MmuINT0039088 @ mm10
Intron Retention
Gene
ENSMUSG00000022371 | Col14a1
Description
collagen, type XIV, alpha 1 [Source:MGI Symbol;Acc:MGI:1341272]
Coordinates
chr15:55518182-55520803:+
Coord C1 exon
chr15:55518182-55518337
Coord A exon
chr15:55518338-55519932
Coord C2 exon
chr15:55519933-55520803
Length
1595 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
CCCCCACTTTTCCTCTTTAGTGT
3' ss Score
10.38
Exon sequences
Seq C1 exon
GACCTTCAGGGGAAAGTCGTCCTGGAAGTCCTGGGCCACCTGGCTCTCCTGGACCAAGGGGTCCCCCGGGCCACCTGGGAGTACCTGGACCTCAGGGTCCTTCTGGCCAGCCTGGGTATTGTGACCCCTCCTCGTGCTCTGCTTATGGCGTTGGAG
Seq A exon
GTAAGTGCCAGTCTCTTGAGGGCTTTGCCCAGTTATACAATGGTTAATACTAACCTGTGTGTGTGTGGGGGGGTGGTGGTGGTGGAAATTAAACAGGGAGGGCAGCAGAACCTGGGCTCCATACTCCCTTACATCATCTTTAGAGTGCAAATTACTGCACAGTCTACTCACATCCCTTAGGAGAGACTTAAATAACACCGCAGCCATGTTTTCTTTGCTTCTAAATGTTGATTTCTGGACTGAGGATATAGCATATTGGTAGAGCATTTGCCAAATGGTGACCCATAAAGACTTGGCCTCCTAGTGGGTCACTTGTCACATATGGTTGAACATTTAGATATTTTCCATGCTGTTTCTGTTATGGTGTGCCCGTGACCTCCTGCAAAATTTCACTCTCTGTTTAAGTTCTCCCCCCATAATAAGCGAGGTCCCCAAAATTCTTTTAGATGACATCTGCCCACCATGTGACAAGAAAGGTCTTAAGATCAAAGTTGCCAGCTGTTTTTGCTTCATCACTAAGTGATAGGCTGAGATTTTGAGAGCTGAAGCATCTCCCACACATGGCAGCAGTCTGCCTGCTCACCCTGGGGCCTTTCTGAATTATCGAGAGAGAGGTTCAGAGACCCGCTCTAGGTCTGTGAGGAGATTAGTCAGCAAATGCACGTTTTTCCTTTTTAAGAGAAATTTAACCTTAGTTGCCAGAGAAATTGGTCCAAGTTTTGTTGATGTGTTTTTTTTTTTTTTTTTCTGTTCATCTTTTCCCTCCCTGTCCTCTCAAATCTGTCCCCTGTCCCTTAAGATCTCATCCCGTACAATGATTACCAGCACTGAAGTGCTAATCCTGCCTTTGGTTGCATTGGCCTGGGGATTTGGCTATGGATACACAAGTGGTTCACCACCACTACTAAGCTCCTGCCCCTGACTGTGGTCACCTCTTTCCTCTCTCACCTGCTTCTCCATCTCAGACTTTCAAGTCCCCTGCCTACCCGGCTCCAGACATGCTGGAGTGATAACATTGTAACAAAGTATAACAAAGTGCAACAAAGTAACATAAATCAACCATAGTAGAACCAGACTTCCGGTCAATCTGAATGGAGGTCTGGGCCTCTGAACCAAGACTCTATCCCAAAGGCCACTTTACTGAGGCTCTATCCTGTTCCACACAATAGGATGAGTATCTTCCTCCTGGCTCTTTTGCTCCACCTCCCTCTCTTGGCATCCCCTTCTTTCCACTCTCCCCTGGTGATGGACTTGTAACACGAGACTGGGTTTTTAATTTTATATTTTCTTCTACGATTCTACTGTATTTCAGGGTTTCTTTTGTAAATAAAAAACATCCGGTATTTAAGCAATTGGCCATGGTTCCAGTTTTCTAACTCCATTGTTTAGTTTGTCTTTCTCTTCCTCCTTTTAACAACTATAAAGCCTCCTGGGGAAGCGGCATAGCAGGCTCGGCAGTGAGTGCTTTCTCCTCACACATTGCACCTCTCTGCTTTATTGACCAAATCTGTGTCCCTAAGGACCCAGATAGGGGAGATTATCCATTTATGGTTCCTGGGCCCCATCAGTACCCCACCCCCACTTTTCCTCTTTAG
Seq C2 exon
TGTCCCATCCTGATCAGCCTGAGTTCACACCGGTCCAGGACGAGCAGGAGGCCATGGATCTGTGGAGCGCAGGCATCTGATGACCTCAGGAGACATTTGAAGAGCAGGGGCAGGCCCTCTTCTGGAGCTTCACTTACCAAATGCTGTCACGTGGTTTGTCCTCTACTTTGCAGAGGGAGGCAGGGCTGATGGTATGGGGTATATTTCCTCTGTGGATAACGTCAATATTACCGTTTTTTAAAAATTGTGTTTTGAAACCGCCCCTTTCTGTGACACTGTTTTAACTGTACACCAGTTACTTTGGACTTCTTCCAATGAAGAGTGCTGAGAAGGATACACCCTGGAGTGTCTTCTCTGTTACATCATTTCAAGTTGTAAAATTAATAAGAGAAGCGTGGTTATATCAGAGGGAATTTGGGGCCCTATCAGCAGAAGAGCGAATTCAGAGATTCCCAGTTTATACCACTGTCCCTGTACCCATGTCAGTGACCTTGCTGGTAATTGAATAACACCATCACTGAGGAAACTACCTCCTACTTGTTTAACCTGATCTGTCTAACTCATAGATTACTCAGTAACTGGTTTTCACGGGTGTTCAGAAATAAGAGCTAGAATATAGCCTTTCTCGATTCTGTAATTAAAAACAAAACCATAGAGTCTGTTTTCCAGTAGTCTTGATTCGTATAAAATAATGACTTCCTTCCAGTTCCGATGCAGAAAAGACCCATCTTTTGGCAGATCATTTGTCCAGGAGTGTGTTTCAGGGCTTGCCTCTCCTCGACTTACAGGGATTGCTTTGTAAATGCAGATATGTTTTTGAAGACTTGTTTTTATCCTTTTTTTTATAAGCAAATAAAAACTTAAAACACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022371:ENSMUST00000023053:47
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.995 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(75.0=79.2)
A:
NA
C2:
NO
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:
CTGGGAGTACCTGGACCTCAG
R:
AGGGGCGGTTTCAAAACACAA
Band lengths:
347-1942
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