RnoINT0132948 @ rn6
Intron Retention
Gene
ENSRNOG00000016254 | Sema4c
Description
semaphorin 4C [Source:RGD Symbol;Acc:1562837]
Coordinates
chr9:43129415-43131358:-
Coord C1 exon
chr9:43131288-43131358
Coord A exon
chr9:43131139-43131287
Coord C2 exon
chr9:43129415-43131138
Length
149 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCTCATTTCTGCCTCTGCAGCCA
3' ss Score
8.62
Exon sequences
Seq C1 exon
GTCCCTTCTGGTCCAACACGTGGCAAATTTGGACCCTTCAAAGATGTGTATCCAGTATGCCATTAAAAAAG
Seq A exon
GTGAGCTTTTTTTTGTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTGCCTGGATCACAGCCAGAGTTCGTGCATCTCCTCACTGTGAGGCCTGGGGTTCCTGTGTTAACACTTGGTTCTCTCTCATTTCTGCCTCTGCAG
Seq C2 exon
CCAGACCTGTTGTTCCCAAAAATATCACAGTTGTAGCAGGCACAGACCTGGTCCTACCCTGCCACCTCTCCTCCAATTTGGCTCATGCCCTCTGGACCTTCAGAGGCCGGGACCTGCCTGCAGAACAACCTGGCTCCTTCCTTTATGACACGGGACTCCAGGCGCTGGTGGTGATGGCCGCCCAGTCCCGCCACTCTGGGCCCTATCATTGCTATTCAGAGGAGCAGGGGACAAAACTGGCTGCAGAAAGCTACCTTGTTTCTGTCGTGGCTGGCTCATCGGTGACCCTGGAGGCACGGGCTCCCTTGGAAAACCTGGGGCTTGTGTGGCTAGCCGTGGTGGCCCTGGGGGCTGTGTGCCTGGTGTTGCTGCTGTTGGTTCTCTCGCTCCGCCGGCGCCTGCGAGAAGAGCTGGAAAAGGGTTCCAAGGCAGCCGAGAGGACACTGGTGTACCCCCTGGAACTGCCCAAGGAGCCAGCCAGTCCCCCCTTCCGTCCTGGCCCAGAAACCGATGAGAAACTTTGGGATCCTGTTGGTTACTACTATTCAGATGGCTCTCTCAAGATTGTGCCTGGTCACGCCCGGTGCCAGCCCGGGGGTGGGCCCCCTTCCCCACCTCCTGGCATCCCCGGCCAGCCCTTGCCTTCTCCAACTCGGCTTCACCTAGGAGGTGGTCGGAACTCAAATGCCAACGGTTATGTGCGCTTACAGTTGGGTGGAGAGGACCGAGAAGGATCTGGGCACCCACTGCCTGAGATTGCTGATGAATTACGACGGAAACTGCAGCAGCGCCAGCCGCTGCCTGACTCCAACCCAGAGGAGTCTTCAGTATGAGGGAACCCCCCCACCTCAGTGGCGGGGGGTTTTCATGGGAGGTGCACTCTTAACTTTTGCACAGGCACCAGCTACCTCAGGGACATGGCAGGGGCAGCATTTGCCCAGCCATGAGGACCTGCTCAGCATGGGCACTGCCACTTGCTATGGCTCACCGGGGCATCAGCCTCACAGGAGGCACACCCTCCTCTGTGAATTTCACATACGTGGGACCCCAGCAGCCAAAACTTTGCAAGGAAGAGGTTTCAAGATGTGGGTGTGTTTGTGCATATATGTGTTGGTGTGTGTATGGAGGGGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGATAACCTTCCTGTCTCTGTCAAGTCTTCCCTTGGCCTGGGGTCCTCCTGGTTGAGCCTTTGCAGCTATGAAGGGGAAGGGGGTCATAGCACTTTGCTTCTCCTACCCCCAGCTGTCCCGAGCTTGGGATGGTGATGTACATACATATGGGGATGGGATGGACAGGGTGTTGTACCCCTTTAGGGGGAGTGCGGGACTTGGGGGTGGGCCTAGCCCTGCTCCTAGGGCTGTGAATGTTTTCAGGGCGGGGATTGGGGGGTAGAGATGGAACCTCCTGCTTCAGGGGGAAGGGTGGGCAGGGCCTCCCACTTGCCTGCCACCTGGTTCGGTGGTATTTTATATTTGTGCTCTTCTGACAGGGCTGGGAAGGGTTGTTGGGGGGAGGGAAGGGAGAAGGTGGGCGTGCTGTGGATACTGGCCTATCTTCTCCCAGCTCTGGGAAAAGGGCTAACAGTGTAACTTATTGTGTCCCCACATATTTATTTGTTGTAAATATTTGAGTATTTTTATATTGACGAATAAAATGGAGAAAATGAAACTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016254:ENSRNOT00000021956:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.390
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(25.8=100)
A:
NA
C2:
PF0143720=PSI=PD(35.5=11.9),PF138951=Ig_2=WD(100=34.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGGACCCTTCAAAGATGTGT
R:
AGCAATGATAGGGCCCAGAGT
Band lengths:
256-405
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]