RnoINT0132961 @ rn6
Intron Retention
Gene
ENSRNOG00000013679 | Sema4d
Description
semaphorin 4D [Source:RGD Symbol;Acc:1310554]
Coordinates
chr17:13528889-13530290:+
Coord C1 exon
chr17:13528889-13529045
Coord A exon
chr17:13529046-13530067
Coord C2 exon
chr17:13530068-13530290
Length
1022 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGC
5' ss Score
8.99
3' ss Seq
ACGGTGCTTTTACCCCACAGTGT
3' ss Score
9.06
Exon sequences
Seq C1 exon
GAACAACGTGGGTCTGTCAGCGGTCTGTGCCTACACGCTGTCCACGGTGGAGGCCGTCTTCTCCCGAGGAAAGTACATGCAGAGTGCCACAGTGGAGCAGTCTCACACCAAGTGGGTACGCTACAATGGCCCAGTGCCCACTCCCCGGCCTGGAGCG
Seq A exon
GTAAGCAGGGTGTCAGGATCTGGGGAGGGCTCATCTTTTCTCTGGATCTCAAGGCCCCACGCATGAAACCACACAGGTCCCAGAGCCTCCTAGCAGCAGGTTGCATGGCAACAGGAATCTGGGCGCCGGGCTGAGTGGCTGTTGGGCCTAGGGTGAAGAGTGAAGCTATTCTTTTCTCATTTCTTCTGTGTTGGGTAACAGGTCTCACTGCCTGCTGCCCGGACGAGAAAGCGTACCACCGGGCTCTTTTGAGAAACGGGCATTGCACAATGGCCGGCTTGCTTCATTTTCTGTTTCCCGCAGAGAAAACCTGTTTGTCAGCATAGCCTAGGCCGTCTCCTGAGCCTGCCTGTCAGCTGGATAATAGGAACCATATTCTTTCCTCCTAGAGACAGTAAATTTGTAAAGAAATTTCTAGGGTTGCTGAACGTTGTTGCCACACTGTGAGTGGGCATGGGGCAGGGTGGCGTTTGGATAGCACCCTGTCTGGCTCTTGAGGCTCTCCCAGGTCAGACCTCTCTGTGGGTGTCTAGCCTTGACCCCTGGTTATTCTTACCTGCGCGCTGTGTTCAATGAAACATGGAGAGAGGGGGCTGGGACAAAACAAAAAAAATCTTTCCAACCTTGTTTTCTTTCGTGCTACCTAGGTAGAATTTGGCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAAACAATATTTAACAAGCTTCCTTTGGCACACTTTCTTCTCGAGCTCTCTTCTCACAGAAAAGCTGCTAAATGCATGCTTTTTAATTTGAGAAGTTTGCTGAGTGTTTTCATTGACTACTAATTTCCTTCACCGACCCTGAGACAAGTATGTCACGTGACTGTGATTTAAAAATACAGCTCTTTGTTTCTGGGGAAGCCACCTTCGCCCGTTAGTCTTGGGAGAAGTGTGACTGGGGCCCTTCAGGGCTCTTCTTCTGTGCTCCGTTGATGCTAAGTGGGTGTGTCTCCACGGTGCTTTTACCCCACAG
Seq C2 exon
TGTATCGACAGTGAGGCCCGGGCAGCCAACTACACCAGCTCCTTGAATCTCCCAGACAAAACGCTGCAGTTTGTCAAAGACCACCCTTTGATGGACGACTCGGTGACGCCAATAGACAACAGGCCGAAACTGATCAAAAAAGATGTCAACTACACCCAGATAGTGGTAGACAGGACCCAGGCCCTGGATGGGACCTTCTACGACGTCATGTTCCTCAGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013679:ENSRNOT00000018378:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.094 A=NA C2=0.013
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(12.0=100)
A:
NA
C2:
PF0140314=Sema=FE(17.1=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:
CTGTCAGCGGTCTGTGCCTA
R:
CGTCGTAGAAGGTCCCATCCA
Band lengths:
349-1371
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]