RnoINT0132971 @ rn6
Intron Retention
Gene
ENSRNOG00000013679 | Sema4d
Description
semaphorin 4D [Source:RGD Symbol;Acc:1310554]
Coordinates
chr17:13524638-13526444:+
Coord C1 exon
chr17:13524638-13524731
Coord A exon
chr17:13524732-13526330
Coord C2 exon
chr17:13526331-13526444
Length
1599 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
TTCCCTCTTTACCACCGCAGGGG
3' ss Score
9.46
Exon sequences
Seq C1 exon
AACTTGACCTCTTTCAAGTTTCTGGGGAAAAGCGAAGATGGCAAAGGAAGATGCCCCTTCGACCCCGCCCATAGCTACACATCCGTCATGGTCG
Seq A exon
GTGAGTCCTGCGTCTGAGGCTCCTTCAAGCTCTTGAGTTTATGGTGGCTTGTGATGTTGCCACCTGGGCTTCTCAGCTCTTCCCTCCTCAGTGCCGCCTTCCTTGGCTTCCTTTTGACCCCGAGCTCCCTTCAGAGAAGGTGAGCGGCACACGGCATAGACTCCTCAGGGAGAGCTTTTGAGTTTATCATTCAGCCGGAAACTCAGGCCCCACTGAGGCATCGAGTGCTTCTGTCAGTTGTTGTGCTCACCAGCTGGATGCTCCCTGGCTGCGTGCCTCCTGCTGTGGTCCATCTGAGGCTGGGGGGGGGGGGGGTAACACGCTGTTGTACAGACAGTTTACACTGGGATGACGGTTCAGGCTTCACTGTCAGTGTATAATATCTAGTGAGCTTTGAGGTATTCAGTACTATATTATAAACTTTTAAAAAAATTTTATATTTATGAGTACACTGTAGCTGTTTTCAGACACACCAGAAGAGGGCATCAGATCTCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCGCTGAGCCATCTCTCCAGCCCCCTAGGTACTATATTATAATACAGGCGTCGTGAGTGACACTTCTGTGCAGTCCTAGGCTAAAGTGTGTATTCTGAGTGTACTAAAGTAGGTGAGGCAGGGTCCCCAGTGGAGGAGTTAGAGAAAGGACTGAAGTAGCTGAAGGGGTTTGCTACCCCCATCAGAAGAACACAGTATCAACCAACCAGACTCCCAGAGCTCCCAGAGACAAAACCACCATCCCAAGAGAACACAGGAATGGACCTAGGGCTCCATCCACACATATAGCAGAGGAGGGGCCTTGTCGGGCATCAGTGGGAGGAGAGGCCCTTGGTCCTGTCAAGGCTCGATGCCCCAGCATAGGGGAATGTCAGGGCAGGGAGGTGGGAGGGAGTGTGTGGGTGAGTGAGGGAGCACCCTCACAGAAGTGGTGGGTGGGGGATGGGATAGCGGGTCTCTGGAGGGGAAGCCAGGAAATGGGTTAACATTTAAAATGTAAATAAAAATATGCAATTAAAAAATAAATCTTTAAAAAAGGGATAAAATAAATAAAGCAGGTGAGGTTGGACCACGCTACCTGGCAGTGTAGGGGCCTTACACATCTTTTTCGACCTACAGTGCTTTTTACTTAGGATGGCTTTCTGGGGTGTCAGACACTGAGGAGTGTCTGTCTGCTGTCTCGATACTGACTGCGGGGAATTCTCATTTGTGACTAGCTATTACCGGTTAACCTGGAAAAACACAGTTAAATTTGGTGACTGTGACTGTTCTGGTGAAAGGCGCTGAAGTAGGGAGCAGAAATTCGTATCGCAGAAGACGGGGAGGCCCCCTTCCCAGCAAGGAATAAATGAATTATGGCAGCCTGGTAGGGGTGTGATAGCCCGGTGGAGGTGGAAGCATGAGGCTTGCTTACGGGCCAGCCTGGGCTAATGTCAGAACTTGTGTTAAACAGTTGTCCCCGGTCTCCACCACAGGCAGAAAAGCTCTGACTGGATCCCCTTCTTGATTCCCTCTTTACCACCGCAG
Seq C2 exon
GGGGAGAGCTCTACTCTGGGACTTCATATAATTTCTTGGGCAGCGAACCCATCATCTCTCGAAACTCTTCCCACAGTCCCCTGAGGACAGAGTACGCCATCCCTTGGCTAAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013679:ENSRNOT00000018378:9
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(7.2=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:
TTGACCTCTTTCAAGTTTCTGGGG
R:
CCAAGGGATGGCGTACTCTGT
Band lengths:
198-1797
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]