MmuINT0039678 @ mm9
Intron Retention
Gene
ENSMUSG00000045672 | Col27a1
Description
collagen, type XXVII, alpha 1 [Source:MGI Symbol;Acc:MGI:2672118]
Coordinates
chr4:62919186-62924806:+
Coord C1 exon
chr4:62919186-62919230
Coord A exon
chr4:62919231-62924752
Coord C2 exon
chr4:62924753-62924806
Length
5522 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAAG
5' ss Score
6.84
3' ss Seq
CTTCTCTCTCATCCCCTCAGGGC
3' ss Score
12.07
Exon sequences
Seq C1 exon
GGTCTCCCTGGCGTTCCTGGCAAGAGGGGCGAGATGGGTAGGCCG
Seq A exon
GTAAAGATTTTCCGTGTCTATTACGCAGACTCTACGGGTAGTCCCACCTCCTGCCGGCCGCGTACTGCACTGGTGGTCCCTGAGACCTGGCACTGTCTGCCTCTCAGCTCTGTTTCTCTGCTCTGGGTGTAGGGCAGGGTAACCAGGGGCAATCACTGGCCTGGGATGCTGCCCGGAGTTCTGGCTGCTCCAGGTGGCTCCTCTATCCCTAAATGCTTCAGCAGCTTGCGGGTAAAGCTTTACGTCTGGGGTGTCTGTCCCGATGTTTTTATTAGTGGCCAGCAGGCACTAGGGGACCTAAGTCCTCCCCTGGACAGCACAGGGTCCCCAGTGTCAGGTCTCCCACTCTGACTTCATTTATGCACATGCAAGGCTAGATGACTAGGGAGTATGGTAGGCCTCAAGAGGAATCCCAGAAATGGTTCAGTATTGACCCCCACCCAAATCCACGAGCCCTCTTTAGATCGCTTCAATGCCATAAGGGATTAGTTTTCCTCTTGCCAACCATCTATAGGGCATAAAGAGAAAGACAAGGCCCCAAAAGGTGTCCAAGGCATTGCAGCCCCTGAACAGCTGGAGCAGGGCACATCCAAGACTGACTCTTGGGAATACCAAATGGTACCAATATCATAAAAGTAGGTTTCCTTGACTCTGTTAGGAAAGCCATTGATTCTGTAAGGGGAATCTGAGTCTCTAAGAGATAGACCTCTGGGTGAGGCCTTGTGACTGTCACCAAGACAACTTTCTTCGGGTCCTATCCCAGTTGGTGGCTTAGCTCTTTGCTGCCATCCTGCAGGTCATCTAATCAGACCTACCACTGACTAGGGAATGCAAGCCACTTGACCAGGGTCACACAGAAAATAGGGAGCCAAGTCTGGATCTGAACCTAAGACCATTGATAATGCAGGGCGTTTCCCACAGGGTCTCTTTTCTCCCCATCAACTCCCTTTTCCTCCAGCGAAATCTACAGTTCTCACCCTTGCCTCACCTCTCATGCTAGAAAGGGGGTGTGCAATTTTGGAAGAAGGTCCAAATATAAAATGTTGGCAGTTAGCTAGTGCTGGCAGGACTTCTGGCCCGGCTGGTTCAGGGTTACGCACAGCAGACGGCTGAGCCACATGCTAGCCAGAATCTCTCATTGAGTCTAGAAAGAGGCTATAGTGATTCTTCTTATCTAGTGCGCTCTCTCTCTCTCCCTCTCTGTCTCTGTCTCTCTCTGTCTCTGTCTGTCTGTCTGTCTGTCTCTCTCTCTCTCTCTCTCTGTGTCTCTCTCTTTCTCTCTGTCTCTGTCTGTCTCTCTCTCTGTCTCTCTCTCTTTCTTTCTGTCTCTGTCTCTGCCTCTCTCTGTCTGTCTGTCTCTCTCTCTCTGTGTCTCTCTCTCTCTTTCTCTCTGTCTCTGTCTGTCTCTCTCTCTGTCTCTCTCTCCCTTTCTTTCTGTCTCTGTCTCTCTCTTTCTCTGTCTCTCTCTGTCTGTCTCTCTGTCTCTATCTCTGTCTCTGTCTCTCTCTCTCTCATCAGTGTACTGGGGATTCCTACCCCTACCATGCTGTTTAGGGCCTGGATCTGCCTGTTGTGACCAGGCCTGCACAGAGTCAGGAAGGCAGTCCCAACACTAGATCAGTTGACCCAGGCTTGGCTCTGTCTCCCACTCTGTGACTCAGAGATGCTGAGAGCTTGCCTGAGGACACACAGCTATCTGGTTCAGGTCAGGAATTCCTGCCCTGGGTTTTTCCTAGTCATCAGATAGGGAAGGAGAGAGTATATATCCCCATGTGGGGAAACTGAGGCCCAAAATGATGAGGGGGAGGGTCTGGTTTTTCATTTACATGTGAGCCTCCGGTGTTGGTGGCCTGTGAGTCTCCGTAAGACTTCTGCCTGTCTGTCTCCATCTCTTTCTCCCTTGATAGCATAACTGGAGAGATTTTCTAGTTTCCTTCACAGGGCAGAGTAGTATATGACCTGTATCATGAAACAAGGGATCTGGGAAATTCAGAGGCCTTCCCTATCAGCGTATTTCAAGCACAGTAGAAAGCATGCAAGCTTGACCTGTGGAAGGACTTCCAGAAATTAAATATTTTGTTCTTATAGCTCTCTAAGTTCGGTGGCTCCTCCTGGAGGCTGCTGAATAGTCCCGTGGTGGGTACCACCCCTGACAAGTGATATAATGATAAACATCAGCTTGCCGGAGAATTGTTAATGATGCTTAGCTTGGTCTTGACTAGGGCACAAAGAGGTGGCTGGTTTATAGGCTAGGAGACAGAGCCTGGAAGCTCAGTAGGTCATCTGTTGAATGCTCAGGCTGCGCTGGTCCTGCATCCACCCTCTGTATCAGAGGAGCAGATTCTGGAGGCCCGAGCTTGGCTGAAATGCTTTTAGATGTCTGGGCCTTGGCATGTTGCTGTCCACACCTCTGGCCCTGTGAACTGTTGCCATCCAGAGTGAGGGTGGAGCCTTGCCCTAGTCTATTTTCTTCCGCCCAGCCTGGTTCTGCTCACAGTATAAGGCGAGGCGTTCAGTCCCAGAGGGGCCCAACCTGGGAAAGCGGAGGAGCCACGTAGCACGCCCGGCAGTGAGCCAAGTTCATTCCTTGGGCCATGGGCCAGGCTGCTGCAGTCAGGGGTTGGGGCAACGGAAGAAGGTAGTGCCTGCTGCCATAGGCTAATGTGCAGTCATCACGCATACATCAGGCACAGCCAGTAGGCACTGGATGGCCAGCTGGGCAAGGAATAGAGGCCTTGGGTTGCTGGTAGATGTGGCTGTCTGCTCGGGAGTGGAGTGGTAGAAGCTTTGAATCTCAGTTTCCTACTGGGGCAACAAACTGCTGTTCACTTAAGCTATGGGCTTCCTCCATCTCAGACCACCTTCAATTGTTCCAGCATCTTTAAAGCTTCATTGTTTCCTAACGGTCTTTTTAAAATAAAAGGCCTAGAGTCCTAGAGGTTGCCCGTCAGCAGAAGCAACGCTAGAGATGGAGAAGGAGAGCTGGTCCCCAGGGCCATCATCTATGTCCAGGCGGAACCAGATTTAATATTCATCAGTCTGGAGCCACAATGGCCCTTTGCGATGCTGGACTTCTAATTCTTCTGTTTGTGCTTGATGCCACTACATAAATACCAGGAGAACAGTTCCGGGGCCAGACCACCTGGATTCAAATACAAACCATGCTATCCCAAAGCTGTGTGACTTTGGACGGGTTTCTTAACATCTCTGGGTCTCTTGATATCTAAAACAAGGTCTGCACAAAGTCCCTTTCATGAGTCTGCTACAGTTGGTTGTTACTGTCATGGCTGTGTCTATTGTCACTCATAGGCTGGCCCAGTCTACTGCTGAACTGCAACAGGGTCTCACTGCGGTTTGAACTCAACCTTCAGAAGGCTATGTCTTAAGACTCTCCCTGGTCTTAACAGTCTCTGAAGGAAAGCAGACATAACTCAGATTCTTAGAGCCTTCTGGGTGGTAGAGCCAGGGTAGCTCAGGGGTGTTGGCCTGACTACTGGGTCTGAGGGGAGTGGTGGGTCAGCTTGGAGCTGCCCTGTGTGTTGCTACCTAGAAACTACCGGCCTTGTGCCCAGGATATACCAACACATCCTCTTCCTCCCCAGTCTTGTCAGTGGGTCAGGCCAGGCTAGCATATATTTTGGGATCAGCCCTCAATCAACACAGTGAACGTCTTCCTATCACACAGATGCCTAGAGAAGACCAGATGGCCCTGGTCTCCTCTAGACTCTGGACCTAGAGAATAAAGCTAGCAATCACCAGGCCTTGCCCCTGGGACCATGTGGAGCGAGCCAGGATGCTGCTACACTTTGTCCTTATTCCATGAGAGACCGCCTTCCTACCCTGTCCCAGCCTTCACGACCAACACAAAGAAAAAGTCAGTGCCTTCAAAAGATGTCCCATATCACAGCCCATCTGACAGATGACTCCAGCCCCAAGAGGGGACACCAGTCAGCATCATGACAGAGAGTCAGGGTTGGCTGGTATCAGCTAGCTGAGACTCCTAGAACACGGGAAGAGGAAGCCCTTGTGGGCTGAATGCACTCTACAGAGACAGGACTGTGCATGGCAGCACCCTGTCACCCCGTGTGCCAGGTGGATACTCTCACTCCTCAGGCCAGGCTGGGCCCATTTGAAACTCACAGGAGTGGAACTGGGCAGAAGCAGAACCCAAGCTCACCTGAGCCACACACTGGTTTTATGGCCTTGGTCAGGTGACTTCCTGCCTGAGCCTCACCTTTCCCATCAGTTAAATAGGATGGGTCACCTTTACCCAGGGGTGAATGCCAGACACACATGCAGGCTGGCACACAAAACAACAACCTGGTCTCAGACCCATCAAATGTCTGCATTTTCTCGAGTCTGAGTAAGCCATGCTTCCTGGGGAGTGAATGTTACCCTGTGCTGTGCCGGTTCATGAATAGGACCTGTATGCTTGCATGCATACATGCCCAGAAACGCAGGATCAGGGTCCCTGCTTACTGGTACAGGCTATGTGACTGCTTCCTAGGGCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTTCTCTCTCTCTCTCTCTCTTCCTTTCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTTCTTCCTTTCTTCCTTTCTTCCTTTCTTCCTTTCTTCCTTTCTTCCTTTCTTCCTTTCTTGTTGTTGCTGGATATCTGCTGAATAAAAGTACTAGCAACCTGAGGCACGAGGCTCCTCCAGGCAGTTATCACAGTCTGGCCACCTTTGCATTCATTCTTTCTGTCAGGCAAATGTGAGCTATGCTTGTCATTCCTCTTGGGAAAGCCACAGTTGGAACTGGAAGAGGGGAAGGGGTTTACAGGCTCTAGCTAAATCCCTCCCTTTCCTTTGAAGTAGGAATGGATTCCCCACCCCCATCCCCCAGGCCTCCCTACAGCTGATGTTTTTCCAGCTGTCTGGCTCCCTGAGGACTGTGAAGCTTCTTAGTCAGGTCACAGAAGGGCTGAAGGGCCAGACCTGCTCAGGCTGGTGGCCTCTTTGTGGCCACAGTGCTCATTCTCCCTAGCAGTGTGACCTTGCGTGACCTTGCCACTTTCCCAGTCACAGCCTTAGTTTGTAACATAGGAACTGTATTTCCACAGAACCTTCCTTTAACCAGTGGGGAAACTGAGGCCAATGGACTCTGAGAAATGTGCACTGCAAACTTCATCAGTCTGCAGTGGTCTAGGTCTGGACCTCGCTTCCTGCCTCAGTCTGTCATTTCCACAAGGAGTCCCAGTGCAGTCCCAGACCTGGGGGTGGTGCCTGTCCCATCTCTCAGATCAGCTGTGACCTGTCCCTTGGTTCCATGTGTGCCAATGTTTGTGGTTAGCAGGAAGGACATCAGAACCCCAGATCCGAGGAGTGAGCCTGCTCAGATATTGTCCTTGCATCCTGCTGGGAATGTGGCTCAGAGCCGAACTGCAGCCTTGAGCGCTAACCTCCATATTTCTTCTCTCTCATCCCCTCAG
Seq C2 exon
GGCTTCCCTGGAGACTTTGGGGAAAGAGGCCCCCCTGGACTTGATGGCAACCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045672-Col27a1:NM_025685:12
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(15.1=100)
A:
NA
C2:
PF0139113=Collagen=PD(8.6=44.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
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: