MmuINT0040078 @ mm10
Intron Retention
Gene
ENSMUSG00000067158 | Col4a4
Description
collagen, type IV, alpha 4 [Source:MGI Symbol;Acc:MGI:104687]
Coordinates
chr1:82456779-82462176:-
Coord C1 exon
chr1:82462051-82462176
Coord A exon
chr1:82456896-82462050
Coord C2 exon
chr1:82456779-82456895
Length
5155 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
TATCATGAACTTTCATGCAGGGT
3' ss Score
6.88
Exon sequences
Seq C1 exon
GTGAACCTGGGCCTCCTGCAGACGTGGATTCCTGTCCTCGAATCCCAGGACTTCCTGGAGTGCCAGGTCCCAGAGGACCAGAAGGAGCTATGGGGGAACCTGGACGGAGAGGCCTGCCTGGACCAG
Seq A exon
GTATGAGCTTCTCTGAGTTCACTGTCAAAATGAAAATCTAGATGTTTTAAGATGTTCTTCAAAAGGAATCTAAGTAGCTCATGATAGCAAATCTGTGAGAACTTTCTTCCTCCTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAACACAAAAGAAATTGGGCTCACGATCTACACATCCTTTCCTATTCTTCTGTTGAACTATTGAAATCTTTTATATTTGGCCAGCTTATGGAGGGTGTGCTTGGCAACCCCAGGAGTAGGTGTCCTGTTCTCATTAACTGCTGGCTTGGTTTTGAACAACAACAACAACAACAACAACAACAACTAAAAATAAAAACCCAGCCAACCAAGCAAACAAGAGCAATGGAATTGGGAGCTGGGGGAACAGGAACAGCTCGAGAGAAGAGAAAAGGAAAGGAGCCGCTCAGAAGATGGAAGGAAAACACAGAGTGTTTCTATGTGTTGGCAATGGCGGCATTATTCCTGGAACTGAGCTGATGAGCGCTGCTCGGTCATTATCGGGCTAGGAGGACCGTTGTTAGCACACAAACCAAACCATCCTGACAAAAAGTCTTCTGCATAGAGTTTATTTTCTTCTTGCAAATCCTGCCCACATTGGGTAATTTTATGCTGAGCTAGGGAGCCCTGGACATCTGGAAAGCACAGACCTCTTCAGACCAGTGGCAGTGGCTTTGAGCTCAGCATCTGTGTGAAGAGTACCAGAAGGGAGGCTCCGGGCCAGCACCTCTCTTCTTTCCTCCACTGCCTGGCTGTGACATGGTTCTTTTCAGTGTGGTGCCAAAGGCTGCGGAAGTGGAATGGAATTTTGTATCACTTGTTTTCTTCCTGCCCTAGAGACCAGAGCAGCCTGGGAGCACAGGCTTCTCATTGCTCACTGTTGGATCTCCACAGGGTTCGGGGTCATGGGAGGTGTCTGCTAAATGCTTGATGGAGAAATACATGATGCCCTGAGTGCCCACTGCAGCGGAGAGCAGCCTTTCTCAGTCGAGTGCTATTGACCTGGGGGCCAAATAATCTGCTCTGTGAAGGGCCACTCATTGTGGGGAGTTGAGTAGTGTCCCTGGTCTATCCTGGTGTTGAGGATATCCTGGATCCTTAACTTTGTGACAACCAAGAACATCTGGCTTCCAGATGTTATCAAATGTGCCCTTGGGAAACAGAAACACCTAAGGCTGAGAACTGTTTGTGGAAAGATAGGAGGTTATCTGAAATCTAAGAAGTTTAAAACACATACACACACGCACACGCACACGCACACGCACACACACCAAAACCCAAAACCTTATTGTAGGACTAGGGAGATGACTCAGTTACTAAGGATCTGTGCCTCCCCAATCTCCCTCTCTCCCAATCAATCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCTCTCTCTCTCTTTCTCTCTCTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCTTTCTCTCTCTCTTTCTTTCTTTCTTTCTTCCTTTCTCTCTTTCTCTTTCTCTTCTCTCTCTCTCGCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCTCTCTCAACTTCCTTTCTGTTATTTTTTATGTTTGTTTTTGAGGCAGAGTTTCTTTGTATAGCCCTGGCTATCCTGGAACTTGCTTTGTAGACCTGGTGGCCTTGAACTCACAGAGAGATCCCTGCCTCTGCCTCCTAAGGCGTGTGTCACCACCTTGCTTGGAAAGCACTCTCTGCATAAGTATGGGGAGCTGAGATGTATCCCCCAGAACCCATATAAAAGAGCTGAGTGCAGCAGCCAGTGTGCTCAGAACCCAGGGCTGGGCAGCCAGATCCAGTTAGGAGCCCAGGGACTTGCTGGGTAGTCAGTCTCGAAAGACAGTGAGCTTCAGGTTCTGTGAGAGACCCTGTCTACAAACCAAGCAGAGGGTGACTGGAAGGAAGATGACTGTCAAGGAAGACTTCAACTTCTGGTCTCTGCATAAATGCATACTTATGTACAATGATACACATAAGCAGGTGAACACACACACACACACACACACACACACACACACAAACAACAACAAAAACAACAACAAACTTATTAAAGGTGTTTAAACATAAAAGAAAAACAAAGTAAACTCAGCCTAAAAAGGCACAGCTGGCTGGCTGGCTGCCCACCCTTATTTCTGCACGTTTGTAAAAGAGTCTATCCTACCCCCCTGTTTTTGCAAACTGGTGGTCTTAGCATGACATCAGTTCTGTGTCATTACATATTTTCCAACAGTATCGTCTGTGGTGTGGTGGCTGCAGAGTATTGCATTATTTGATTGTGCCATAACTCATTTAACCACCACTTTCATGAACTATTTATCGAATGCTTTGGTGCCAGCACTCTGCAAGGAATAAATGAATCCAGCAAGGCTCTGCACTTGGAGCAGCAGGCCAAGGAAAAGAGAAGGTCCTGACAACAGCCCCGAAGTCCTGAAGGTTAGCCTGGTCAATGGAACTTATCCAGAAATAGGAGAGAGCCTAGGATTTCAAGCCTTTTGGAACTTCACAATCCTTCCCTTTACTCACCCCCCGCAGAGAGCATTTAAAAAATACATATTACTGGTCCCAGCCTAGACTTTCTGGCTTCTCAAGTGTAGACTGGGCTGTGAGGTTCGTTTTTCTTAAGAAAAATGCTGCTGCTGTTCTGGGACCACCTTAAATGCATTTAAGGTGGTCTTACTTTTTCACTCTGATCAGCAGCTCTTAAAGCATGTCTGCCTGGGTGATGGACATTTCATACTTAAGCATCCATGATTATATCAGAGGGGAAGTACGGTGGCTAGGAAGGGACACTCTGAAACTTGACTGCATGCACTCTGCTCGGGTTCTCGGTCTCCTCACCTCAGAGACTTGTATGTTAACTGCCATTGATGACATCACAAAGGAACAGAATGAGCAGGACATCTCTTTGCTATCGTTATTGCAGGTATTGGTTCCTTACTGTAAGTTCCTTGGGTACCATTTATGGTGTTAAGAGTTGGCAGAAAGAGGCTGGAGAGATGACCCAAGGGTTAAGTGCTTGCTTGCTAGGAGGCAGAGGCAGATCTCTAAGCCAGCATGGTCTACAGAGCAAGTTCCGGGGGAGAAAGGGCTATAAAGAGAAACGCTGTCTCAATAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAGCAAACAAGCAAGCAAGCAAACAAATAAACAGAGTTATAAGGACCAGAGTTCATATCCCAGCACCACCCATATTGGGCAGCTCAAAAACACCTGTAACTCCATCTTTGAAAAATTCATCTTGAGGACTCCATATGCTAGTTACTAGAGCAAGGGTACAAAACCCAGGCAGAGCATATACTGGAGCAGCAGAGGGAAGTGCTCTAAAGGGACAGGTTTTAGAGCCACCCAGGGTAGGAAGTGATGTCTCTCATCCCTGATGTTGCTTGCTTGCCAAGCCCAGGCCCTGCAGCCTTCTTCAGGGCAGGGCTGATGCTCGGATGGAACAGAATTTGGACAGTGTCTTTGGTCAGTCCCTTTGTTTTCTAGGATCAGCTCTGTCATCAGCAAAGTGACTTCACATTCCATCGCCTTTGGCTACAGGGCTGGTGTCAAGCTATGTTTCTGTTTGCTCTGGCAGCCATAGCAAATGTACAGAGCAAGAGCTATACAAACACCTCATCCTTTGGCTCTGGAGGGAAGTCTCAGATTAAGGCAGCCATGGGATTGATTGGTTTCTTTTGAGAGTCCTTTGCCCTTGGTGGCCTTTTCTCTTTTCCTATAGATATCCCAGCCAGGTTGGGTTTGCCTGCCCTAAGGACCTTGAGATGCCTTGAGCATACCTTTAAAGATATTGTTGCCAAATACAGACATTCTAAGCCACTGGGGGTAGGAATTCAATATGAATTTGGAGGAAGGGTGGTACACAGCAGCCAGTGATCAGTTTATTCAAGGAAGGAGTTTAACAAGTAGCATCTAGAAACATGGAGAGGGCAAATTAGTCAGCTAAATGGGTCTAATGGTATAAACGGCCAGACATGGGTGCTGCCATGACCCCATAGAAACTTCAGTTAAGGAACAAAAGGAAGAAAAAGGATGCCAAGCAGTTAAAATACTCTGCAGGACTAGTGAGGCTGTGCCAAGATCCATAAGGATGTATCTGAGCCTTGTCAAGGGTGGGGGCAGGGGGCTGATGGATACCACCTCTGTCCTTGCTGCCAGCCAGGTTAGTCCATGTGACACCACCTCTGTCCTTGCTGCCAGCCAGGTTAGTCCATGTGTGCTCTCCATGCCTGTTGAAGTTTCTCTCTCGGAGTAAGTGTAGTCTGGGCCATATGTGGCTGCTATGAAGACTCAGTTGATAACTTTTATGAAGGGGTTGGTTAGCTTGAAATGAGTACATCATAAACCCTTGATAACAATCCATTCTTGGAAACCAAATCCTAAGCCAGGCAGTGGTGGCACACACCTTTAATCCCAGCATTTGGGAGTGAGAGGCAGGTGGATCTCTGAGTCCAAGGCCAGCCTGGTCTACGAGCAAGTTCTGGGACAGCCAGGGGTACAGAGAGAGTGTGTCTCAAAAGAAAAAAAACCAAAAAACCAAAAACCCAACAGCAGCAGACACTACCAACAAAATGAATCCTAATAAATTTATCTCATTCCTCTACTCATCATGAAAGAATATTTGAACATAAAGGCATTGCATGTTCAATGTTTTCTAAAAGCAAAAAGCCAAAAACCAACCAACCAACCAATATTGAAGAAAATGGGATAGGCTCCCTCTCAACCCTCCCTGGTCTAGAGCTACAGAGATGATCTAGCCCTTTACTAGACCATGTCATAATCTAGGTCAATTTGTTGTACTTCTCAGGACCTCCATCGCCCCAGTTGCTTCGTGGAGGTCATAAGCCAATGCCATGTACTTGTGCAAACCAAATGAGTAGATCCAATGTCATGGGGGGGGGGGGGAGGCTCAGAGTCAGCCCATAGGATGCATAGGCAGTAGTTACCACTACCACTATCATGAACTTTCATGCAG
Seq C2 exon
GGTGCAAAGGAGAGCCTGGACCGGATGGCAGACGGGGCCAGGATGGCATCCCTGGATCTCCCGGGCCTCCTGGACGCAAAGGTGACACTGGAGAGGCAGGGTGTCCTGGAGCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000067158:ENSMUST00000087050:44
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=PU(5.0=7.0)
A:
NA
C2:
PF0139113=Collagen=FE(65.0=100)
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
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types