MmuINT0108497 @ mm10
Intron Retention
Gene
ENSMUSG00000005397 | Nid1
Description
nidogen 1 [Source:MGI Symbol;Acc:MGI:97342]
Coordinates
chr13:13509433-13512275:+
Coord C1 exon
chr13:13509433-13509545
Coord A exon
chr13:13509546-13509945
Coord C2 exon
chr13:13509946-13512275
Length
400 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACA
5' ss Score
8.92
3' ss Seq
CTGATTTCCATCTTTTCCAGGCC
3' ss Score
10.32
Exon sequences
Seq C1 exon
GAATTCAGTGATTGCCATGGACCTTGCTATATCCAAAGAGATGGATACCTTCCACCCACACAAGCAGACCCGGCTATATGGCATCACCATCGCCCTGTCCCAGTGTCCCCAAG
Seq A exon
GTAACATCCATGCTGCTGAATGGAGGTCAACACTCAGAGTCTCTAAGAGAATCAGGGTGGCCTAAGTACATCCATGGGCCTGCTTCCTATAGGTATCTCAGCCTGGATATCCCTTCCTGAAGGATTCTTGGATTTTCCCACCTCAAGGAACTTAATCTAGAACCTCCTTATAGACATACCCAGAGGTGTATTTCTGTTGTGATTCTACCAACTTGATAATCAAGATTATCACACACCTCCAAGTCAGGAATACATGTACTTGCCTGTCTTATTTATGATAAAGAAACAAACAGCAGCTCAACTTGGCTCCTTGAGCCCACAAGGAGGTAAATGGGGAGCCTGCTGTAGGTACCAAGTCAGTCAGAGGTAAGACTATGATGCTGATTTCCATCTTTTCCAG
Seq C2 exon
GCCACAATTACTGCTCAGTGAATAATGGTGGATGTACCCACCTCTGCTTGCCCACTCCAGGGAGCAGGACCTGCCGATGTCCTGACAACACCCTGGGAGTTGACTGCATTGAACGGAAATGATGTCAAGAATTCCTTGTTCCCTCTCCAAGTATTTCATAGTAACACTCTACTTGAAGTGACTTGATCCAGACTGAAAAGTGTCCTGCAGTGGAATGACCACCAGGCCCAGATCTAGCCTAGCCTGAGCTCTCACAACCTCTCCTTAACCTTCCCTAGAACAATTACCTTTAGCTCAGTAATGGGAAAATCTCTACCCTAACATGAGGGCAGGACACACACACACACACACACACCCTTTGATCTCAGTCTTTAGACAAGTTTATAAAGTTCTGGATAAAAAGCCAAGGGTAGTGGTACATGCCTGCAACCCTAGCACTTGGGAGGCAGAGGCAGGAGAATCAGGAGTTCAAGGCCAATTATCTTGTCTGTATAGCAGGGTTTAGAAATAACCCGAGTTACGTGAGTCCCTTCCAAAAAAAAAATCAGGATAAAAATTATGTGTCCATTCTAGAGCCATAGGACTTCTTCCTAATTCTAGACTCTCCCATGGTAAGCAGAGCCTTAGCGACCTAAGGAGGCTACTTCTTGGTGGCATTACAAACTCAGATATTACCCAGTTTCTCAACATACCACCCAGATCCAGCTTAGGCAAGGTCATACTTTTTCTCTTGGTTATGCTCCCATCTAACTACTCTCCTGTTGTATACCTTCATTCTGCCCAAGACTGCTTTCAGTGCCTTCTCTGCCATATGATCAAAACCCAACCATATTCCAGGGATTCATGGTATTTGGTAGATGGTAAAAAGCAACCCCTCCCAAATTACAAAGTCCTGGCATTTCAGCAGTGGCCATTGATAATCACATAGGTAAGTCAAGGAAAAGTCCTGAGAGAGGGATTTGAAGTCAAGATGTTTGAAGATAGGAGATTATTATCTTGATGTGTCTTGAATTGTAGCAAATTCTTCTTCTTTGCCAAAGTACCTGTATTAGTTTCTGGTCTATGACGTCATGGGAATCTTCAGCCCACTCCTGGTACCAGTTTTCAAGTCTTCTCATGGAGAGTCATCTGGAGCTCAGGTTGGGGTAGGACTTTGACAAAGTAGTGTCCAGTCATAGTCCCTCACCTTTAGAATTGTGTCTCTGTTTCTCCCTCTCTCTGTGGCCCTTTCTGACTAGATCCTCATCTGAAGACACAATCTAGGAAGATCTAGTTGGGCATTTCTAGTAGTGGTTCGGATCCTTATTTGATCATCAGTATAGTTTGAGGGACTGTTGCTGCCTTCCATGTTTCTGTCTGTGATTTGTTTCAAAAATATCCGCTGGCCAGATGCATAGCTACTCTCCTGTCTGTTTTGAGGTGTCTGTGTTATTGATTCCATTCTAGGGACAACAGTATAAACTTAGTAATCATTTGTTCTTTTCTTTTTAAAAAACAAAACAACCCTTGTCCCCTCTCTCTTCCTTCTATCTACTATTATCTATCACCTATCTCTCTACTTATCTGTCATCTATCTCTATCTATCTCCTGTTTTCCACTGCTTCCTAGACACTCAAAGGATTAATAATTTTGGATTGGAAGTCAAGCATCAGAAGTTCGGTTTGCATGGTGTAAGGTGAGGGCACAGACAAGACTCAGGCAGAACTATTACAAGTGGTGGATAAGGATGGAGAACAGGGATGGAAAATCCCAGAAGAAACAGCAGTGGAGAGGCTTAAAGGCAGCTAAAACTAAAAGCCTTAAACAACTTCAGAGAAAAGTGGCACATTTGCCAAAAGAATGTTTATCCTTGAAGACATAAAAGAACTTGGCCTGATGTTTTTCTTGGGGAACAGAGCCCCCTACCTCCTTTTCTTCTACTTTCACTGTACTCAGCCCCCAACCCTATCTCCTACCTCCACCTCGACCTGCTTACATTGGACTGGGAATCTAAATTGGGAGGGAGTCTTTACTTAAATAATTGGAATTTAAATCACAAAGTTTAGGGAACGTGTGACTCTTTCATGCACCCTCATAAAGTACCCCTAGTTTTTTTTGTCATGTTCCTCATGATATATATCTTTTATAACTTTTATTCATTTTTACTAGATTCCTTCTAAAATGTTTTACATGGTAAATTGTTAAGCTGTGGAAACCACTGAAGGTGCTTATTAATGGTTCTCCAGATGTATACAAGTATTGGATGATTCCTCAAGTTTACAGCTGTACAAATATTAGTGCAGAAAAAAAATAATTAAAATACAACTGTTAAAAATAAAATCTTATTTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000005397:ENSMUST00000005532:19
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:
NO
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=75.6)
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:
GTGATTGCCATGGACCTTGCT
R:
CTAGGCTAGATCTGGGCCTGG
Band lengths:
348-748
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