RnoINT0132921 @ rn6
Intron Retention
Gene
ENSRNOG00000019737 | Sema4a
Description
semaphorin 4A [Source:RGD Symbol;Acc:1304636]
Coordinates
chr2:187812333-187813268:-
Coord C1 exon
chr2:187813163-187813268
Coord A exon
chr2:187812450-187813162
Coord C2 exon
chr2:187812333-187812449
Length
713 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
CTCCCTCTCCCTGGTCTTAGATG
3' ss Score
10.03
Exon sequences
Seq C1 exon
GAACTCCAAGATTCCTTCCTGTTGCCCATCTTGAAGGACAAGGTCACAGATGGGAAGGGTCAAAGCCCCTTTGACCCTGCTCACAAGCACACAGCTGTCTTGGTCG
Seq A exon
GTGAGTGCTAGGCTTTGCGGACTGTCCTGAAACTTCCCCTTTGTAGTAACTCTAGGGAAAGTGAGATACGATAATTTTCCAAAGAAAGGGGCAGAGCAAACCAGGAGCCTCAGAGCCAGGGCAGGATCAGAGGGAGAACCAGGCAGCCCAGTCACTACCCCTTCTGAAACTGTCCCCAAAGGGGTGCAAGGAAGTCCACATGGGTAGATACAAGGCCCAACGGCACCAGGTGACCCCTGAGGTTCGGCCGCTTGTTTAACCACTTTGCATGGTGGAGATGACTCTTCTGAATGGCCTACGTGTGGAGCAGAAGTGGCTACGACAAAGTCCTGTGCCTCTGCCTGGCCACGAGTCATCACACACCTCCCACCCTGGTTTCCTACAGGAGATGGCTATTGCCTTTTGAGCAGACTTAAAAGATAAACAGGGACCCGAGGTGTGTGAGCACAAGTCAGTCATTTCTCTGGGATTGGTGTTTGAGGAAGGACCAGAGAAAGGCTGCCAAGTGCTGAATACAGAAATCTACACAGGCCATTGCCTGTGGGCAGAGGGATCTGAAGGGTGCTGGGTGTGTGTGTGTGGTGGTGGTGGTGGGGCAGTATGAGCTCTGCCGTGGGATTCTGCAAGAGGGAAAGAATAGAAGGAAGGCATGTCTGAGGAGGGCAGGCAGCCTTCCCCTGATACTTGCTTCTCCTCCCTCTCCCTGGTCTTAG
Seq C2 exon
ATGGGATGCTTTATTCTGGCACCATGAACAACTTCCTGGGCAGCGAACCCATCCTGATGCGGACACTGGGATCCCAGCCTGTTCTCAAGACTGACATCTTCCTACGCTGGCTGCACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019737:ENSRNOT00000056862:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.041 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(19.1=100)
A:
NA
C2:
PF0140314=Sema=FE(21.3=100)
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:
TCCAAGATTCCTTCCTGTTGCC
R:
CAGCCAGCGTAGGAAGATGTC
Band lengths:
215-928
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]