RnoINT0132962 @ rn6
Intron Retention
Gene
ENSRNOG00000013679 | Sema4d
Description
semaphorin 4D [Source:RGD Symbol;Acc:1310554]
Coordinates
chr17:13530068-13531632:+
Coord C1 exon
chr17:13530068-13530290
Coord A exon
chr17:13530291-13531516
Coord C2 exon
chr17:13531517-13531632
Length
1226 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
CCTGTGTTTTGACCTTGCAGACC
3' ss Score
10.99
Exon sequences
Seq C1 exon
TGTATCGACAGTGAGGCCCGGGCAGCCAACTACACCAGCTCCTTGAATCTCCCAGACAAAACGCTGCAGTTTGTCAAAGACCACCCTTTGATGGACGACTCGGTGACGCCAATAGACAACAGGCCGAAACTGATCAAAAAAGATGTCAACTACACCCAGATAGTGGTAGACAGGACCCAGGCCCTGGATGGGACCTTCTACGACGTCATGTTCCTCAGCACAG
Seq A exon
GTGGGTTCCCGGGTGAGATTGGGAAATTCGCTTAGTCATTTGTGGGTAAGAGCTGGTCTCTCCAGGTGCAGGAAGGCTTGTGACAGGAGAAGAAGTTTCTGAGGCATCACAGCATCTGGAATTCTGAATCTCCGTGACTATCAGGCACCTCAGGGGCTGGTTACTAATGCAGGCTCCACACCATACCTGGGCTGGAGTGGAGTTAAATAGTCCCTGTTGTCCTGGGACCAGTGGGGTGGCCTGGTATTTCCGAATTGGTAGTGGGAGACTCCACCCCTACTGAGACTCCACCCCCTTCTGAGACTCCACCCCTTTCTGAGACTCCACCCCTACTGAGACTCCACCCACTACCGAGACTCCACCCCCTTCTGAGACTGCTCCCTTCTGGGAGCCAGGGTCCGTCCCGCCCTTAACTGCCTTTGGAAGCACAAATCTCGGACAAGTCTTCTGGGATGGTGATGGAGAGCTGGAGCTTGGCAGATGCTAGAGCCCCGGGGGCTACCCTTAGAGCTTCCCAGGTGGCTTGAACACTTTGCCCTCGCTTGCCTGGCTGGGCCCTAACCTCCCCAGTGGAGTGCAACAGCCACCTTACACCGAGTGTGGCTCAGGTGTCAGGGTGTGATCCTGTTGATGAAGGTCATTGGACTCCACCATGGGACAGAGCTGTCCTCTTTTGAGTGAGCGCCCCATTGAGGGGGTGACTTTGAGCGTGAGTGGTCGCCTTCAAGGCTGGAGTCTCTGCTGGTTTCATTTCTGTTGCCGGGCAAAATTAAAACGCCCCGACAGAAGCACACCTAGGGGAAGAGGGTTTATTTGCCTTTTATGTTGGGTATCGTCTGTCATTTTGAGGGAGTCAGGGCAGGAACTTAAGCAGCGAGTCACGTCATATTTGTAGTCTAGAGCACAGAGAAATGAATGGACCCTCGTTGTCCGCTTGCTGTGTCGCTTGCTGGGATACCTCTGCCTAGCTAGCCAGCTCTCTTCACTTAACATTGTCCACGGGATGGTGCCTTCCACAGTGGGCCAGGCCTTCCCACGTCCGTCGACAATCAAGACAGTCCTCCACAGACCTTTCAGCAGACCAAACAGATCTAGGCCATTCCTCAGTGGAGGCTCTTTCCAGACGATTCCAGGTCGCACTAAGTTGTCACTTAAAACTAACCAAGGTGGCGCCCTTGGCATTTCCCTCTAGGACCTCCTTGCTCACCTGTGTTTTGACCTTGCAG
Seq C2 exon
ACCGGGGCGCTCTGCATAAAGCTGTCATCCTTGCAAAAGAGGTACACGTGGTTGAGGAGACCCAACTCTTCCAGGACTTCGAACCGGTCCTGTCTCTGCTGCTATCATCAAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013679:ENSRNOT00000018378:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.013 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(17.1=100)
A:
NA
C2:
PF0140314=Sema=FE(8.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTATCGACAGTGAGGCCCG
R:
TTGATGATAGCAGCAGAGACAGG
Band lengths:
334-1560
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]