RnoINT0132917 @ rn6
Intron Retention
Gene
ENSRNOG00000019737 | Sema4a
Description
semaphorin 4A [Source:RGD Symbol;Acc:1304636]
Coordinates
chr2:187814653-187816677:-
Coord C1 exon
chr2:187816510-187816677
Coord A exon
chr2:187814814-187816509
Coord C2 exon
chr2:187814653-187814813
Length
1696 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGT
5' ss Score
10.75
3' ss Seq
TTATCACTGCCTCCCAACAGGAG
3' ss Score
10.23
Exon sequences
Seq C1 exon
AACCATCTGGTGACTGTCTCCGGATGACCATGGCCCTACCATCCCTGGGCCAAGACCCCTGGAGTCTCCTGAGTGTTTTTTTCTTCCAACTGTTCCTGCTGCTGTCACTGCCACCAGCTTCCGGGACTGGTGGGCAGGGACCCGTGCCCAGAGTCAAGTACCATGCGG
Seq A exon
GTAAGTGTCTGCTACCTGGGAGGCATGGATGCGTGGTAGAGATGAAGGGACTGAGGAAGGAGAAGAGTGTGCCAGAGAGAATGAAACAGGATGGAGAAACAGATGTCAGGTAGCCTCGGAGGGCCTGGGAGAAGAGGAGGCTACTCGAGGCACAAGTTGGTGTGGAAGGGAAGGAAGGGTCACTGTCACTCTCCCGTCTCTGCCAAGTTTTTCTCCCTCAAGTGTCACAGTAACCAAGCAGGGAACCTTAAATTCCTGACTACTTGCTCAGCACCAGGGGCCCTAAAGCCAAAGTTCAGGCTAGATTGTCTGAGGAGCTGGAAGCCCGAGCCAATGGCAGAGGTCACACCAGGCCAGATCCTGTCCAGTAGGATGGGCACCAGGAGAAGGGATCCTAGCAGCTCACCCAGTCAAAATGGTTTCTTGATAAGGCTGTTGGGCTTCTGACACCTTTAGTTCCAGGAAATGCCCCAGGGGAAGTCACCCACACGCTTGCACACACACACACTGGCACACACACACACACACACACCCCTCGCTCACGAATACAGAAGTAAGGCAGTTCGGTTCACAGCTATAGCTTAGCATCCTTCTGAGGCAAAATGGTAAAGGAGGTGGACCGGCCAGCAGAAAGAGAGGGCATCTCTGGGTGGGACAGGAGTGCAGACACAAACAAGGCTGCATTTCAAGGGGACAAACAAGGAGGAGCCCTCTTCAGAGTTGAGGGGAGGCCAACCTATGTACCACCTTTTCCCATTTTGTTTTCAGAGTCCTCTTGGCCCCCAAATTTCCTGAGGACAAAACAGTAACAACCAGGTTGTCCTCTGACTAAAGTAAAAGGCCAAATGTGCTCACGAGAGAATTTCTGAAGTGCTCACTCCTCCCTGCTGATGGGCCCGTGTGGCAGGAGCCTACACACTCCACAAGGCTAGGTAGCAAATATGCTCTACTAACCAACATATTCGGCACCAGGTGGCACCGAGGCATGCCCACACTGATGGGGCTCAGGCATGCCCACGCTGATGGGCCTCAGAGACAGAGGAAGCAGCGTTTTCAGCCGCAGCCCTGCTAGTGACGGGCAACTCTTATAACAGAGCAAGGGGAGGAAACAGAGGAAATGGGGGTGGCAGGAATCTGTAACCATGATAAGTCTTGTGGCAAATGACAGCTACCTCTGCTGCTTGTGGTTGAGAACTCCTTTCTGTGTCTACCTGTCAGCTCTTCCCTCTCCTATCCTGCCTCACTGAACCCTCCAGGCCTGAGAATGCATCATCTCCTTTTTTTTTTTTTTTTTTTTGTGCCCCAACAAGGCTATTCATTGCTATCTATGCAGTTGGAACCCAGGGTCAGTCCATGTATAGTCTTTGGGTAGTGGCTTAGTCCCTGGAAGCTCTAAGAATGTATTTTCTACCTCACTTCATGTCTGTGTCTTGAGCAGGCTTTCCCCCTAATCCCTGCAACAGCCTGAAGCTATCACTACCCTATCTTGGGCACTTTTCTGGGGACTCAGCACACAAAGTTCAGATGCCTGCTATTGGGGGTGCAGGAAACTGGGGGGGGGAGTCTGCCAGTGAAGAGTGATCTCGGGAGTGGGACGAAGCTGCTGAGGCCTGCCACCCTCCCCCACCTCTGCCTCAGAGATCAGCTACTGCTCACAGCTCCTCCTCATCCTCTCCTTATCACTGCCTCCCAACAG
Seq C2 exon
GAGATGGGCACAGGGCCCTCAGCTTCTTTCAACAAAAAGGCCTCCGGGACTTTGACACCCTGCTCCTGAGTGGAGATGGCAACACTCTGTATGTGGGGGCTCGGGAGGCCATCTTGGCCCTGAATATCGAGAATCCAGGAATCCCAAGGCTGAGGAACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019737:ENSRNOT00000056862:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.122 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(36.4=66.7)
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:
CCATCTGGTGACTGTCTCCGG
R:
CATGTTCCTCAGCCTTGGGAT
Band lengths:
327-2023
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]