DreINT0098271 @ danRer10
Intron Retention
Gene
ENSDARG00000103308 | mst1
Description
macrophage stimulating 1 [Source:ZFIN;Acc:ZDB-GENE-020806-3]
Coordinates
chr6:53416851-53418403:-
Coord C1 exon
chr6:53418283-53418403
Coord A exon
chr6:53416970-53418282
Coord C2 exon
chr6:53416851-53416969
Length
1313 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAAT
5' ss Score
-0.24
3' ss Seq
TGGGTGTTTTTTGTAACCAGATA
3' ss Score
7.05
Exon sequences
Seq C1 exon
AGGTGTGCATCACTTGTAATGGTGAAGACTACAGAGGGCAAGTGGATCACACTGTCAGCGGAAAAGAGTGTCAGAGATGGGACCAACAGTTTCCACATCAACACATCTACCAGCCGGAGAA
Seq A exon
GTGAATATGACATTACTATAAATCCAGAGGGGTACCTGGCAAACATGAAAGGAAAAGTGCAGATACTGTACTGCAAATTTGCTTTATTCATTCATTCATTCATTTTCTTTTCGGCTTAGTCCCTTTATTAATCTGCGGAATCAACCGCCAACTTATCCAGCATATGTCCATATGCTGGACACTCATACACTCTCATCCACTACGGACAATTTAGCTTACCCAATTCACTTACTGTATAGAGCATGTCTTTGGACTTGTGGGGGAAACCGGAGCACCCGAAGGAAACCCACATCAACATGGAGAGAACATGCAAACTCCACAGAGAAATGCCAACTGACCCAGCCGAGGCTCAAACCAGTGACTTTCTTGCTGTGAGGCAGTTGTGCTACCAACTGCACCACCGTGATGTGCTTTATTACAAATCACCGATTTTTTTTAAAATCAGTCCTAACGTGAGACTAAGGGTGCTTTCACACCTACACTTTTGTTTCGGAACGTATCTCGTTTGCCCAGTTAGTGCGGTTCGATTGGCATATGTGAACAGGGCAATCGCGCTCTGTTCCGCGCCAAAGTAATCGCTCCGAGATCGCTTGAATGAGGTGGTCTCGGCTCGATTGAAACGAACCCTGGAGCGGTTCGATTGCAGTGAGAAAGCGATCCGATCCGAGCGCGGTTATATCACAGTGTTTTATGCATACGTAATAGGCTTACGGCTATATGAAGAGAGAATTATGAGTAGGGCTGGAAGTTTCGCGAGTCTCCGGATGTCAGCAAACGAGTGATGATCTCCCGGTAATCTTGCCTCTCCCTCCCTCAAATAGGCATCGTCGCGCACCCTTCTCACCCCTCCCCACCGCGTCTCTCCTCAGACATGTCGCGCGCGCGCACCCTGTCAATCACCACCAAACCACCACCTCTCCTGACAGCTGAGCCGGACGCTGCAAAATAAACCCTGACACTGACCAATGTGAGGAGAGTTTACTCGCACGTGACTTGTTTTAGCTCTTTTGGTCCGTTTAGAAACTTTGCAGTGTGAAAGCGAACCGCTCCAAGAGCAAAGAGCAACAATGTAACAATTGTAATCTCTGTTTCGGAACAACTGAATCGATTCACAGGTGTGAAAGCACCCTTAGTAACGAAAAGAAAATTTCTCTCATTATTTCATCATCTTACACTTGTTTCAAACCTGTTTGAGTTTCTTTCTTCCGTTGAACACAATTACTCATCTTATACCAACTTGACCTGCAGTTCCTTCAGTAAATGCTGTTGTAATCGTGTAAAATGTCTTTGTCTTGGGTGTTTTTTGTAACCAG
Seq C2 exon
ATATCCGGATAAAAGTTTGGATGATAATTATTGTCGCAACCCGGATGCGTCTCCGGTGCCCTGGTGTTACACCACTGACCCAACAATGGAGAGAGAGAGCTGTGATATAAGCAAGTGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103308:ENSDART00000162791:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.098 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005113=Kringle=PU(48.7=92.7)
A:
NA
C2:
PF0005113=Kringle=PD(50.0=95.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
AGGTGTGCATCACTTGTAATGGT
R:
GGCACTTGCTTATATCACAGCTCT
Band lengths:
240-1553
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]