RnoINT0132918 @ rn6
Intron Retention
Gene
ENSRNOG00000019737 | Sema4a
Description
semaphorin 4A [Source:RGD Symbol;Acc:1304636]
Coordinates
chr2:187813816-187814813:-
Coord C1 exon
chr2:187814653-187814813
Coord A exon
chr2:187813879-187814652
Coord C2 exon
chr2:187813816-187813878
Length
774 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
CTTTCAACTCTCCACTTTAGATA
3' ss Score
8.88
Exon sequences
Seq C1 exon
GAGATGGGCACAGGGCCCTCAGCTTCTTTCAACAAAAAGGCCTCCGGGACTTTGACACCCTGCTCCTGAGTGGAGATGGCAACACTCTGTATGTGGGGGCTCGGGAGGCCATCTTGGCCCTGAATATCGAGAATCCAGGAATCCCAAGGCTGAGGAACATG
Seq A exon
GTGAGGAGGCCAGGGACTTGGGTCCAGGCCAGCAGCTTCCCTGGACCAGCTTCCATATGAACAGCCACCTGCCACTCTGAATCAGCAGTGACAGAAGGGACATGCTGCCGTGGCCTCACAGTGACATCAGCCACTCAAATGGCTGATACGGAAATCACTGGCTTAGGAGATTTAAAACATTGATGCAAATCAGTGACTCAAATAATTTGATGTGCACCTATGAGAGAGAAATCCGAGATTCCTGAGTTATCATCGCCCTCATGGCATCGATGTGAGGGGAGGGGGGTGGGGGAGGAAGAAGTCACCTGTCATGGCTCTTTCTCAGTGCGTGGTCTCTTGATCTTCGCCATATGTGGGGTCTGATATCTACACCCCTCCTCTGCAGTTTCTCTGAGGGGTTGACAGGCTCCCCCAGGAAATGTTTGGTTTATAACCACTGCTGTATATGCCAGGCACTTACACACGCATTCTGGCTGTAACCAACGGGCTGTGAAATGGAGCCAGAGTGCTCAGTTGAGTTGGTGGCCGAGCCTTAATTTGAACTCCAGATCTATCTGGTTCTACCACAGAGCCATGTCCTGATGAATCCTAATACTATGGAAGTTATGGTCCTGATCAAATTGGCATTATGACTGCCTACCAGAACATCACTAAGCACTTGCTGGTGGTTTTACATCAGAGCTGCGGTGTGCGGGGGTACAGGGGGTGGGGGTGGCTTACAGAAAAACCCAAAGATCTTTCCTTTCATCTACCCCTTTCAACTCTCCACTTTAG
Seq C2 exon
ATACCCTGGCCAGCCAGTGAGAAAAAAAAGAACGAATGTGCCTTTAAGAAGAAAAGCAATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019737:ENSRNOT00000056862:3
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=PU(36.4=66.7)
A:
NA
C2:
PF0140314=Sema=FE(20.2=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:
ACAGGGCCCTCAGCTTCTTTC
R:
TCATTGCTTTTCTTCTTAAAGGCACA
Band lengths:
214-988
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]