MmuINT0040080 @ mm9
Intron Retention
Gene
ENSMUSG00000067158 | Col4a4
Description
collagen, type IV, alpha 4 [Source:MGI Symbol;Acc:MGI:104687]
Coordinates
chr1:82450352-82452486:-
Coord C1 exon
chr1:82452298-82452486
Coord A exon
chr1:82450639-82452297
Coord C2 exon
chr1:82450352-82450638
Length
1659 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGG
5' ss Score
5.53
3' ss Seq
TGTATCTTCTTCTCTCCAAGGTT
3' ss Score
8.36
Exon sequences
Seq C1 exon
GCCCTCCTGGTCCAACTGGTGATCCTGGGCCCAAGGGGTTTGGCCCTGGATCGCTCAGTGGCTTCCTCCTGGTTCTCCACAGTCAGACTGACCAGGAACCGGCCTGCCCCGTGGGCATGCCTCGGCTTTGGACAGGGTACAGCTTGTTGTACATGGAAGGACAGGAGAAGGCGCACAATCAAGATCTTG
Seq A exon
GTATGGATACCTCAAGAATAAGCTGTCATGTGCTGTAAGGGGTCATTCATGCTCTGGCTCAGAGAAAAAAACCTAGGAGTTAGCCTTTACACTTTCATCAACTTCTTAAGCACTTATCTTCCACAGCTTTATTACTAAAATAGGAAAAAATGAAGGAAGAGCAAGCCTGCTATGCTAATTCTCATGACCCTGTTATATGCCACAGAGGCTCATTCTGGTGCCTATTTAATCCTGGTTTTTGTTGTTGATGTTGTGGTGGAGTTGGTTGTTTTGCTTGTTTGCTTTGTTTTGTTTTGTTTTGTTTTGAGACAAGGTTTCACTAGGTAGCCCTGGCTGACCTGAAACTGTGTAGACCAGGCTGGCCTCAAACTCACAGAAGCCTGCCTGTCTCTGCTTCCTAAGAACTGAAATTAAAGGCGTGGGATACCACAAGCATGAGCCTTGATTGTTCTTTTTTGTATTTGTTTTTAGTAGTCTTCTGCAATGGGATAGATATAACTTCGCTATAGAATTCGACTTTTAGTGTTACTAAATGTAAATTATTTAATTGGGCATGTTGAGTCCCCATGATTAGGTATGGACTGGCTGAAGGCAGAACTTGTTGGGTTATGCTACAGCACTGGCAAGCACTGACTTTTAACCCTGTTCTGTTTTGTTTGGGATCACTAGACTAAGCACCATCCCTCTGTGTTCCTTCCCATCTTTCAACAGCAGATTTGTAAGCTGCAGGACTTGATGTCAAGGCATATAATGACAGTGACAGGGATGGTGGATACAGGGAGTGTGTCAGTCAATGGGTCAGTTGACAGTTAGGTGGGTCTCACTGCCTTCACCAGGCTGGTCCCTAGCTAGTAAGAGGATGACGATGTGGCAGCCCGATGACTGACAGATATTCAGACACCCATCTTTGTTTTCTGCTTGGTACTGCCACCACACTACCTGGCTTGGATTCCTAGATTCCTTCAGGATGGGGTGGGGGTGGGTGGAGAGAGGAAGAACTATTTATCTTGAACCTGCTTTCTTTCTCCTCCTAATATCAGGTACTTTCCTTGCCCTGGTTGGGCTGGAACACCTATCTAAAAGTTCTATAGAACTCCCCTAGGTAAAATCAAAGCCCCTTGACAAGACTGCCGAAGCCCACATCCTGTGGTCTGAATTCTCTCCAGATACCAAGAGATGAAGTCACACATATGCGCTCTCCCTGGCTCCCACAAGCCACCACTGAGCTCTAAGCTGATGCTCTGTGTTCTCTGGCTCTCTCCATCTTAGCATCCTCTTTGAATGGTCACCACCATCTCCAAACCTGGTTCCATCATTTTCATCTTTGGTATCCCAGTTTAGAATAAAGTCTAGTCACCCTTATGGGAGTTTTGGGCAACCCTCACCTCTCATCCACAGGGATTCTCTGTCTCATCTGTGACCATCTGTTTGCTCATTTGTACTGAGAAGACAAATGTATCTGTGCTCATCGCTAGCCCTTGGTGGGTTGTTGGGCTCCAGGGAGAGGAAAGAATGATGGAGGCTGGTCCACAGATCAGGGAGGTGGCCAAAGCGGCAGTCAGCTCAGGCATGGGTCTCCATGGGCGTCTGTAAAATGCCACATGTGGCTGCTTGCATTCAACTAGCTGCTCATATACTGTGTATCTTCTTCTCTCCAAG
Seq C2 exon
GTTTGGCAGGCTCTTGTCTTCCTGTGTTTAGCACTCTGCCCTTTGCCTACTGCAACATCCACCAAGTGTGCCACTACGCCCAGAGAAATGACAGGTCCTACTGGCTGTCCAGTGCGGCTCCTCTTCCTATGATGCCACTCTCAGAGGAAGAGATCCGCTCTTACATCAGCCGCTGTGCGGTGTGTGAGGCCCCAGCACAGGCCGTGGCGGTCCACAGTCAGGACCAATCCATCCCACCGTGTCCACGGACATGGAGGAGTCTCTGGATTGGGTACTCATTTCTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000067158-Col4a4:NM_007735:46
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.438 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(28.3=26.6),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
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCCTGGTTCTCCACAGTCA
R:
TGGATTGGTCCTGACTGTGGA
Band lengths:
356-2015
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: