MmuINT0039660 @ mm9
Intron Retention
Gene
ENSMUSG00000058897 | Col25a1
Description
collagen, type XXV, alpha 1 [Source:MGI Symbol;Acc:MGI:1924268]
Coordinates
chr3:130288601-130292955:+
Coord C1 exon
chr3:130288601-130288654
Coord A exon
chr3:130288655-130292877
Coord C2 exon
chr3:130292878-130292955
Length
4223 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACT
5' ss Score
6.64
3' ss Seq
GAGTTAATTTTTACAAACAGGGA
3' ss Score
6.24
Exon sequences
Seq C1 exon
GGCTTCCCTGGTCCTCGAGGCGAGAAGGGTGACCTGGGAGAAAAGGGAGAAAAG
Seq A exon
GTGACTTCTCCCAGCATGCATCTCATGTGTATCTACCAGCAGAGCTCCCAGCATGCATCTCGTGTGTGTTGGCCAGCAGAGCTCCCAGCATGCATCTCGTGTGTGTTTGCTAGCGCTGTCTACTTTTCTGCTGAACCCACAGGCTTCCACCAGGCACCTTTCCCGTGTCCATCCTGTGTTCCAAAAACATACAGATGGCTGATCTAAGGAATCAGGTCTTCAAAGAGGGCTAAAGAAGGCTATACAGCTAGAAATGAGGGCACCTTCCAGCATAGGAGGAAGAGTCTAACTCCTGGATATCAAAGCTACAGTCTTTCAACTTCCTGACACTAATTTTGTTTTTTAATATAGTGTCCAAGGGAATCGACTTCCTTTTTTTTTTCATAAAAGTTAGATCACATTGCACAAACCTCAATGGTATTTTGGCAAAGCCTGACTTACCCGCAGGCCAGGGTCTCCTTTATCTTCCCGAAGTTCCCAGGAGAGATACTGATGCATGATACATTTTGATATTTTTAAATTCAGAAGTAGAAAACAGGCTCTATCACAGAGCTCAGTGTGCCCTGCCACTGCACAGGAGCTGCTTGGCTAGCTGTAAATCCAATAGTTACAGATGACTTAATGAAGACATTACTTTAAGGATTTCTTGGGACCATCAACACCATAGGTTGTTAGGGGGTCAATATCAAGCAATGATTTTTTATGACCGAAAGAAAAGTCTCAATTGAGAATTTTAAACTTCACTTTTTCTGTTTCTCTTTTGTTCTGCTTCTCTCTCTCTCTCCTCTCTCTTTTCTCCTCTCTCTTTTCTCCTCTCTCCTTTCTCTCCCTCCCTTCCTCCCTTTCTCTTTAACCCAATAGTAAATCAAGTAAGTGTTTACATTGGATGAAGCAAAAAAGCAACAAAACCTCGATAATGAAAATCTTAAAGTAGCTGAATATCCGTCCACCCCATGATTCCAGGGTAAACCAGTCCTCCTTAGATTCATGTGTGCCCTGATATACTTAACAACACAATGATTTTAAAAGTCTAGTAGATTCTCTTGAACAGTGAAACTCATTCCTGTTATGATGCAAGACCAAAAGAGATGTGTCAAAGAAAAGCAACGAAGCCCCTGCATGTGTTTTAGGAATTAGGAGTTTCTCAGCCTCCCGTTGGTAAGAGCCCATACCATGGTCATCTCAAGCTCCGCCTTCCACATCATCACATACCGTGAGCACCTGTGCATTCCTCTCCCACGATAAACCTTAAAATCGTCACACTGCCACCCCAAGGTGGGTGCTGTTATTTCCCTATTTCAAAAACGAGGAAAAGTATGCTATAAGAAGTTCTTTTCCACATTATAAATCCTGACTACAAATTGTAATGCAGTTTGAGACAGGTTCTATGTGAGACCATTGAACACAGCAAATTGTTTTTAAAAGATCTGCTTAATTGTTATATATTTACCTAGTGGGTTGTATGGGTCTAAAATGTTACACAAGGAAAAAAATTTATCATGCAGTACTCAGTTTTATTATCTTTAAAGAAGTTGGAAATTATACCAGTATTGGCTCAGTGTAGAGTTCTTACTGAGCATGTGCAAAGCCCTGAGTTCATTCTCCCAGCATAGCAAAGAAAAAAGAATGAAGAGTCTAGGGGAGAGGAGAAATTTTCATTACTGTAGCTTATAAAACCATAAGCTACTCACATATCCTCCCTCAGAAAAATGCTAGTCACTCACACAAAAATATTTCCACAATTATTCCAAGTTTTATATTTAGGAAAATTAGATTCTAAAGGTTAAACACTTTGTATATATCTCTTTCATCAGTATAAGAAATGAAAACTGACAATAATTATCACATTTCAACTGCTCATACACACGATGACACATAACTTTGAAGAATATAGATTATCACTTCATTTTACAACATGCTGTTGATTGATAATGTTGACATGTTCTTCTCTGTGATAGCATTAACATATCATTCTTCATAATGGCTCTTTTCCATAAAGCTTGCTGTTCGCTGAAATATCAACCCCAAATCATTGCCTATCACAGTAATTCCAGTAGTTAGTCTGAAGTCCATTTGCCAATCAAGCAATGAATGCCACTTAACCAACACACCTGGTCTTGGTTAGTCCTACTCAAAGATGGCTCCGCTGCCTTCAGGAAGGGCAAAGCACAGGTAAAAAGTTTCTATCAGTTCATGTCATGACACTGAAGCTGCTCGCTGAAGTGGGTGCTGATTCTTCATGAGTGAGCACTTGCTTCCAAAGGCATCGTCCATTTCCTGTCTCACCTGCTCCTCCTTCCCTCTCCCTGTCACAGCTTTGCCTTCACCCATGCTCTAGTGAACCACACCAAATTTCTATCCCCTGTATCCAAGAAGCCCAAGTGGTTTTGATTCCAAGCCTTCTGCCCCCATGTTCTTGGCACACAGGAGATGACCAAGGCGGAGCTTTCGGCCCATGCTGTCAGAGTGAATGTATTAATTTGAATGAGTGTCTCATACTTCAATGCGGTGTGCGCATTGTTCTGTCTATTTTCCTTTGAATATTCATGTTGCTTGCTTCAGACTGTTCGGTTTTATTGCAACTGCCATCCAGATTGCAGGATGAATGCTCTCATCTACGTATGTATCTATGTACTGTCTTCTGCATTCTGCACAGCACCAACTGCCTGTCTATACGTTTGCAGATGTCTCCGTTAATGTGAACCAGCTGGGGTGCATTCCTTCCCTCCTCTCCTTTCGCCTCCTTTCCTAAATTCCTCCATCCCTAGGACCCATGCCGACATCCTACAAACCTTGACCTTGATTCCCAAATACTAATTTCCATGGCTACATTCCCACTACGTAATTATCCTGCCTACCTCATTTTAATGAGCCCAGACTGCTTTTCCTATCTGCAGCGTTGTGGGCTGGAAACTCATTTACCATTGTGAACAACAAAGATTGAAGAAGACCGCCTAGGTTTATCCAACTGTTTCTCCAGTTGGCATTGCTGCCGTGTACTAGCACCTGAAATCTGTGTTTAACTCAATCAGTCAAGTGTTCACTTTTATTTTTGCCAGAGAGGAAAAGTTAAACACAATAGAGGCACGTTTTAATACTGGAATGTTTTTACTGGGAGCTGCAGAATAGAGTACGACTGGACAGCCTTGGGAGAGAGCAAAGCTGTAGCCTCTCCCTCTGAGTCTGTACAGCCATTATGTGTTAAAGAATACGGAGGGTAAAGGCAAGTTAAAATTACTCACAATTGGGTAGAGCATCCATTACCCTAAGCCCAGCTCCACCTGATACCAACTGGCTTCAGTGTAACTTGTCCGCCATCTTTGCCTGGTCCACAGAACAAATCCCTAATTCACTGTTGACTCAGATATTTTGACAGTCAGCACTGGTCTGCCTTTCTGATGCATCAGCCCTTTTGGTATCCTCCTTTCTTTTTGTTGAATGTCATAAATAAATAATCAATCAATCAGCCAACCAACCAATCTATCCTGTTTCCAGAATCCATTGTCAGCATGGCAGCTTAAGTTATTTTTTTTATAGCATCGTGTCATATGTACATCAGTAAACAATGGTAAATGCCTCCAGACTATTTCTAGCTAAGCCATACTTTGGATAATTTTTATTCTACACCCCCTCAAAATAAAACCTGTCTTTTATTTAAACCCTTGTATCCACAGGGGGAAAAGGGAAAGAAAGGCAAAAGGGGGCCTAAAGGGGAGAAAGGAGAACAGGGCGCTCCTGGATTAGATGCACCCTGCCCGTTGGTATGTCTAACTGATGCAACCGTCTCCAGATGTCTTGTGATGGGATGAGGATAAGATGGGAGAGGAGCAGGCCAGAGGGGTCAGTAACAGCAGGTCCTGGGAGGGCCACTTAACACAGACTTTCCGACGGTGTTCAGAAGTACGAGGCTACACTGGTGTCCTTGACATCTTGTTGCCAGCCACTCAACACTACTCGTTTCTAAATTTACAAGCAGTGCTGGCTGTCAGGAACCTGACTGTAGGGTGTGAAGAAGAGCCAACAGCATCCCATATCCCTCCAAACAGGAGGCCAATGGTTTCCTGTCAAAGGCTTTGTCATGATAATGTGAAACTTCTCTGCGTGTTACTACCCCTTCTAGGCTGTTCCTCTCCTGGCTTTGTCTTCTAGTTGTCTCTTTAGCAGATTTTTGCTTTCAATGAATTCTTGGATTAGTAACGTTATGAGTTAATTTTTACAAACAG
Seq C2 exon
GGATTCCGTGGCGTTAAGGGGGAAAAGGGGGAGCCAGGCCAGCCTGGCCTGGATGGGCTGGATGCTCCTTGCCAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058897-Col25a1:NM_029838:35
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=PD(9.9=50.0),PF0139113=Collagen=FE(22.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(33.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: