RnoINT0132965 @ rn6
Intron Retention
Gene
ENSRNOG00000013679 | Sema4d
Description
semaphorin 4D [Source:RGD Symbol;Acc:1310554]
Coordinates
chr17:13534885-13537114:+
Coord C1 exon
chr17:13534885-13534928
Coord A exon
chr17:13534929-13536188
Coord C2 exon
chr17:13536189-13537114
Length
1260 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CATTTATTTTGATGTTCCAGATA
3' ss Score
8.25
Exon sequences
Seq C1 exon
GGGCTGGATTCAGGACATGAGTGGCGACACGTCCTCGTGCCTGG
Seq A exon
GTGAGTGGATCTCCTTTGTTTCCGCCCTTGGGTTGGCAAAGTTCCTGGGGCGTCAGTTCCGCGGTGTCCGGTATCCCTGTACAACTCGTTTTCCTCCTCTCCAGACAGAAGTCAAGTGTCACGCAGCAGACCTGGTGGACCTGTGGTCTTTCTCTGTCCCTTTGGTTACAGAAAGAGGGCTCACAGCCACACGGGGTATATCGGTTCACGGGAAAGCATGCCCTGTCCCACACCAAGTTCTTCTGTTCCGCTTAGCGGGGCCCCGTAGACAAAACCCGAGCCTGCTAGGAATTGAGAAGGAAGGAGTCCTTGGGTATGGTTTGATAGCCCTAACCTAAAAACAGCACTCAGGAACAGTGGGGATCAGTGTCATGCTTCGAGGAGCAAAGTCTTACCCTAGAAAGTAGTATCTTGACGCTAGGGAGACGGCTCCATTGGTAGGATCTGAGTTCGATCCCCAGAACCCATGTAACAACTGGGCATTGGTGGTCCATGCTTGTGATCCCAGCCCTAACGAGGGTGAGGCAGGTGGGTCCCTGGAGCTGCTGGCCTCACACAGCCTAGTTGGCTAGACAAGTACCAGAAAAAGACAAAGTGGGGTGGAGGTGGGGAAAACTGCTACCTGAGGGTGACACTTGGTAGATTTCTGGCCTCTTTCTATATAAACACACACTTGGCATCAGATTGCTTTCAGGCTCTCTGTGTAAGGTGACACAAATGACAAAGAATTCATGTTGAGACTTCGGCCCCCTTCCAAAGATAGTCGTCTTGTTTTCTACGTGCAAATATTCCCAAACCCAAAGCGTTTCCCATCTCCCGTATTTCAGACAACAGACACAGTTGTGATTAGTTCTGGTGTCCTCTTGGGGGAGGGGGCAACCTTGCTGATGGCTAGCTGTCAGGGAATAGCTGTCCCTGGTTGCTAGCTGGCCTGCTTCATCCATTAGCAGAAGTGTTTGTCAGCTGACTGGGTGTAGGTGGGGCTGCTGAGAATGCCCAGTCCCTCAGTCTGCTGAGTTCTCTCCAGGGCCAGGGTGAGACTAGAATTTCTCTGAGCTGTCACCAGTTTGTTCACTGTGGTGGGGTTGGAGCTGCTGTAGGGTCACGGATGTCTTTACCATGGTCCTGAAGATGGCACCTGGCCTCCAGTGGGCAGACGTCTCGTGCCGCCGTCCCGTGGGTATTAACCTGTTTTTTGAAAGCAGTTGAGCGATCAGGTGGAGGTGTGTGACGGTGAGCACATTTATTTTGATGTTCCAG
Seq C2 exon
ATAAGAGTAAAGAAAGTTTCCATCAGCATTTTTTCAAGCACGGCGGCACAGCAGAACTCAAGTGTTTCCAAAAGTCCAACCTGGCCCGGGTGGTGTGGAAGTTCCAGAACGGCGAGTTGAAGGCTGTGAGTCCCAAGTATGGCTTTGTGGGCAGGAAGCACCTGCTCATCTTTAACCTGTCAGACGGAGACAGCGGTGTGTACCAGTGCCTGTCAGAGGAAAGGGTCAGGAATAAAACGGTCTCCCAGCTGCTCGCCAAGCACATCCTGGAAGTGAAAATGGTAGCTCGGATCCCCCCATCACCTACCTCACAGACTGCTCAGACAGAAGGTAGTAGGATCACATCCAAAATGCCTGTGGCGTCTACCCAGGGGTCCTCTCCCCCTACCCCGGCTCTGTGGGCAACCTCCCCCAGGGCTGCCACCCTACCTCCCAAGTCCTCCTCCACCGGCACGTCCTGTGAACCAAAAATGGTCATCAACACGGTCCCACAGCTCCACTCGGAGAAGACAGTGTATCTCAAGTCCAGTGACAACCGCCTGCTCATGTCTCTCCTCCTCTTCCTCTTTGTCCTCTTCCTCTGCCTCTTTTCCTACAACTGCTACAAGGGCTACCTGCCCGGACAGTGCTTAAAGTTCCGCTCAGCCCTGCTGCTCGCAAAGAAAAAACCCAAGTCAGAGTTCTCTGACCTGGAGCAGAGTGTGAAGGAGACGCTGGTAGAACCTGGGAGCTTCTCGCAGCAGAACGGCGACCAGCCCAAGCCAGCCTTGGATACCGGCTATGAAACCGAGCAGGACACTATCACCAGCAAGGTCCCCACCGATCGAGAGGACTCGCAACGTATCGACGAGCTCTCCGCCAGGGACAAACCGTTTGATGTCAAGTGTGAACTCAAGTTTGCAGACTCGGATGCCGACGGGGACTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013679:ENSRNOT00000018378:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.078 A=NA C2=0.278
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(26.4=87.5)
A:
NA
C2:
PF0768612=V-set=WD(100=26.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATTCAGGACATGAGTGGCG
R:
TCTGTGAGGTAGGTGATGGGG
Band lengths:
354-1614
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]