MmuINT0131813 @ mm10
Intron Retention
Gene
ENSMUSG00000038020 | Rapgefl1
Description
Rap guanine nucleotide exchange factor (GEF)-like 1 [Source:MGI Symbol;Acc:MGI:3611446]
Coordinates
chr11:98836785-98840338:+
Coord C1 exon
chr11:98836785-98837673
Coord A exon
chr11:98837674-98840259
Coord C2 exon
chr11:98840260-98840338
Length
2586 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
ACGCCCATTGCTCTCCACAGATA
3' ss Score
8.55
Exon sequences
Seq C1 exon
CCCGGGGCCAGGAGCGCAGCCGCCGCCGCGTCCTCAGCCTTGCGCTCCGCCCGCTGCCTCTGTCGCCTCAGCCCGGCCCCGGAGCGCTGAGACGGGGACACCAGCCCCTCAGCCTGCCAACCCTTCGGCCGCAGCCGGCATGGGGGGCCGCTGAGAGCGAGCTCCTCTTCCCTCTGGCACCTCCCCCGGCCACTGGCCACTGGACTCTGGCCAGCGAGGCTCGGCCACCTCTCGCTCGCAGTCCGACGCCTGGCACGGCCCTCGGCTCTGCTCCCCCGGCTCTGAGCATCGTGTCCCCGCCTCCCCCCGCCCGCGCCTGGGACACCTGGGTCCCCCGGCGGCCCCTAAGAGAGGGGCGGGGGGGGGGGCATGAAGCCACTGGAGAAATTTTTGAAGAAGCAGACGTCTCAGCTGGCGGGGCGAGCGGTGACTGGAGGTCCCGGCGGGGGTCCGGGTTGCTGCGGAGGGCCTGGAGGGGGTGGGGGCCCTGGTGGGGGCGGCGGTCCGGCCGGGGGACTGCGGCCACTGCAGCGGCGTCAGAGCGTGTCTCGCCTGCTGCTCCCAGCTTTCCTCCGAGAGCCCCCAACCGAGCCCGGGCTGGAGCCGCCCGTTGAGGAGGAAGGGGGAGAGCCATTAGGGGTCTCTGAGGAGCCGGGCAGTGGGGGGCCCTGTTGGCTGCAGCTAGAGGAGGTTCCCGGGCCTGGGCCGATAGGATCTGGGGTGCCCCTGCGCTCTCCTTCCTCGTACTCCTCAGATGAGCTATCCCCCGGCGAACCCCTGGCTTCACCACCCTGGGCCCCCCTGGGCGCCCCCGAGCGGCCAGAGCATCTTCTGAACCGGGTTCTGGAGCGCCTGGCTGGAGGGACCACCAGGGACAGCAGCGCCTCAG
Seq A exon
GTAAGCCTGCTCATCCATCCCAGAGCAAGAGAGCACGGGGTTGGGGGTGGGAGGTGAGGGATTGGCCCGGGGGATGCTCCCTGATTGTTTTTTCTTGTCCTCAGTGTTGGTGTAGAGGATGAGGGGAAGCCCGAAGTAATGTAGGGGAAGGGGCATGGTAATGCGCACCCACCTTCCTCCCCACATTAGCTTCATTCTAGGGGAAGAAGGGAAACCATCTCTCTCCTTCAACTACCCTCCCTCTCTCTCGGCTATTTAAGCCAGTCTCCCACGAGCCCTTGATACTGCCTACCTCCTCCCACGCCCCTAAATTAGGGCCTGACACCCTAAGGTGGACGCTTTCCCGCTGAGGTTGTACGCTGCCCTCCAGACCATAGCTGAGGCCTGAAAACCGCTGACAGGAGTCCCTGGCTGTGTAGGAGCGCCTCACTTGGTGGGGCCATGTGGATAGTCACAGAACTCGGCTGCTTTTATTGGGGATGAATTCGAAGGTCTCTAAGGGAAGATACCAGGAGACTGCAGCATCCAGAAGGCTTTGGGCCTCCGTAGCACCCACCCTTCCCATGCCATGCCTCAGCAGAGGGCCTTTTTTAAAAAAATAATAACCACACCCTGAGAAGCCTGAGATGATGCCATTTCACCCACTATGAGAATGCCAGCACCCTATTAAAGGGCTTCTGAGGAACGTAGGCCCCCACATCGCTAGTTGGAATAGATGTAGAGATATCAGGGTCTTTAGATCTAACTAGGCACTCCACTAAACCCAGAAGGGGCTTAGGGTTGAGAGACCAAGCTTGAGACCCTAAAGAGGAGGGTGTTAGGAGTTACCCTTCCTTCTCTGCAAGGCATTCTGGCTCTAGGAGTGGAGTGTCACCCTCTACTCCATTTTTGTCCTGAAGGTCGGGGTCCCCTCTTTTGGCTCAGGCTGCAGTTGCCCTGGGGAGCTGACACCTTTTGGATTTAATTAGAAAAATATCAGACACACACAGCTCTCTTAACCATAACTTCCCGCCTACACCACACACCCTGTGTCTCTATGACACATTCCCCAGGGAGGCTGTGCGTTGGACCGGAGCCTACTTTGGAAGAAACAGATGCCAAACTGGAGCCCCCGTATCAGCATCTCTCCACTCTGCCCGCGTTCCTTGTCCTTTACTCCCATTTTAACATTCACACTCTAGTGAGAGAAAGATGCGAGGAAGGATGTCAGGCCTCTTTATGCCGAGGCCCCAAACCTGGAGCTGGGCGTGAGGGCTGGGGACCCTTCTGACTGACTCTCAGAACATAGCTGGGTAGCTGGGTAGAAAGGGAAAGAGAGGCTGTCCAGTTTGGACAGCGGATTGTCCAGTTTCCCCTGGGTTAAGACTCCCCATTTGTCACCCATATTATCTGGCCCGACAGGCTAAATCTCCAGAGTAACTAGTTTGGGAATCCTCCCCATTTAAACTGCCACTCCAATATTTTTAATATAAGCCACGTTATCAAGCCTCTTGATTTCTGCCCAGGCTGCATGGGAGGCGACAAATGCTTAGTGAGGGCTCTCCTCACCTAGCCAGAGCTCCTTCAAAGGTCTAGGCAGCCCCTTGTGGCCAGTAGGTACTAGGCCCCCCCCCCCACCCCCATACTCTGCTTGCCCCTGTATTGAGTTGAGAACACAGCATTCTAAGTTCATCTGGCTCCGGGCCTCAGTTTCTCCTCTGTGAAACAAAATGAATTCAAGTAGACAATCTTGTGTTGCTCCTCCACCTCCACCTTCGTGGCTGGCATTGGCAGCAGGGCATGACAACCATGGGTTGTCAGAAGCCATGGTTTTGTCCTGGAGCAGTGCCTGGGGACCTGGCCCTAACCTGTCCTGGTGAGGACACCTGGCTCCCTCCCTGTGCCCTGCCTGTCTGTGTGTGCCAAGCAAGCCCTGCCCCACCCCAAGGCTGGCGGCAAGTCAGGGCGACCGACCTTGTACCTGGCTGACTGGCTGAGCCAGGCCCAGACAGGGGTGTGGAGGGAAAAGGGTGGAGAGAGGAGCCCCTCCCCTGTCCTTCTCATCATTAACCCTTCCACCTCTGGGCACCCAGTGGACACAGGACTTCTATTTAAAGACTGAGATAAAGAGATGGCGGCCTGTCTCCGCTGTCAATTTTCATGGGGATGGTCCCCACCCTGCCCTGTGGAAATTCAAAACTGTGAGGTTGGGAGTGATCGAGGAGGATGGACACACATCCCACACATCCACATCCCTCTGACTGGAACCTCTGCTTGCCAATTCTCCGTCGATGGTCCCTTCTGTGGACCCCTTTTTCTCCTGAGCAGATCTCAGGCATGGTGGTATTATCTGACCAACTTCCCCCACACTGAAGAGAAGGGTGCATGGCCTTCAAAGGCACCCCCCCTCCCTCCAGCTGCCTTGGCAGCTGCCAGCCCCACCCCCGCAGCGGCTGCCCAGAACCTTCACACATGTGTGCACTCGCGTGCAGAGCATGACGGGACAGGTGGCCGGGGCTCCAGGCTTACCAAAGAGGAAAAAAAAAAAAGAGGGTTCAAGGTTTGCAGCCCCCTTCTGACCTCTGTGACGCCCATTGCTCTCCACAG
Seq C2 exon
ATATTCTTCTTGACGACATTGTTCTTACCCATTCCCTCTTCCTGCCAACAGAAAAGTTTCTACAAGAGCTACACCAGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038020:ENSMUST00000107479:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.874 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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