RnoINT0139615 @ rn6
Intron Retention
Gene
ENSRNOG00000026065 | Slit1
Description
slit guidance ligand 1 [Source:RGD Symbol;Acc:69307]
Coordinates
chr1:260855612-260858939:-
Coord C1 exon
chr1:260858842-260858939
Coord A exon
chr1:260855752-260858841
Coord C2 exon
chr1:260855612-260855751
Length
3090 bp
Sequences
Splice sites
5' ss Seq
CACGTGAGT
5' ss Score
9.3
3' ss Seq
TCCTCTGCCCCCTACCACAGGTG
3' ss Score
10.72
Exon sequences
Seq C1 exon
GGCCGAAACTGTGAGGTGTCTCTGGACAGCTGTTCCAGCAACCCATGTGGAAATGGGGGAACCTGCCATGCCCAGGAGGGCGAGGATGCTGGCTTCAC
Seq A exon
GTGAGTTCCCAAGGAGCTCTGAGATGGGGTTGGGGACTGCTGCTGGGTCCAGCCTCCAAGCCTCCTCGTGCAAGAGATGAGGGTCGGTAGAGGGAATAGACCTGTGCTCCAAATAGTGGTCATCAGTTCTCTAAGCCCCCAGAGGACAGCAGGCACCAGACAGTGCGGGTTCACAGAAGAGAGCCTGGGGTTGGGGCTGCCTCCTGGTGAAGGTACCAGGAGTGTCTTCCTGCACCATGGGAACCTACAACCAAAGAGCACATGCCATGGTAGTGCCACGAAATGGTTGAGGACATCTAAGACTCTTTTAAACTTCCACACACCCTCCTGAGCTTCCACTTTAAGCTGAACAAGTCTCTAGAGGCTGTACCGGGACCATGCAGGCCTTAGCTAGCCCTGTGTAACAGCTGAGATGACCAAAGTGAAGCCACATCCTGGTCACTCCTTCTGGGGTCCAACCTTCACACAACTCTCACTGACTGGCCACCTAGGGAGGGGTCCCACTAGGCGTGGCATTTCCCATGCTCTTGGTATAGCTGTGCTCACCATATAGCACATCTGAATCCCTCCAGGGCAGATGTCAGACCCCCCACACCCACATACACACATACCCCACTAGCCTGCTTTCCCCCAGGAAGCCCCAGCCCCCATCCCTGGCCTCCCAGAGCTTTCCTGAGGAGCACAGTACTTAGTCGCTGGAGACAAATTGCCTACTGAACAAATTGGCTCTTCAGAAAATGATGTTGAATCTGCGGGCGGAAATGGCCAAACCTGCCTCTGCAGACCCAAATTACCAGATGTAAAAAATAAAGCGCTAAGTGCCTCTCCTCCAGCGTTGCCTTGGAAACGCAGCCTTACAATAGGCAGGCCCTCCTCAGGGGCGGGCAGCAGCCTAGGCTAAGCTTCCTGCCTGGTCCACTGCTCAGCTCCTGCTCAGGGCTGGGACGCACCTTCAGGGCGTAGGGGACAGCTAGGGTGGCCCTACCTATCCAACAGCCGGGCAGCCCATAGCACCAGGTAGAGGGGAGATCCCCTCCCTTATGCCTTAGATTGTGCCAGTGGGGACTTTCTGCCCTAACTCAAAATCGAACTCCAGAAGAAGGCTGTGATAGAACCTTCAGGCCTCTTTACTTGCCTCACTCTCCAGAAAAGACGTGAACACCACCTGCGCAAATTTTCTTAGACCAACAGCTACATTTGCTTTTTACTGTAAGTTTATTTTTTCATGCAAAGGAGACAGTATCATAGACATCATAAATATCATTGCCATTTTAAAGTAAAGCAACTAGGTTACACACACTATCCCTATCCTCCTGTGGTATCCTCTTGAGCATAGCAACGGGGGTGCCATTTTAGTATGTATTCATTAATTTTTTTTTTGTTTTGAGACAGGGTCTCTTGTATAGCCAAGGCTGCTCTGGAGTTCTCAACCATGCATGCTTCCCTTTGGCCTCCCGAGTGCTTTGCGCGCCTTTTAAAAATGCCACCAGCAAGCTCCCCCATAGCACTGAAATGACTATGCCAGGAACATCTGCCACTGAGAGTCTGAGGGCTGAAGCCTGATGTCCCTCTCCATTTCCTGTCACCAAGAGCTCCTAATTAGACGTCTCTTTTGTCTGGATTTGGTGGTACACATAGGTAATCCTAGGGTTTAGGAGTCCGAGGGCAGGAGGATTGTGAATTTGAAGCCAGCGTGAGCTAGCTACCTAGGGAAATCCTATCTCCCAAATTGTATTTTATTAAAATTACTTTGGAGCATGGAGAGATGGCTCAGTGGGTAAGAGCATTGGTTGCTCTTCGAGGACCTGGGTTTGAGTCCCAGCACCCCACATGCTGGTTCACAACCATCTATAACTCCAGTCTCAGAGGACCATATGCCCTTTTCTAGCCTCCAGGGGAGTCAGGCATGATAAAGACATGCAGACAATGCACCCTTACACACAAAAACACAAATAGATACGATTACAAAAAAATAGTTTCTTGTGTCTCACTTATCAGTAAGATGGCTAATACCATGCAAAACAATGTAACTGTTATAAATTCGGCAGCTATTACCTGTAAGGTAATGTGTGCCGGGACAAACTCCTTTATAGTGTGTCTGTTTTCTTTGTAAGCTGGTCCATGTGTCCGCAGATGGTCTGGGCATGACAGGAGTGAGCAGCTGCCCTGCTGTTTTATTTGCATGAATATTTTATTCTGGGAAGGTCTGTTCACATAAATCCACTGTCAGGATTAGTAGATTCATCATGGACCTGCCACTCAGCTATTGGAAACCCTTCCAGTTTATAGGACAAAAATCTCCAGCCTGAGCAGGTGGCAGCAACATTTCAGTTCGGTTAGAGACTCAGTTCCAGGAGTCTCCTGTCAGTTATTTTTGTCTGCTTGCTGCCTTCTTTGGCACCTGGAGGCACAGCCCCCACCTCCTGCTTAGGCGGAATGCCACCTGAGCATGACAGGAGAGAGGCAGCTATTCCACTGTCTCTGAGTCCTGTGGGATGTTTGAAGCGCTGGATGGGAGCTCCTCAGACGACTGTCTCTGACCCTTGGGAAAGTTCACATGTCCTGAGCTATTGACTACCCTGGTTAGAAAATCACCAACTTCAAGAACCTTCTCCAACCCAGCGACTGCTCAGTCCAGCTCCATTCTTTCTCTGTCCCTGAGGTCTGTGTCCTCAAAGACTTGAGCAATGTAGGTGAGCAGGTCCTACCTTCTCACTTCAGACTTTATGCATCCTTTTGGGCTCACAGTCTCCCCTCCCCTGTTGGGACTCTTGCTGAGGTTAGTCCATCATCTCTGCCTGACCATGTGCTGGTAAGGAGGTGTTAGGGGCTCTTTGCCCATGCCTGGCTTCAGAGCCTCCACCATCATGATTACACTTCTCCTTGGGCCATTGTCTTCTATTTGTCTCCCCCATCAGACTGTAAGCCAGAGGATTCCTTAAAGGCAGGCCTGGTCTTGTTACCCTCTAACCTGTTCGCCCTCTGACAAGGGCCTGGTTTAGAGTAGAGCTCTAGCCTCGTGGAATAAGGGTTCTGACCAGCGGCCAAAGGCTTTCCCAGCTCCTTTCCATCCTCTGCCCCCTACCACAG
Seq C2 exon
GTGCTCCTGTCCTTCCGGCTTTGAAGGGCTGACGTGTGGAATGAACACAGATGATTGTGTGAAGCACGACTGTGTCAATGGGGGTGTCTGTGTGGATGGCATAGGGAATTACACATGTCAGTGCCCCCTGCAGTACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000026065:ENSRNOT00000034758:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=PD(6.2=6.1),PF0000822=EGF=PU(64.7=66.7)
A:
NA
C2:
PF0000822=EGF=PD(32.4=22.9),PF0000822=EGF=PU(90.3=58.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
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]