACTAGCGACACAATTCTGATGTGCTACAGTCAGAATTATAGCTTTCCAACTGTGCTTTCAGCCCTAATGGACACTGGAATCATCGTGGGAGTTAAACAAACAAACAAACCAAAAACTACTGACACCCGGGTCCCACCCCCAGAAATTCCTATTTAATTAGTCTAGATGGGGCCCCAGTATTCATGAGTACTTTTGAAAAGCTCACCAGCTGAGTTTATTATGCAGCCAATGATGAGGACACTGCTCAGGCCACATCCTATTATCAAGTAAATCAGTATTTCTGGGAGTGGGACCCAGGCATCAGTATATTTCCATGACTCCCCTGGATAAGTCCAATGTTCACTCAAGGTTGAAAGTCACTGCTTCTGAGCCTCTAGCAATCCTGAAATTCTATGTTAGTGACTGACACTATGGAAACCCACGTGGCTGCAGTGTAGAGTAAGGACTCAGGGACACATGAAGCTGAGCTTTAGGAACCCACCAGTCCCTCTTGCAATGCTACCTGTGGCTGCTACTCCAGTAAAAAATGG
Seq C2 exon
CCCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000081052-COL4A4:NM_000092:42
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(5.3=10.8),PF0139113=Collagen=FE(57.1=100)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
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]
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)