MmuINT0023987 @ mm9
Intron Retention
Gene
NA
Description
NA
Coordinates
chr1:164653241-164655000:-
Coord C1 exon
chr1:164654835-164655000
Coord A exon
chr1:164653419-164654834
Coord C2 exon
chr1:164653241-164653418
Length
1416 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGATGTTACTGATCTTTTAGTTG
3' ss Score
5.85
Exon sequences
Seq C1 exon
ACTACTTTTAAGGGGTGTGTCAGGAGGTTTTGGACTAGATGAGTTTCCACCGAAATGTCGGAGAAGTCAGGCCAGAGCACAAAAGCCAAGGATGGGAAGAAGTATGCAACACTCAGTTTGTTTAACACTTACAAAGGAAAGTCCTTGGAAACACAGAAGACTACAG
Seq A exon
GTGAGTAGATGCAGTAGCCCACGTTATCTGGTTTGTGGGTTTGTTGATGCAAAGACACTGTGTCTAATGTGTATGATTAGAAGCTAGGGTGAACCCGTTTATTTTAGCCTTTTTGTATGTATTCACATTCTTTCCAGGGAATAAGAATTAAATATTTTACCTTTGAAAATTTGTTTTAATTTTTTAATGATACTTAGATGTTGTAGATGTGTGTGTTTGTGTGTGGATATGGGGAAGTGAGTGCAGGTGCCTGCAGAGGTCAGAGCTATGATATATCCCTTTGGAGCTGAAGTTACATAGAGATAGGTGTGACTTAGAACTTAACAGCTACTGTTCTTAACCTCACAGAACTTTGTATATATACACTTCTCTATACACTTGTGTCTATAGGAAAGAAACCATATAAGAGACGAAGAGGGGAGTGGGTGGGTGTGTTCGTGCTACAGGGGGAAAAAAGTCCTGTCTTTTTGACCTGGGTCCCTTGCACCACCAGTACATACAGTGAAAAGTAGAGCATTTGCTGCAGTATTGTGAACATTGTGGGCTTTGTTTGTGGGGTTAGGGGGTGATGAGACAAGGACTTGTTGCTGTGTATTTTAGTTAGGGTTTTATTTACTGCTATGAAGAGACACCATGACCAAGGCAAGGCAACTCTTCTAAGGAAAACATTTAATTGGGGCTGGCTTACAGGTTCAGAGGTTCAGTCCATTGTCAACAGGGTGGGATCATGGCAGCATCCAGGCAGGCATGGTGCAGGAAAGAGCTGAGAATTCTTATATCTTATTCTGAAGGCAGACAGGAGAAGACTGGCTTCCAGGCAGCTAGGACAAGGGTATTAAAGCCTGTATCCACAATGATAACACTTCCTCCAACAGGGCCACACCTCTTAATAGTGCCACTCCCTGGGGCCAAGCATATACAAGCCATCACACTGTGTAACCCTAAAGGGCTTAGAACTTAACAGTGGATCAGGCCAGCCTCCAACATGAAGCTATTTTCCCACTTTCACCTTCCAAGTTGTGTAGTTTGAACTTTCTTCTCTTAACATTTTAAGTTTTTTACTTAAAATAGATTGCCTGAAAACATTTCAAAACTAGCATTTCCCCTTCCCATATTCCCAGTATATAGTGTTCCATATTTAGAAGTTAAGGGGTTCTGGTGGGTGGGTTTGTTTTGTTTTTTGAGACAAATTTTGCTGGGGTCCCAAGATGGCTTAATATTTTGAGTGGATTGTTTACTTTTTACCTTCAATTAATGTTGTAGGTTATAAACTGAGTTTATAGAGCTCTACTTTAACATTGGGGACTAGTCAGAGATTGTTAACTCCTGTTCATGTATATTATTTGTTGAATAAAATGTATAATAGAGTGATGAACAGTAGATGTTCTAAGGAAATTGATGTTACTGATCTTTTAG
Seq C2 exon
TTGCAGCTCGACATGGGTTACAAAGTCTTGGAAAAGTTGGTATTTCACGGCGAATGCCCCCACCTGCTAACCTTCCAAGTCTCAAAGCAGAGAACAAAGGCAATGATCCTAATGTGAATATTGTGCCCAAAGATGGGACAGGATGGGCATCGAAACAAGAGCAACATGAAGAAGAAAA
VastDB Features
Vast-tools module Information
Secondary ID
-Bat2l2:NM_001081290:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTACTTTTAAGGGGTGTGTCAGG
R:
TTCTTCTTCATGTTGCTCTTGTTTCG
Band lengths:
342-1758
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: