RnoINT0133063 @ rn6
Intron Retention
Gene
ENSRNOG00000045998 | Sema6b
Description
semaphorin 6B [Source:RGD Symbol;Acc:69278]
Coordinates
chr9:10948904-10951252:+
Coord C1 exon
chr9:10948904-10948962
Coord A exon
chr9:10948963-10949361
Coord C2 exon
chr9:10949362-10951252
Length
399 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGC
5' ss Score
8.69
3' ss Seq
GCCACCTTCTTTGTCCCCAGGAC
3' ss Score
11.79
Exon sequences
Seq C1 exon
TGCCACGTTTGAGCAAGATGTGTCCGGGGCCAGCACCTCTGGCTTAGGTGACTGCACTG
Seq A exon
GTAAGCTGAGAAAGGGACTCCCTTGTGTGCTGTGACACAGCCAGAGACACTCAGTCCTGGGAATGGAGGGTGGACACATGGCAGACTTCCTTAGTGAGCTGGGAGCCATGAAAAGCTAAGTTCACCCAGTGTTCACGGTCGCCCTCTGGTGGCCGCTGCGATGAAGGGTGAAAATGAGACCATCTAATAGGGAGATGAAAGATACTGATTCCAGAAAAAATAGGCACAAAGGGTCATGGCTCAGGCGTAGAGCCCTTGCCTAGAATGCCCTTGTGAGAGGCCTGGGGCGTGGTCATGGATGGAACCCCGCCTAGAATGGAGCGTAGCTCAGTGTAGGGACTGTATTGCCACCTTCTTCTTTTTTTTTTTTTTTTGTATTGCCACCTTCTTTGTCCCCAG
Seq C2 exon
GACTCTTGCGCGCCAGCCTCTCAGATGACCGCGCAGGGCTGGTATCGGTGAACCTGCTGGTGACGTCCTCGGTGGCAGCGTTCGTGGTGGGTGCCGTGGTGTCCGGTTTCAGCGTGGGCTGGTTCGTGGGTCTCCGCGAGCGGCGGGAGCTGGCCCGGCGCAAGGACAAGGAAGCCATCCTGGCGCATGGCGGCAGCGAGGCAGTGCTGAGCGTGAGCCGACTGGGCGAGCGCAGGGGAACCGGGACTGGGGGTCGTGGGGGAGCCGGCGGCGGTCCCGGGGGTCCCCCGGAGGCCCTGCTGGCCCCGCTTATGCAGAATGGCTGGACAAAGGCGGCACTGCTGCATGGTGGTCCTCACGACCTGGATTCGGGGCTGCTGCCCACCCCTGAGCAGACGCCTCTGCCCCAGAAACGCCTGCCCACAACACACCCACACGCCCACGCCCTAGGACCGCGAGCCTGGGACCACAGCCACGCGCTGCTGTCGGCCTCTGCCTCCACATCCTTGCTCCTGCTGGCGCACACCCGCGCCCCTGAGCAGCCCCCAGTGCCGACTGAGTCAGGCCCGGAATCTCGCCTCTGCGCCCCAAGATCCTGCCGGGCCTCTCACCCAGGCGACTTCCCACTCACGCCTCACGCCAGCCCGGACCGCCGGCGGGTTGTGTCCGCACCCACGGGCCCCTTGGACTCTTCTTCGGTGGGCGACGACCTTCCAGGGCCATGGAGCCCACCTGCAACCAGCAGCCTGCGGAGGCCGGGCCCCCATGGGCCCCCAACAGCCGCCCTGCGGCGCACACACACATTCAACAGCGGCGAGGCGAGGCCCGGGGGTCACCGTCCTCGCCGCCACGCACCCGCGGACTCTACACACTTGCTGCCCTGCGGGACGGGCGAGCGGACTGCACCCCCGGTACCCTAGGCCGGGCGGATGCCTCGACGGTGCCAACCACAGCGACCCGGGCGTCAGCCCAGGTCACCGAGCCCTACTGGCGCCGAGTGGGACGCGTTCGTTCCCCACCCTCGCGGGTGGGGATCTCCTCGCCACAGGGAAGCACAAGAGCCCCCTCCATCCCGGAAGATGCAGAACATGAAGCCCCGGGGTGGGCGGGAAGAGGCTGACCTTTTACCTGAGCATAGACTTTGATTTTTGTTTATTTTGAGTTTGGTTTTTTTTTTTTTCTAAGAAATTGCACAGCCCCATTCTTACTTGGGGTGTCGGCCGGGGTGGGAGGTGAGGATATGGGGTAACGGGAGGCAGAGCTGCAGACACGAGCCTTCCTGCCTCAACACATCCTCCCTAGAAGGGACCCCCTCCCCTTTCCTGGGCTCCTGCGCGCGCGCGCGCGCGCGCGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTCCGTGTGCATGGCCTGTTTGTGTGCAAAGGCCCGAGGCAGAAGTATGTGTGCGTGCGTGTGAGACAGGGCTGCCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGACTCAGAATGTGGGTGGTGGTGCCCTCAGAGACCCTGGCATTGGCTGAGCCAATGTTGGTACTTCTGGAAAGAAACCCAGGGGATGGAGCCTCTGAGGTGCCGGTTGGAGTTCAAATCCTGCTCCTGCAGAGGGAATCTGGGGATCCAGGCTGGGAGATGGGGGAACCTACTTCTAAAGGGCTTGTGGGGGGTTTTGGGAGGGTGGAAGTGGGCAGACACCCCTGTAAATACAGCCCTGGGGTGGTCAGAGAGGCCCATGCCACCTGTCCCCACTTGTGACATGCCCTCTGACTGCCAACTGACCATGCATGCCACGTGGCCAGCTGAGTCCAGGACCCTCCTCAGCCCTATCCCTGTCAATAAAACTCTTGTTTACATCCACCGGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000045998:ENSRNOT00000070794:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.048 A=NA C2=0.735
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(35.7=100)
A:
NA
C2:
PF0143720=PSI=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGCTTAGGTGACTGCACTG
R:
TCCAGCCATTCTGCATAAGCG
Band lengths:
348-747
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]