MmuINT0089730 @ mm10
Intron Retention
Gene
ENSMUSG00000026478 | Lamc1
Description
laminin, gamma 1 [Source:MGI Symbol;Acc:MGI:99914]
Coordinates
chr1:153218922-153223758:-
Coord C1 exon
chr1:153223659-153223758
Coord A exon
chr1:153221730-153223658
Coord C2 exon
chr1:153218922-153221729
Length
1929 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGT
5' ss Score
9.66
3' ss Seq
TGTCCACTTCCTGTCTACAGGAC
3' ss Score
11.08
Exon sequences
Seq C1 exon
GCTTCGCAGGCTGCTCAGGAGGCTGAGCTCAATGCCAGAAAGGCCAAAAACTCTGTCAGCAGCCTCCTCAGCCAGCTGAACAACCTCTTGGATCAGCTAG
Seq A exon
GTAAGTAACAGAAGGGTTGCTGCAGCCACCGCTTGCAGGGCTGAGTCCACTGATGCAGAGTCACATTCTCTAAAAGCATCATTAAGGCATTCATATTAATGTTTTGTTTAGCTCTTGCTTATTTAAAGACACCTTGTACACAGTGTCTTGCTTGGCAGAACCTTGTAAGGGCAGCTTGCATCGGCGCGACACTGATAGGCTGTCGATTCTAGAGTGAAGGCGAATGGGACTCTATTAAGTTCAAGTACTTAGGTGCCTTCCCTGGGGCTGAGATGAGCTGCCAGCTAGGGATGCCACTATGGCCAAGGTCCAGCCTACAGTTAAACAGCCATTTCCTCTTAGTTCTGCCTGCTGGTGGAGCGTCTTTAAGGGATTTGAAGAGAAAGGCTCAGTGGGAGAATAAAATAATACTTGAACCTGACTGCACTTCAGAGCTCAGAATTCTCTCCACTTGCCAACCAAAGAACAATTTGATGAAGTGAAAACTTTCACACCAAACAAGAGAAAAGCTTTGTTTTGTCTTATCTTGTTTCAGGGACATATAAGCGCTGAGCTCTCAATTTAACCCAGTGTGGTAGAGAACTGAGCTTTCTTAGGACCTCCATTACGAGAGAGTCATATAGCCACCAAAGACTGGGGATGGATTCTTTTATGTTTTTTTTTTTCTTAAAGGGAAGAGAGATAATATTTTATCTGTCTCAGAGACCAATAATAATAAATTATGTGCCTAGAATGAAAGCAAGCTAAAGCAGGGGCTTTACACCTTCTTTATCCGTTAGGTTGTATAAATGCATGCAAATAATTCTTGACCGTCTGTACTTGCTGGTTTTGTGTCAACTTGACACAGGCTGGAGTTATCACAGAGAAAGGAGCTTCAGTTGAGGAAATGCCTCCATGAGATCCAGCTGTAAGACATTTTCTCAATTAGTGATCAAGGGAGGAGGGCCCTTGTGGGTGGTATCATCCCTGGGCTGGTAGTCTTGGCTGTATAAGAGAGCAGGCTGAGCAAGCCAGGGAAAGCAAGCCAGTAAAGAACATCCCTCCATGGCCTCTGCATCAGTTTCTGCTTCCTGACCTGCTTCAGTTCCAGTCTTGACTTCCTTTGGTGATGAACAGCAACATGAAAGTGTAAGCTGAATAAACCCTTTCCTCCCCAGCTTGCTTCTTGGTCATGATGTTTGTGCAAGAATAGAAACCCTGACTAAGACACCATCTGAGAGTTGGTGAGGTAGACTGGGCTCAGGAAACTGCTTGTCTTTCTGTATGATTTTATTTTCTATAGAGCATCTTCTTCCAAAAGAAACTATTATTTTTTTCTTGATATATTTAGAGCAAAGCTTTGCTTACAGATCTCGGCATTTTAACCTTGGTCGTTTTTCATCAAAAGGTTGCTAGTGGTGTGTAACGCCTACAAGCAGAAAGTGACCCCCAAACGGCCCCATTTGAATCCCAGGAGTTGAGGATGTATGCTTCTATCTTAGAGACTTTGGCATTCTTTGACGATACTGAAATGGACCACAGATTACACCTAGATTACACATAGAAACCTGCAGAGGATTGAGTCTTACCAAGTCACCTTCTTCAGCATAAGCGAGGTCTAAGACATGGTGCTTATACATTTAGAAACACATCCTCCGAGGGCTAGAGAGATGGCTCAGTGGATAAAAGCACTAGCTGCCAAGTTGGACAACCCGAGTTCAATCCCTGGAAACCTCATAGTGGAAAGAGAACCAAGTCCTGCAAGTTGTCCTCTGACATCCACACACATGCTATGGCATTCATGCAGACACGCATGTACACACATGTGCATAGTGATAAGTAATAAATATCAAATTAAAATATTGTGTGAACAAAGCTTTGTCAAAAAAGAAATCTGTCCTAGTATTAATGATACACGCTACTTCTCCTCTGTCCACTTCCTGTCTACAG
Seq C2 exon
GACAGCTGGACACAGTGGACCTGAACAAGCTCAATGAGATCGAAGGCTCCCTGAACAAAGCCAAAGACGAAATGAAGGCCAGCGACCTGGACAGGAAGGTGTCTGACCTGGAGAGCGAGGCTCGGAAGCAGGAGGCAGCCATCATGGACTATAACCGGGACATAGCAGAGATCATTAAGGATATTCACAACCTGGAGGACATCAAGAAGACCCTACCAACCGGCTGCTTCAACACCCCGTCCATCGAGAAGCCCTAGTGGCGAGAGGGCTGTAAGGCAGTGTCCCTGACAGGGGACCCTGTGAGGCCTCGGTGCCTTGACACAAAGATTACACTTTTCAGACCCCCACTTCTCTGCTGCTCTCCATCACTGTCCTTTTGACCCAAGAAAAGTCAGAGTTTAAAGAGAAGCAAGTTAAACATCTTTAACCAGGAACAAAGGGTTTTGCCTAATAAAGTCTCTCCTCCACTTCTGTCAGCACCCTACCGGAACTTTCCCTTGTTTGCCTGAAGTCACGGCATCTTCCAGGGGCCTACCCACATCATGTGAACCTTTTAATGCCAGGGCAGACCCAGCCCCCTCCCCTCTCTCAACACCAGCAGGACCTATCTCAGTACTCATGTTTCTATGAAGGAAATCTTTGGCTCCTCATCGTAGCATTGAGATGGCCAGTATGTCCGCTCTGCATCTTCTGCCTCCTCTTTGAAAGGAAATAAACATCCTGTGCCAAAGGTATTGGTCATTTAGAATGGTGATGGCCATCCATCAGACATGCTGGCTGGCTGAGCATAGGACACAGAGCCATCGTGGGTGACAGCGTAGTTACATGTGGGTCCCCAGGAGAACATGGCTCAAAGATGCTTAGGGTTTCCTCCTGTTTTCATTGACTAGGAAGATGAATGTTTCCCAAATCCTCAGGCAGCTGATAAAAAGTCTGGATGGGCAGCTCGCACGCACCACTACGTGAGGTAGCTTTTGATATTTTTATAAGCAGGACTTAATGCAGAAGAAACAGATGTGATAACCCACTCAAGTTTTTTTCCCCAAGTAGTACTAATTCTTGAAGCTTTGTTAGTGTTAGTCTTGGAACTGTTGGTAAGATATCTGTCAAAACAGTTGTCCTCTAAGGTCTTGACCAATGAAAGAAGAGCAAATCTCCTTTTCCCCATATTTTCTGGGAAGTGGCTGTAATTGGGATGTAACCGCTCTCATTAGGATTCCATGAGTGCATTTCTTTTTCTCTTTTTCTTGGAGAGAGATGTGACATTTGGCCCTTAGCTCCATTCTCTTCTGATGTTTCCGTTCTTTCTAGAACTCTTCAGAGCACATCGTTGTTTGCCAGGTCCTGGTGGCAAACACCCGCTCTCAGTGTTTCTCAAGGCTGCCAACCCCATCTAGTTCCTGCACTTTGTGGCTCTGCCCACTCCAAGCCTTTCCTCTGTGTGGAGAGGGAAGATCCATGCGTGGCATTTCCTAGTGGGCTTCTCAACCTCTGATCCTCAGCTCGGTGGTCTCCTTAAGACCACACTGTGACAGTTCCCTGCCACACATCCCCTTCCTCCTACCTACCTGCCTCTGAGATTCATATTTAGCCTTTAACACTATGCAATTTTGTACTTTGCGTAGCGGGGGAAAGAAACTATTATCTGACACACTGGTGCTATTAATTATTTGAAATTTATATTTTTTGTGTGAATGGATTTTGTTTATCATGATTATAGAGTAAGGAATTTATGTAAATATCCCCGGTCCTCCTAGAACGGCACTGTCTGCTCACGTCTCTGCTCAGTTGTCCCTCTCACTGGCACAGGAACCTGTACCATGCCTGGTCACGTCGTGCCTAGTCCCCAGTGTTTTGCTCCACCTCTGCCTTGTGTTTGCAGCACCTTCACTGTCTGACGGGAAGCCTGCTCACCTCCACAACCTGACCGAAGAGGGCCCTCTTCCCCGTGGCTCTGACCATCTGAGCTGCAGCTCCTCAAGGTTCTCATGCCTGCCCCGGAGCAGTAGCCAAGCTGACAGGGTAAAGGGATTAGGAACGTTTGTTTGTGGAACCTTCCCACACGGGTCAGTTTTCTAAGGGAGCATGTGATGACTGAACACTTGAGGGCATCAGCACCGTGCTACTGATGACAGAGGGGAGGCTCTGTTCAGCCTGTCTCCATCTCGGAGATTGCCACAAAATCTCAGCTTGGCATCCTCCGAGGCCTTTTGTGCCACGGCAGAGGCGTGGCCTCACCAAGTTCAGTGCTGATTGGCTAGTTCCTCTATTCCGAGCTCACCACCTTAACATTTTGGTCACAGTTGCAAGAAAATGGCTGAAACAGACCACCACCAGCATTCTTTGGGTCAACTCCACTCCAGCAGGCCCGAGGCGCTGGTGGGTGGGGTGTTTTGGTTTGTTTTCTCCAGCTTTTGTGGTATATTTTTAAACAGAATTTTATTTTTTAAAATGAAAGTTATTTACAAGATGATACCTTATTACACTCCTTCGACACAGCCATTGCTTTATTGTATAGTTCCAATAACCTGTATTTTATGTAATGAAATGGACAGAATGGCTGCTGTAGAATGCGGGGTGCCGCACAGAACAGATTGTTTTATCCCTCCCCCGCCCCCGCCCATGGAATTTTCCTTTGATTCCAACTGTGGCCCTTTTCAATGTGCCTTCACTTTAGCTGTTTGCCTTAATCTCTACAGCCTTCCCCCCTCAGGGAGGGCAATAAAGCGCAACACTTGGCATTTTTTTATGTTTAAAAAGAAAACAGTATTTTATTTATAATAAAATCTGAATATTTGTAACCCTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026478:ENSMUST00000027752:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.529 A=NA C2=0.439
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF115703=E2R135=PD(22.2=48.5)
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:
AGCCAGCTGAACAACCTCTTG
R:
TCTTTGTGTCAAGGCACCGAG
Band lengths:
358-2287
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