RnoINT0132963 @ rn6
Intron Retention
Gene
ENSRNOG00000013679 | Sema4d
Description
semaphorin 4D [Source:RGD Symbol;Acc:1310554]
Coordinates
chr17:13531517-13534812:+
Coord C1 exon
chr17:13531517-13531632
Coord A exon
chr17:13531633-13534639
Coord C2 exon
chr17:13534640-13534812
Length
3007 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATG
5' ss Score
8.99
3' ss Seq
CGTCTGTCTCTCATGCACAGGGG
3' ss Score
8.85
Exon sequences
Seq C1 exon
ACCGGGGCGCTCTGCATAAAGCTGTCATCCTTGCAAAAGAGGTACACGTGGTTGAGGAGACCCAACTCTTCCAGGACTTCGAACCGGTCCTGTCTCTGCTGCTATCATCAAAGAAG
Seq A exon
GTAATGTGGTCTGAGGGGCAGGTCCAGGCGCTTGTCTCCCTCGGGAGCTTCTCTGTGACTAGGACTAGATAGGATGGTCTCTCAAGGCTTGGCAGCCTCTGGTCTTCCTGGCCCGGGTGAGCTGACCTTTAGACTCTCAGCAGTCTTCCATGGGATCTGAGGCCTGGGAGGAGGACGGTAGAGCCAGGGAGGTTGATGTGCTAAGCCCCTAGAGCTTTTAGGAGGTCACTAACCTGGGAAAATGTCTTTGTGCCGTGAACTTGAAAGAATGCAGACTGTGCTGCTGGGACAGGACACTCATTTTTAAGGAGAAATAGCAGGTCACCCTCTAGAGCTCCCATTGCCACACCATCCTGTGTATCCAGCTGCCTTTGCAGAGGCCTCAGTCATGGTCGCTTGGCTCTGCACTGTGGCTCCCACAAAGCCATGGAAACACATAGATGACCAAACCTGCCCTTGAACCCTTGAAGCCAAGCTCTGCGTCACCTGAGGTTTTCATAAGAAGCTTCAGCCAGGTAGTGGTAGTGCACACCTTTGATCCTGGCACTCGGGAGGCAGAGACAGGTAGATCTCTGTGAGTTCAAGGCCAGCCTGGTCTTCATAGTGTGTTCCAGGCCAGCCAGAACGATGTAGGGAGACCCTGTCTTCAAACAACAACAACAACAACAGCAAATTAACTAATTAAATATTTTTTAAACCCCTGAATGGAGCACAGTGGTTCTTCATACCTATAGTTTCAGACCTTAGAACATGGAAGATCAAGAGTTCAAGGCTAGTCTTAGCCACATCACAAAATCAAGGCCAACCTGAACTAAGTGAAACCCCATTGCAAAAGTCAAGTGATACACAAAAGTCCTTTAGGTGGTGGAGTCTATAGAAAAGGCCCAGGGGCTGGGTTTGGTTCACTGGCTGGAACTTGTTTCTTATCCACTGGCCTTGGGAAGGCCTGGACACCACATTTTACGTCTAGGATAGAGCAGTGAGATTCAGAATGTGGGCTGTCTCCCAGTCCTGATTATGCTATGCTGCCATGTGACCCTGGGCGTCACTGTGTGATCCTCATAAGGTGGTCTCTCTGTGTGTAAGCTTCTCATTAATGTGACTGTGAGCATGTGAGCCTCCTGGGTGCTAAGGACGGGCTTTGAGCAGCACTGAACCCAGGGACAACTAGGAGCAGGATCAGCGGCCACCTGCCCTGCTTCATAGCTGCTGGCCAGAGGTGCTCCCCTCTCCTTGCTAGGACTGTGCTGTAACCCACTGAACAGATGGGTCCAGGGACACACTTATGGCTTCAAGTGTCTCTGATGCCTGCCTCTGGGACACTGCTGAACTCTGTGGCCTGGTGTTACCTTTCCCTGTGGACTGCACATCTGTGGGCTCCATGTCTGCTGTTCAGTTCTCTTTAGGTAGCTGGCCACGGCAGATACCCAGGGCCCATCAGTCTCACCCGTGTGCTGGCCTCCTGCCAGCGCCAGGTACGGTGCTGACCTTGGCCTAGCAACCACATGGTACGCTCCTGTCCTGGAAGTCAGAGCCTTGTATGTGCTAAGCTCTGTGTGGTTACACACGGTGGTGGGGGTGGTATGTGTGTGGAGGGAATGGCCTATTTTTGCGGCTCTGTGCTCACAAATGCAGGCAAATGGGAAATCAAACGGCAGTGTCTCTTGCTGGGTTAAGCTTGATGGCCTTCCGTTTGTTCTTTGCACGACGTTGATAGACGTGGTCACATTGGCCTGCCGGATTCAGAGATGAATGATAAGGAAGTGTCCTTAGCACAGGTACCTACTGTCTGTCACAAGACAAGGCTGGCATTTAAAGGCTCTGCCCTGTGGCTTCCAGCTGCAGTGCTGCGTCACCTACAGAGAGTCCAGGAGAGCAGTGGGGGATGTCAAATTAGGAGTGGGAAGCAGCTGAAGAGGTCTGTTACATGGGTTTTCTCAAGACACAAATGAAAGTCTCTTTACCCCAGGCAGGGCACTGAGGACAGACCAGTCCAGCTCAGCGAGCCAGTGAGTTATGGGGGAGTTAGCTACAGAGGAAGAGGGAGGGTTGATTTACAAGCCCGTGGGTGACTCAGAGGCAGCTGCATGGACAGCCTACCCCAGCATAAGTGACATTCACAAAAGCTGCAGCGAAGGAACTCCCTGCACGACTGGTAGGCAGCTCGGCAGGACAGAGCCCCGTCTCTGACAGCACTTGTGTATTGCTTATATAGCCCTGACGGAGCGGGAGCTTGTGAATCTTATTACTTGTCAGGCTTCCTAGATTTCCTTTACTGAGAGTCTTGTGAGCCTCCCTCCGCCCTCCGGGAGGACACGTTTCAGTTGGGCAGAAACAGGAACAGAGTTGTCTTTTCTCGAAAGAGAAGCTACTTCGGGAGGGACTGCAGTACGCCCCGCCACAGGTCTAGCCCCAGATATGGAAGGGTGGCATCAGATCTGCAATTCCTTGGGTGGTGTTTGAACCCTCCTGGGGTACAGGACACCCTATATTTCCATACGAGATTTCTGTCTTAGTGTGCTTTTTTTTCTGTTGCCATGATAAACCACTCTGACCAAAAGCAGCTTGGAGAGGAAAACGTCTGTTCCGGCTCAAACATCCAGGTTGTAGTCTGTCGTTGAGGGAAGCCAGGGCAGGACCAGAGACCATGGAGGAAAATGGCTTATTGGCCAGCCCTCCTGGCTTCTGCTTAGCTACTGTTTTACAAAGTCTAGGACTATCTGGGTGCCATCCCCCACAGCAGGCTGAACCCACCTACCATTACCTAGCAAATAAGAAAATGCCCCACGGACAGGTCCTGGGTTGATCTGATGTAGGCAATTCCTCAGCCGCAGTTCTCTGCCCCGCAAGCGTGTCAAGGTGACAATGAAAACTAATTTCAGGACACTGTCGTTTAGGCCAGGGAGTCTTTTCCTCCCTGCAGTACTTGAACGCAATGTCTTCCCAGTCTCGGGACTTCCCAGTGCCCATGTCCTCCTTACACCTGCCGTCTGTCTCTCATGCACAG
Seq C2 exon
GGGAGGAAGTTTGTCTATGCTGGCTCCAACTCAGGAGTGGTCCAAGCTCCCCTGGCCTTCTGCGGAAAGCACAGTAGCTGTGAAGACTGTGTGCTAGCACGGGACCCCTACTGCGCCTGGAGCCCAGCCATCAAGGCCTGTGTTACCTTGCACCAGGCAGAGGGCTCTAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013679:ENSRNOT00000018378:15
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(8.8=100)
A:
NA
C2:
PF0143720=PSI=PU(71.7=65.5)
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]