MmuINT1031417 @ mm10
Intron Retention
Gene
ENSMUSG00000011486 | Slc25a41
Description
solute carrier family 25, member 41 [Source:MGI Symbol;Acc:MGI:2144215]
Coordinates
chr17:57039818-57041654:-
Coord C1 exon
chr17:57041574-57041654
Coord A exon
chr17:57039974-57041573
Coord C2 exon
chr17:57039818-57039973
Length
1600 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACT
5' ss Score
8.77
3' ss Seq
AGCAGCGGCTGTTCTTGCAGGTT
3' ss Score
6.46
Exon sequences
Seq C1 exon
AGCTGGGAGCCAGATAGACGCCCCAGAGGACGCTGAGACTGGGACCTTAATCCTTCAGCAACTATGGGAGTCCATCTCGAG
Seq A exon
GTAACTCAGCATCCTCGTTTGAAGGTTCAAACCTTGCTTAAGAGGGTCAAGGCTCAGCCGGGCGTGGTGGTGCACGCCTTTAATCCCAGCACTCAGGAGGCAGAGGCAGGCGGATTTCTGAGTTCAAGGTCAGCCTGGTCTACAGAATGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCGGGAAAAAAAAAAAAAAAAAAAAGAAGGGTCAAGGCCTTATTTAGGAAAGCTCCACCCTGCCCTACCCCCACCCCTCTCCAGCCTACCCTACCACCATCTGAAGCATGGAACCCAAGGTGCACACACATGTATGAGTATGTTTGGACATGTGGGTGAGAACAACCCTGAGCATCCTTCATCATAGCAGGTAAGTCTGGGGAGTGAGATGGCACAGGCTGGACCAAAGGGAAAAAGCTTTGAGGCCCATATGGTACGGAGCACCTCCCTCCAGACAGAGTAGAACAACCTACACTGAGACCATGTGTGAGACCACGTGGTAGTTCACACCTGTTATCCCAGCACTCAGGAAGCTGCAGGCAGGACATCAAGAAAGGTCAAGGTCATTCTTGACTGTTTTAGTGAGTTAGAGACCAGTATGGGCTACTTGAGACCCTGTCTTAAAAGGGGAAAGGGGAAGAAGAGAAGGAGGCTGGGGCTGGCTAAGGAGACGAAGTGCCTGACACTCCAAAGCATAAGGCTGGACTTCAGAACCCTAGAACCTGTGTAAATGCTGGGCAAGCCTGACAGCCATCTGTAACCCCAACAGCACAGAAGTGAGACAGAGATGGGGGAGCAAGCTGGCTGGCTAGACCAGATCAACTGCTGAGCCTCTGGGCTCAAGTGAGGAACTCTGCCCCCACATATAAGGTAGAGAGTGGTCCAGGATGACCCTGCACATCAATTTCTGGCCTAAACACACTCACACACAAGAGACACATGCCACTTCAAACACGCACGTACTCTCTCTCACATAGTCCCACTCACATGCATGCACTCTCTCTGACACACACACAGAGTCACACATATCACTACACACACACTCACATACACACAGTAACACATACATGCATACACTCTCTCACGCTCACACGCACAAAGATAGGAAAACAGACTGGAGAGGTTAAGAGCTCTCACAGAGGACAAGAACTCAGTTCCCAGCAACCACATGCTGGTCCACAACCAGATGCATTGAATCCAGTGTGTTTTTCTGTTCCTCTTGGATACCTTCATACACAAACAAAAAGTAAATCATTAAGAAAGTCAGAAATCAGCTAGTGGCGTATGCCTTTAATCCCAACACTTAGGAGACAGAGACAGAGATCTCTGTGAATTAGAAGCCAACCTGATCTACACAGTGTGTCCCAGGACAGCCAGAGCTACAAAGTGAGACCCTGCCACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACCACCTAATCACCCCCTCCAAAGAATTGTCCACATTGAGGCAGCAAACAGAAACAGCTCCTTTAGGGCTCCGGAGGGAGTGAGCTCTTTTAGGACTGAGTGTGGCCAAGCAGCGGCTGTTCTTGCAG
Seq C2 exon
GTTCTGGACACGGGAGAGCAGCTGATGGTCCCTGTGGATGTCTTGGAAGAGGAAAACAAGGGGACCCTGTGGAAGTTTCTGCTCTCTGGAGCCATGGCTGGGGCAGTGTCTCGCACAGGGACAGCACCTCTGGACAGAGCCAGGGTGTACATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000011486:ENSMUST00000058661:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0015322=Mito_carr=PU(35.1=63.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGGAGCCAGATAGACGCC
R:
ATGTACACCCTGGCTCTGTCC
Band lengths:
230-1830
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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