RnoINT0132941 @ rn6
Intron Retention
Gene
ENSRNOG00000025167 | Sema4b
Description
semaphorin 4B [Source:RGD Symbol;Acc:1307872]
Coordinates
chr1:142007234-142008362:+
Coord C1 exon
chr1:142007234-142007384
Coord A exon
chr1:142007385-142008151
Coord C2 exon
chr1:142008152-142008362
Length
767 bp
Sequences
Splice sites
5' ss Seq
GCGGTAGGT
5' ss Score
9
3' ss Seq
TCATGCTTCTGCCTTTTCAGTGT
3' ss Score
9.25
Exon sequences
Seq C1 exon
GCACAGAGGGACCACAGAAGGCTCTGCCATCTGCGTCTTCACCATGAATGACGTGCAGAAGGCCTTTGATGGTCTGTATAAGAAAGTGAACAGAGAGACACAGCAGTGGTATACTGAGACCCACCCAGTGCCCACTCCCCGGCCGGGAGCG
Seq A exon
GTAGGTATCAGTAGGGTTGTGCTCAGAGTGGCTTCTGGGCAGGCTTGGTCCCTGGACCATGCCGAGAGCAAGGCTGTATGGTCTCATACAAACTGTGAAGCTTCTCTGAATCTGATTTCTCATCTTTGAAATAGGGCATAATAGACCCTTACCAAAGAAGATGGCCCGTGAATGACAAAACGCCATCAGTCCTGTCTGTCTTGTCAGCCTGACCTCTGTACAGTGGTGTAGATTGTTTTTAGTTGTCAACAACAGCAGTCTCGTGTGGTCTAGGTTCTTTGAACTCCTGATCCTCCTGCCTCCACCCCAAGTACTAGGAGTACAGGAGAATGCTACTGCATCCAGCTTTGCACAAGACTGTACTACTGTTGTACCTTACCTTGTCCACCCAGCTAAGCCTTGTGCACAGAGAAACCCTTGGGCAGAGAGAAACAGGGCCCGGGTAGGTGTGGGAATTGGGTATGGCTAGCTGTGCTGAGATAATGATGCCGAGAACCCTAGGGTAACATTCATGGGTAAGACCCCAGGCAAAATAAGTCACACCTTTTGAGGGCTGTGTGCAAATTTTTAAGGATCAGAAGGCCATAGGCCAGCAGGAAACCAGGGCCTTGCTTTCCTCACACGTCAGATCTGCCTTTGGACCAGCGCTGTGCAGAAAGGCAGATGTGCCATGATTTCTGAAGCATAGTTAGTGGGGCAGGGGCTGCTACTGTCCCTGTGGGGCATGCTCCATGCTGATCCTGCTCCTCATGCTTCTGCCTTTTCAG
Seq C2 exon
TGTATCACCAACAGTGCCCGGGAACGGAAGATCAACTCGTCGCTGCAGCTCCCGGACCGAGTGCTGAACTTCCTCAAGGATCACTTCTTGATGGATGGGCAGGTCCGCAGCCGCCTGCTGCTGCTCCAGCCACAAGCCCGCTACCAGCGTGTGGCCGTGCACCGAGTGCCTGGCCTGCACAGCACGTATGATGTACTATTTCTGGGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025167:ENSRNOT00000030914:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.216 A=NA C2=0.056
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(11.4=100)
A:
NA
C2:
PF0140314=Sema=FE(16.0=100)
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:
ACAGAGGGACCACAGAAGGC
R:
CATCATACGTGCTGTGCAGGC
Band lengths:
342-1109
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]