RnoINT0132950 @ rn6
Intron Retention
Gene
ENSRNOG00000016254 | Sema4c
Description
semaphorin 4C [Source:RGD Symbol;Acc:1562837]
Coordinates
chr9:43134997-43137076:-
Coord C1 exon
chr9:43136931-43137076
Coord A exon
chr9:43135146-43136930
Coord C2 exon
chr9:43134997-43135145
Length
1785 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
TCTAATCCCTGTTTCTACAGAGC
3' ss Score
8.33
Exon sequences
Seq C1 exon
GGCTGCTGGACTGAAGTTTAGACTCTGGGTGTCTGCCATGGCCCCACACTGGGCTGTCTGGCTGCTGGCAGCAGGGCTGTGGGGCCTGGGCATTGGGGCTGAGATGTGGTGGAACCTTGCGCCTCGGAAGACTGTATCTTCTGGGG
Seq A exon
GTGAGTGCCTGAAGCATGGGAGGCAGGGCCAGAGGGAGCCTGGGGCAGGCTGCTGGGGGAAGGGTGAGGTGGGAGTGATGCTTGTTTGAAGGAAGGAGCGACTGCTGAGGAATTACCCCCAAGCGTACACCTTTATACTGATATGTGTGACTGTGGCTTTCTAAGAAACGTGAGTGGCCCCAGGGACCCAGAACTGGTAGTGCGGGTCTAGATCTGAGCTTTGTCCCTTTCTGACACTGGGATAACTTTGTGGGATCTCTTACCACCCTACCCCCACCCTCATGCTGACCTGGCTGTCCTAGTGTGCGAAGGAGGTAGTTTCTGAATCAACCTCCCTGTTCCTCACTTGAATTGTCACTCATGCTTGGAAGCCTAGACAGAGAAACCTGAACCCCAGAGCAAGTGTAAACCTAACCCCATCTCCAGTCTTTGAGGCTGTCTGTCCCTAGAAGCCCCTTTAATTCACCCTAATGGTCTCCTGTGCTGCTCTAACACTGGAGCCTTCTGATGGCTCTGGGTGGGCATATATAAGCACTGTGCTTTATGGGGGAGGAGGCAGAGTGGACCAGATAGCTTTCCTTTACACACACACACACACACACACACACACACACACACACACACCTGTATGGAGAGGTGGTGATGTCAGGTGTTTGTATCATCCCTGTGCTCTTGGGACGTGGGATGAGCTCACCTCCCACAGGCTGCACTCAGCTGCTATTAAAGCCCCTCCCATGCGGACCCAACTCTCACTGGTCACTGCCTCCAAGCCTGAAGCTGACTTAAGCGGGGATCCTGTGGATAGGTGCAGGTATACGGGCCTCTGGCAGATTACATGGCTGTATGTCTGATCATGTGCTGGATGGCAGCCTAGCTTCCCGAGTTTCAACATCATCAATGATCTCTGAGTCTCTGGTTCCTTTGATCTCCCAGTTCTAACCTCTTCCTCCTTCTCCACGAGCCACCTTGACATCTGTGTGTGTGTCTCTGGCGGCCTAGATGGAGTGAATGGCTTCTTAGACGAGGAATTCTGTGCCTCCCTCCTGCTGCACTAGACCTGCCACTGGGGTCTGCCTGGACCCTGCCGTGGTCAGCAAGTAGCAGAACTGGGAATGGCAACCGAGGAAGCCGGGTTTGGGAGGAAGTGTCTAGCTTTGTGCCTGAGGTACCGCTGACCCTGAGTGAGAGTCATCCATCAGATGGCTTCCTCTGGCCAGAAGCTTTGGCCGAGATATCCTTCCTTCCTCTTTACCGGCCCAGATTGCTTCTCCTCCCCGCCTTGAGGGGGAGGCTGAAGAAGGGTTTTGGAAGCCTGGGTAGGATGGAGCTGTTGTGCCAAAAGGTATACAGAAAAAGTCCTTTATGGGCTGTAGGAGGTTTGACTGTTGTCTGTGTGTGCATGGTGCTAGCTTTTGTGGAGAATCGTGATGATAAGGCCCAGGGGGATCCTTGGACAAAGGAAGATTGATGGGTTCACACAGGGAGGATGCCATCCGCCCCCTGCTCAGCACCACCATGTTGTTGTTGTTCTTCTCCTCCTCCTCTTCCTCCTCCTCCTCTTCTTCTTCTTCATAAAGATTTATTTATTTACTTTATGCATGTGAGTACATGGTAGCTGTCTTCAGACACAGCAGAAGAGGGCATCAGACCCCATTAAAGATGGCTGTGAGCCACCATGTGGTCTCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCACTGAGCCATCTCTCCAGTCCCCCCACCATGTTCTAATCCCTGTTTCTACAG
Seq C2 exon
AGCTGGTCACAGTAGTGAGGCGGTTCTCCCAGACAGGCATCCAGGACTTCCTGACCCTGACCCTGACAGACCGTTCTGGCCTATTATATGTGGGGGCCCGGGAGGCGCTGTTTGCCTTCAGCGTAGAGGCTCTGGAGCTTCAAGGAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016254:ENSRNOT00000021956:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(7.7=66.0)
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:
GGCTGCTGGACTGAAGTTTAGA
R:
CACTCCTTGAAGCTCCAGAG
Band lengths:
295-2080
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]