MmuINT0039965 @ mm10
Intron Retention
Gene
ENSMUSG00000031503 | Col4a2
Description
collagen, type IV, alpha 2 [Source:MGI Symbol;Acc:MGI:88455]
Coordinates
chr8:11445960-11449287:+
Coord C1 exon
chr8:11445960-11446246
Coord A exon
chr8:11446247-11448058
Coord C2 exon
chr8:11448059-11449287
Length
1812 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGT
5' ss Score
8.35
3' ss Seq
ATCTCCTGCTCTCTCTGCAGCAC
3' ss Score
11.5
Exon sequences
Seq C1 exon
GACTGGCAGGCTCCTGCCTGGCACGCTTCAGCACCATGCCTTTCCTGTACTGCAATCCGGGTGACGTCTGCTACTATGCCAGCCGCAACGACAAGTCCTACTGGCTCTCCACCACGGCCCCTCTGCCCATGATGCCCGTGGCTGAGGAGGAAATCAAGCCCTACATCAGCCGCTGCTCTGTGTGCGAGGCTCCGGCCGTGGCCATTGCCGTGCACAGCCAGGATACCTCTATACCCCACTGCCCGGCTGGGTGGCGGAGTTTGTGGATCGGATATTCATTCCTCATG
Seq A exon
GTATGTATCCCTTCTCCATTCTCTGAGCATGGTACCAAGTGGAACCTTCCCCATCTACCTCCTAGCTGGGGCACAGAAAGGACACATATTAAATAAACCAGGGCTGAAGATTTGAGCTCCATGGGTAAAGTTTGGATCTCCAAGAACCATGGAAACACCAGTGAGGTAGAGCTTGCCATGCTGTATCTGTGCCAGGAGACAGACAGTGGGATCCCACTCATTCCCTTGCAGGCTAGACTATCCAAAAAGCGCCAGATTCAAGGTCCAACCCCCTTCTCAGAAGATGAGGTGGAAACCAATTGAAAACCCGTGACCTCCAGATAATCACATACACTAATCATAATTGGCAATTGCCCAAGTTGTGTGTCATACAAGCGCACCTAGTGCAGGAGTGGAAGGCTGTCATTCAGCTGGACCTGGGCTGAGCTGTGTGCTAGGCAAGGGGCTAGCTTCATGCAGTGTGAGGATCGATTTGCCACCCTACCTTTACATACAAGATGCAATGTTTCTGTCTTAGCAACAAAGTCTACACTTTCTGGTTTGCTGCAGTTTAAGTGAATGGAAGAATTCTCTTTCAGACTCTTTCTGGACTATAGAACACTCCTTCCCAGCACGTGCTGGCTAGCTGGTCTCAGCTGCACCCAGCCATGGGACCCTGGAGTCTGGACTCTATTGTACGCAGAGCCCCAGCTCCGGTGGGACTCACTCCGGATGATCAGTTTCTCTGTTTTCTTTTACTTTTGCCTTTTTTGTTTTTGAAAGAGTCTCACTCTTTAGCCCAACTTATCCTTGAATTCTTGGCAATCCTCCTGCCTCAGCTTACAAACATGAGTTACCACTGGTGGTGGTGAATCATGCCTTTCATCCCAGCACTCAGGAGGTAGAGATGGGTAGATCTCTGAGTTTGAGGCCAGCCTGGTCTAAAGAGTAAATTCCAGGACAGCCAGGGCTACAGAGAGAAACCTTGTCTCCAAAACAAAACCAAAAAAACAAAAACAAAACAAAGAAAAAACAAAAACAAAACAAAGAAAAAACAAAAAGAAAACAACAAAAACAACACAACAAAACCGCGTGAGCTACCAAGAATGGCCTATTTTGAGTTGTTGATTTTTGGTTGGTGGTTGGTTGTTTTTTTTCATCTACTGGACATCTTGAATGGATAGTTTAACCAAAATATAGTCAGTCATATCTACAGATTGTATCTACTTCTTGATTGTGGCTTTCATTGAACAACCAGCCATGGATGCTAAGGTTCATGCCATGCCTGCATCTACGACACCCTCCCCCAACATCAGGACCAGTCCCTTCAGTCACCCTGAAGGCAGAGCACCCTCCCCAGGGTCTATGTGACAGATATTCCTGTTATTGACTTAGCAAACAAGCAGGGACCAAACAGGGATGGAGGATGTGGCTTGGTCCAGCATGCACGATGCCCTGAACTTTATCTGCAGCACTGACCAAGCTGGGCACAGGAGCCCACCTGTGAGCCTAGCCCCCGGGAAGTGAAGGTAGAAGGCAGGAGGGGAAGAGTTCAAGGTCAACCTAAGCCACGTATAGAGTCATGTAGAGTTGGAGACTGGCCTGGGCAACAGGAAAGACTGTTAAACCCAGGAGTGCTGTTGCGTGCATTTGATCCAAGCTGCTGGAGACCCTAAGAGAGGAGCAATTATTTGAGTCTAGGACTTCAACACCAACTAGGGCAACATAGTGAGTTTCTGCCTTGAAAGTATGTAATTAGCACAGTTGGCCGTAGTGCCTGGGTGTTTCGGGCATGTGACCTCTAACACACTTCATCTCCTGCTCTCTCTGCAG
Seq C2 exon
CACACTGCAGCCGGGGATGAAGGCGGTGGCCAGTCACTGGTGTCGCCGGGCAGCTGTCTAGAGGACTTCCGTGCAACGCCATTTATCGAGTGTAACGGGGGCCGTGGTACCTGCCACTACTTCGCTAACAAGTACAGCTTCTGGCTGACCACGATCCCAGAGCAGAACTTCCAGAGCACACCATCCGCTGACACGCTCAAGGCTGGCCTCATCCGCACGCACATCAGCCGCTGCCAAGTGTGCATGAAGAATCTGTGAGGCTCCCGCCCTGCCCACGGCAGCTGTGTGGGAAGGCCACGTTGGTGCTTATCCTTCTGTATTTGTTTCAACTTTGTTTGAGACAATGTCTCACTTTTCATCCCTGCCTAGCCTGGAACTATGTAACCCCGGGCTGGCCTCCAACTTGTGGCAAACCTCCTGCCTCAGCTTCCCAGATGCTGGGATTATGGGCATGCGCCACCACACCCAGCTTGGTGCTTACTCTTAACTTATTACCTCAGATGCTGATCCCAAAGTTGATCTTAGTGTTTTCAAACTACCAAAGCAATTCTGCACCAGCACTCATTCCAACCGTCTGTCAGCAAGTGGGCACTAGCTCCTCCGGGATCTACCAGCCTTGGCTCACAGCCCTGCTAACACCCACCTTGGAGAGCCAACACCTAGGAGCAACCCACGGACCTCTCCCCATGTAGGACATAAACATCATGCTACCAGGTGTCCCCAACAATAGCTGTCTCTGTGTCCCTGTGCTTCCCCTGGCAACAGGCTGCTCACCTTCCTGCAGTCTTCCTAAAATGAGGCAGAGTCTAGGGGACAGCAAAGGAATCTATGGCCAATGATAGCTGAGCTCACTGACCCATTTCCACCCAAGGATGCATGCAGTGTGCTTCTGTCTAGACCTGGTTTCTTGGAGGAGGAGATGATAGCACTTTTTTCTATCAAATCCATAACTGCCACCTCCCAAGTCCCTACGTGTTGGCCCCTGCCTTTTTAAGACCCTGACGGCAGCTGGCACACAGCTCATGGCTCTAGCCAAACCCACAGCAAAGGAGACATCTCTCTAGCCCTCACCAGCATCTGCTGGAAGGTACACTTAGCAAATCATTGACAGTGGCGTCCTACAACCTGTGTCACCCTAAACACCTCCCTCCACAACCTGTTCCCTGCGGCAAGCTGTTCTATGGCTTTTCTGTGTAACACCATAAATAAAAGATATTCTAAGGACTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031503:ENSMUST00000033899:47
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(26.1=31.2)
A:
NA
C2:
PF0141314=C4=PD(72.2=96.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCAGCACCATGCCTTTCCT
R:
CTCGATAAATGGCGTTGCACG
Band lengths:
352-2164
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