RnoINT0132936 @ rn6
Intron Retention
Gene
ENSRNOG00000025167 | Sema4b
Description
semaphorin 4B [Source:RGD Symbol;Acc:1307872]
Coordinates
chr1:142003533-142004389:+
Coord C1 exon
chr1:142003533-142003631
Coord A exon
chr1:142003632-142004277
Coord C2 exon
chr1:142004278-142004389
Length
646 bp
Sequences
Splice sites
5' ss Seq
ATTGTGAGT
5' ss Score
7.35
3' ss Seq
ACCTATCTACTCCCCCACAGAAC
3' ss Score
9.81
Exon sequences
Seq C1 exon
CGTGACTGTCAAAACTACATCAAGATCCTTCTGCCCCTCAACAGCAGCCATCTGCTCACCTGTGGCACCGCAGCCTTCAGCCCCCTGTGTGCTTACATT
Seq A exon
GTGAGTTCTCTCCTGCAGCCTTCAGCCCCCTGTGTGCTTACATTGTGAGTTCTCTCCTGCAGCCTTGCTGCAGGAGACTGGGGCACAGCCTTCCTGCCAGGGGGGAATCTTCTCTCACCCTGATACCTGGTGAAGGAAGACCCTAAGGGCAGGCTTCTAGGTAGCAGCAGAGTCTTGAGACCCCTGAGCCCATCATCCTGGCTGCCACCCAGCTCCTACTAGGTCTCCCTGCAGGGGCAGGGAGGGGTGCATGCAGCCACCTTGTCTAGAGATCCTGTCTGACTTCCGGCTTCCTGCCCTCCAGTTTCCTTCCCTTGCTATACTTGATGCTCCGGGTCACCTCGTGCACCTTCAGCATGTGCCCACCCTGTGTTCCCACTGTACACCCTAACACGCTCTAGCAGAGGGTGGCATAAAGGCTGCGTTTTGGAACACAGGACTTGGAGTCAGAAGTTGCTGGGTTTGCATGGTGTTGCTCTCCCTGGCTCTAAGCCACACGTCTTCCTGTTCACTGGGGATCAGGGCCCACTGCACACATGCATTCACACAGACCATGGGGTGAGGAGGACACACACTTACTTCCCTGCTGTACACTCCCTCATCCATGTCTCAGTCCTGAGCAGGCCACCTATCTACTCCCCCACAG
Seq C2 exon
AACACAGCAAGCTTTACATTAGCCCGAGACGAGGCTGGCAGTGTCCTCCTAGAGGATGGCAAGGGCCGGTGTCCCTTTGACCCCAACTTCAAGTCCACGGCTCTGGTGGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025167:ENSRNOT00000030914:4
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:
PF0140314=Sema=FE(7.3=100)
A:
NA
C2:
PF0140314=Sema=FE(8.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGACTGTCAAAACTACATCAAGA
R:
ACCAGAGCCGTGGACTTGAAG
Band lengths:
206-852
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]