RnoINT0132959 @ rn6
Intron Retention
Gene
ENSRNOG00000013679 | Sema4d
Description
semaphorin 4D [Source:RGD Symbol;Acc:1310554]
Coordinates
chr17:13527304-13528803:+
Coord C1 exon
chr17:13527304-13527455
Coord A exon
chr17:13527456-13528627
Coord C2 exon
chr17:13528628-13528803
Length
1172 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
TACTGTCTCTGGAATTCCAGGGC
3' ss Score
4.66
Exon sequences
Seq C1 exon
AGCCTAGCTTCGTCTTTGCTGACGTGATCCACAAGAGCCCAGATGGTACAGAGGCTGAGGATGACAAGGTCTACTTCTTCTTTACGGAGGTGTCCGTGGAGTACGAGTTCGTCTTCAAGTTGATGATCCCGCGAGTTGCCAGGGTGTGCAAG
Seq A exon
GTGGGTGCTGCCTCCCCTGTCCCCACTCACACTCCTGCCGTGGATGCTGCCTCTCCAAGACTCCTCCCTCTGGAATCGCAGCCTTATCCTATGGGTAGAGACCCCGGTGGTAAAGTTTCATGGATAGTTGAGGCACAGTAAGAGACTCAACAGTGACAAGTGATAAAAGATAAGAGATTTGTGTGAACGGTTTCTCTTGACTCCCGGAGTAGGATCGGGAAGATGGCTTAGTGGTTAAAGTGCTCGCCACGAAAGCAAGAGGAACAGAGTTCAAATCTCCAGAACCTATAGATGCTGAGTGAACCCCCTGTAATTCTGACTTAGAAAAGTGGAGATAGGGTCTCACTGGAGCCAACCTGCTAGTGGGACTCTCCTCGTTGGCAAGCTCTGAGTTTGACTGTGAGACTTTGCCTCAAAGAATAAGGTGGATGGGACCTGACATCAACTTCTGGCCTCCATACCCACTGAGACACGAACACTCATGTAGAAGTGCACCATACACACACACACACACACACACACACACACACACACACACATACACACACACACACAAAAGGAAGGAAACTCAAAGGGGAAAAAAGAACCAAGGTGAGCATTTGTGGTATTTTCAGTATGACTAGTCACAGGGTAACTGAAATTGCAGGAAACCAAGACCACTCACACGGGAGCTGGCTTATTTCTTTCCAGCTCACGGTTGGGTGCAGTTGGTAATTGTTTCCGTTGTCTCCGTTGTCGACTCACTGAAAAGACTCAGGGCTCTAGAGCTTTGTCTGGAATCAAGGAGGCAGAGAGGGCAGGAAAGGAGCTCTTAGTGGACACTCAGATGTTTGCCCAGAATGGTCTGTAGGGCTGAGGTCTGTGGTGGGAACGAGGCCACCCATCATATGCTTATCTCCCGTGTGCTCCTCCCTGGGTCACAGCTGGGAAGGCTGCAGGAGCCAAAGCCAGTGGCACGCTGGGGTGACACAGATGTGGTTGTTTTGGTTGTCACTGAATGTGCCTGGCTCTTTTCTCGTTCTGTGACCCTGGCCCACATGGAAGTTTGCTTTGGTGACATGGCTTGTCTGCAGCAGTCTTGGGCTGGGCTGGTGGCTGGGGACATATGGACGCCTGCTTCTGTGGTTGGCCATCTGTGCTGCCTCTACTGTGTACTGTCTCTGGAATTCCAG
Seq C2 exon
GGCGACCAGGGCGGCCTGCGGACTTTGCAAAAAAAGTGGACCTCCTTCCTAAAGGCCAGACTGATCTGCTCCAGGCCAGACAGTGGCCTGGTCTTCAACATTCTTCAAGATGTGTTTGTGCTGAGGGCCCCGGGCCTCAAGGAACCTGTGTTCTATGCGGTCTTCACCCCACAGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013679:ENSRNOT00000018378:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(11.6=100)
A:
NA
C2:
PF0140314=Sema=FE(13.4=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:
AGCCTAGCTTCGTCTTTGCTG
R:
AGCTGTGGGGTGAAGACCG
Band lengths:
328-1500
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]