RnoINT0132969 @ rn6
Intron Retention
Gene
ENSRNOG00000013679 | Sema4d
Description
semaphorin 4D [Source:RGD Symbol;Acc:1310554]
Coordinates
chr17:13519130-13520928:+
Coord C1 exon
chr17:13519130-13519192
Coord A exon
chr17:13519193-13520829
Coord C2 exon
chr17:13520830-13520928
Length
1637 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGTGTGTGTTTCCCTTGCAGACG
3' ss Score
13.12
Exon sequences
Seq C1 exon
GTATACTGGAAGGTCTCTGAAGACAAAAAATCCAAGTGCGCAGAGAAGGGGAAATCAAAGCAG
Seq A exon
GTGAGCACAAAGAGCTCGCCCGCGCACACGCACATTTCGCAGTTATTTGGATCTTTCCCAGTACTGTGACTTCTTTCTGCATGCCCACCTGGTGTCACGTGATTCTGGTGGGCTCGGTCCTGTGGCAGCTCTCCCTGAGCCCCGGCGTCAGGATGGATGCTCTCGGGCCAGTGCTCTGTCTCCTCAGCTCTGGAGAAGCCTGTTCAAATGGCCTGGCATTGTGACTACAGGATACGTCCTGTAGTTTCTGCTGCCCGCTAGGACCTGGTGTGAAATTGGCCTCCCCTCTGTGTTTCTGGGCCTCTCACACATCTGCACCAGCCGTGTGAGGCCTAAGAGGTTTCAGGGATTTGATGGGCATCAGAAATGAACGGTGTGTTGTTGTTGCTTGGTTTTGTTTTGTTTTGTTGTTTTATTTGGTTTGTTCTGTTTTTGTTTTGTTTTTGAATTTTGTTTTCGGATATCCGTGTGCCCACTCCGGGAGACTGAGCCTTGTATCCCTTTTCTCAGGAGCTCTGGGTACCCTCTTGTGCCCACCTGGTGCCCCACAAACGTCCCAGGTGTTTTTTTTTTTTTTTTTTTTTAAGATCACAAATGTTTTTAGATCACAAGAGCCAGGTTGTCACTGATAACGATCTCGGTGGCTCAGCGATGGCAGAGTTTGTCAGTTCTTAGCTGATTTCAAAAACAAAGATTCAAACAGCCGCTCACAGTTTGTTTTTTCTAAGTTAAACTTTCTTGGCCGAATGCTCACTAAGCACTTTTCACCGCCCCTGCTGGTCTCTAATTGGGGTGTTAACTGGGGATCTGAGGCAGGCAGGCAGGCGTTATGATGGGATGACTGCTGCAGGCAGTCTGTGTAGCCAGTGAGCGGATGCTTTACACCGCAGCGCGCACGTGGGGACCCACAGTGAACTTGGTAGGGAGCCCTCCTGTGAATGATACCCCGTCCATTTGAAAACAGTTGTTGGGGGGGACAGACAATAACAACAACAACAACAAAAAAATCCTTTTCCAGTTTGAGATCATTTCAGGCTATAGCCCATGCACTCTAAGCACTGCTCTCTTAAAATAGCACGTAGGTTCCAAATTGTCATCTTTGTTTTCCCACCGGGCCCTCGGGGATGCACACTTGGCCGTCCCCTTGGGTCCAGCCTCTCTCTCTTAGACCCTGCTAGTCGCTATTTCTAGTTCCGTGCTGGCGACAAGAGTATAGGGTGGGGTCCCCAGGAAGGCCGAAGGAGCCTGTACAACGTCTGTTTTGGTGAGATGGCCATCAGAAATGAACGGTGTGTGTTCAGCTAGGGTAACTACATGGCCATTTGTAGTGGGTTCCCCGGTACAATTTGAGGGTCAGCTCTGGTTTGGTCTTGGCTTTGTTTGGTCGCCAGAGACAGGCTGACCATCTATTAGGGACAGAGCTAAAGTCATTCCTGGCACCTGTTCTGCCCGTGGACCTCAGAGATAGAGTTCACGTTGCAGAGCCTGGCTCACGGTGCAGTGCGCCCCTTCTGTAGGCATAGACAGACCAGTCTGAGCAGAGGAGAGAACCGGGCAATGGATGCCTGGCCTTTACGACGTGGACACGCGGATTCTTTGGTGGGTGCCTGTTAATGGTGTGTGTGTTTCCCTTGCAG
Seq C2 exon
ACGGAGTGCCTTAACTACATCCGAGTGCTGCAACCGCTTAGCAGCACTTCCCTCTACGTGTGTGGGACCAATGCGTTCCAGCCCACCTGTGACCACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013679:ENSRNOT00000018378:7
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=PU(5.0=95.2)
A:
NA
C2:
PF0140314=Sema=FE(7.4=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]