MmuINT0039311 @ mm9
Intron Retention
Gene
ENSMUSG00000026141 | Col19a1
Description
collagen, type XIX, alpha 1 [Source:MGI Symbol;Acc:MGI:1095415]
Coordinates
chr1:24330521-24332142:-
Coord C1 exon
chr1:24332089-24332142
Coord A exon
chr1:24330575-24332088
Coord C2 exon
chr1:24330521-24330574
Length
1514 bp
Sequences
Splice sites
5' ss Seq
GTTGTATGT
5' ss Score
4.04
3' ss Seq
TTTCTTCTTGTATTTTCTAGGGA
3' ss Score
11.66
Exon sequences
Seq C1 exon
GGTCAGCAAGGACCTGCAGGTTCCATGGGGCCCAGAGGACCACCAGGAGATGTT
Seq A exon
GTATGTATTGTATCATCACTATTTTGAAATAAAATTGATGTCAGTTAATGAGCTGATTATGCTACATTCCCCAAAACCATAGGTTAACCCCACTACTCAAATTGGTCACTTCTAATGCCAGGGGATTAAGTGGATCTGAATAAACCAATCTTTGAAATTCAAGATAACTCAATTGTCAGTAGTCAATGCTACAGCAGAATGGAGAAAAATAGAAATATCCAAAGAAATAAGAGAAAACCAAAAGAGACAGCAAGTGTTTCCAAATTACATTCATAGACTCGAGTTCAAATAATCATTTTCATGCTATATGATAAGCTCAATATAGCTTGCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCTTCCCATATTTCTACCCTTGGGTAATCTCCTAGTCTCCCCATGGGAACTGAGAGCTAATCATCAAATAATAGATCAAAATGGAGATCTGGCTACAACACTCAGTGACTCTGTGCCCATGACTAGGATGCTAGTTGGCCAGACTTGAGACCTGGCCTCTTTTCACCATCTTGGGAGTGGCCCTATGACTTCTTTCCTTGCTCTCAAGCTTACTGCCTGAGCCTCCTGGAGGCAACTGGTTGGCCTTCATAGTGGGCTTGCTAATCTGAACATCTGATCCATAAGAAATGTTATTTATCCCTCCTAGTCTTAGCTAGGGTTTTACTGCTGTGAACAGACACCAAGATGACAGCATAATGCTTATATTGGGACACTTCATTGGGGCTGGCTTACAGTGTCAGAAGTTCAGTCCATTATCATCACGGCAGGAAGTATGGCAGCATTCAGGCAGACATGGTGCTAAAGCAGGAGCAGAAAGTTCTGCATCTTGATCCAACTACAGACAGGAAAGGATTGTCTGTCTTCTAGGCAGCTAGGAGGAGGGTCTCAAAGCCCATGCCCAAAGTGACACACTTCCTCCAACAAGGCTCCCCCTCCTAATAGTACCACTCCCTGGGCCAAGCATATTCAAACTACCATACTCCTACAAGGCATTATTGAATCACTTCAGGAATACCTTGTGGAAAGACACCATAAAAAAAAATGTTAATAACACAAGAGGAAACATTAAATACTCTGCTTAGACAGAACTGTTGGTACTGAGGAAATAAAATGAGAATTAAAATCAAAAGGAAAAAAGCCCCTGTGCAAAAGCATAATAAAAATATTTTGACATTTTTAGTTGGGATGTAGTGCTTGCTCCCAGCCCCTACCATCCCACTTCCTTCTTAGAAACTATATAGGTGAAACATTTCAATTACTCTTTTCTGTTTCCCATTATGGCTGTTGACTGCACAGACAGGAAGCCACACATATCTCCAAATAGCGCTTCCCCTAAGGCTAAACATCAACATTACCTTGTATATAGACGTTTAAATTCAGTTCTCTGACAAAGATGCATGGCTATTACACTAAGAGATGTTCTAACTGCTAGTTTTCTTTCTTCTTGTATTTTCTAG
Seq C2 exon
GGATTGCCAGGAGAACATGGTATTCCAGGAAAACAAGGCGTTAAGGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026141-Col19a1:NM_007733:23
Average complexity
IR-S
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=FE(25.0=100),PF0139113=Collagen=PU(27.9=94.4)
A:
NA
C2:
PF0139113=Collagen=PD(1.5=5.6),PF0139113=Collagen=FE(27.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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]
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: