RnoINT0139624 @ rn6
Intron Retention
Gene
ENSRNOG00000026065 | Slit1
Description
slit guidance ligand 1 [Source:RGD Symbol;Acc:69307]
Coordinates
chr1:260843483-260844921:-
Coord C1 exon
chr1:260844710-260844921
Coord A exon
chr1:260843917-260844709
Coord C2 exon
chr1:260843483-260843916
Length
793 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGG
5' ss Score
6.23
3' ss Seq
TTGGTGTTTGTCCCATCCAGAGT
3' ss Score
6.9
Exon sequences
Seq C1 exon
GTGTGTCCATGGGAAATGCGTGCCCCTCGATGCACTTGCCTACAGCTGCCAATGCCAGGATGGATACTCGGGGGCTCTGTGCAACCAGGTCGGGGCTGTGGCAGAGCCCTGTGGGGGCTTACAGTGCCTGCATGGTCACTGCCAGGCCTCGGCCACCAGAGGGGCACACTGTGTGTGCAGCCCAGGTTTTTCAGGCGAGCTGTGTGAGCAAG
Seq A exon
GTCAGGGAGCCCCATCCTGACTGCCCTCTGCAGGCTCCCTCCCCACCATCCTGCTGTAACAGCCTCATGTTAGCATCCATGAACCCCCAGCAAGCCCTCTCATTCTCAGCCCCTTCTCTCCCCTCTGGTACTTATGGGACTACCGGGCTTTTGGTGCCCCTGCCCTCTAGGAACAGAGCTTCACCCCTTCTATCTCCTGGGCCCAGCCTGCCTTGCAGCTCCCTTCTGCAGGGCCCTGCCCTTCTTGGCTGAGGCCTATATGAAGTGATCATCCAGGTATGCCCAGTAACAGCTCCTGGCCAGGTTTGAGCATCTTGGCCTATCAGCGTTGGACCTGGGTGTAGCAGGATGCTTGAAAGTTGAGGGATTTCTTCCCAGACGTTCCCTGGGCTCCTTCACCAAGATGCTTTGGTTAGACTCCAGACTGCAGAGGCTGAGAAGAGGGAAGAAGGAGAACTCAGCCTTGGGTACCAGAGAGTCAGTGGGTCACGCTCTCCACAGAGGAATACTTCCACAATGCTATTGCCCTCCAGGCCTCAGCTCTTGCACATCTGCACAGTGGAAATCATCTCATTTGGCCCCGGGCCTGGAGGGCCAGGGCAGTCAGCTGTTTCCCCCTTCCCCAATCACACTGTGGTCCTGGGAGGAAGCACAGCACAGGTGCATGCAGACAGGGGGAGGACAGAGGGATGAGAGAGCCCTCCCAGAGGAGCCCTCCTAGGATGCTGCCCTGTCCCCCTCCTGCCTCCCATGGTGTGCCCTGAGGCTGTGTCTTGGTGTTTGTCCCATCCAG
Seq C2 exon
AGTCCGAGTGCCGGGGGGACCCTGTCCGGGACTTTCACCGGGTCCAGAGGGGCTATGCCATCTGCCAGACCACGCGCCCACTGTCATGGGTGGAATGCCGGGGCGCGTGCCCGGGCCAGGGCTGCTGCCAGGGCCTGCGGCTGAAGCGGAGGAAGCTCACCTTCGAGTGCAGCGATGGGACCTCGTTTGCTGAGGAGGTGGAGAAGCCCACCAAGTGCGGCTGTGCCCCGTGTGCGTAACGTGCGGGTGGCACACTAGCAGCTGGGCTGGGGCGGGCATCACCAGGATAGCGCTTGGGTCCTGGTGGGCGCGGGGACACTGAGCTGCCTTTCCAGCGGACTGCACTGCCAGGGCAGAGGAGCAAGGCCCGGGTTGCCAAGCCCTCTCCCAAAGTGCCTTGCACAGATAGGCGCTTAATAAATATTTGTTGAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000026065:ENSRNOT00000034758:36
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.073
Domain overlap (PFAM):
C1:
PF0000822=EGF=PD(66.7=36.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGCCAGGATGGATACTCGGG
R:
CTCAGCAAACGAGGTCCCATC
Band lengths:
355-1148
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]