RnoINT0132916 @ rn6
Intron Retention
Gene
ENSRNOG00000019737 | Sema4a
Description
semaphorin 4A [Source:RGD Symbol;Acc:1304636]
Coordinates
chr2:187799568-187801464:-
Coord C1 exon
chr2:187801367-187801464
Coord A exon
chr2:187800805-187801366
Coord C2 exon
chr2:187799568-187800804
Length
562 bp
Sequences
Splice sites
5' ss Seq
TCAGTGAGT
5' ss Score
7.68
3' ss Seq
ACCTCTTTGCTTCTCTCCAGTTA
3' ss Score
9.95
Exon sequences
Seq C1 exon
GACTTGGAAGCAGGACATGGAACGCGGCAACCCGGAGTGGGCATGCGCCCGTGGCCCCATGGCCAGGAGCCCCCGGCGTCAGAGCTCCCCTCAACTCA
Seq A exon
GTGAGTGTGGGACTGGAGGAGGTGTCCAGGCACTTGGAGAGCTTCAGGCAGGGCTGGCTTTTCTGCCCCGTGGCTTCTGTCTGCAGCACCCACCTAGGCTGAGATCTAAATTCCCAAATTCAGGATGTGAAGCGGACAATAGAAGGAGAGGCATACTAAGCTGGAGGCCACACTAGGGTTCAGGTTGAGGTCGAAGTGGGTTTGGTGTCTGAGTTGGAATTAGTAATACTGGTGGCTGCCTACAGCCAGGTCACTCTGAGCAGATCCAATCTTGGCTGATCTCAGAAGCTAAGGGTTGATCTGGTTAGATGGAGAAAGACTCGGGGCTAGTTTGGGGCTTAGCTTGGAGATAGAGAAGGGTTGGGTCTTGAGCTTGAGAGTTGAAATGGAATTAGAATACAGACAGGCATGGTGGTCCATAGCAGTAATCCCAGACTCCAGGACTGCTGAGAGTTCAAGGCCAGCCTGGGCTACAGAGTGAGACCAGATGTGAGTAAGACTGGCTCTCCCACCCCCCTCCCTCCCTCCCCATTGAACGTGCCACCTCTTTGCTTCTCTCCAG
Seq C2 exon
TTAAAGAAGTCCTGACAGTCCCCAACTCCATCCTGGAGCTGCCCTGCCCCCAGCTGTCAGCACTGGCCTCTTACCACTGGAGTCACGGCAAAGCCAAAATCCCAGAAGCCTCTTCTACTGTCTATAATGGCTCCCTCTTGTTGCTGCCACAGGATGGCGTTGGGGGCCTCTACCAGTGCGTGGCCACTGAAAACGGCTATTCGTACCCTGTAGTCTCCTACTGGGTAGACAGCCAGGACCAGCCCCTGGCACTGGATCCTGAGCTGGCGGGCGTTCCCCGGGAGCGAGTGCAGGTCCCACTGACCAGGGTCGGAGGCGGGGCTTCTATGGCTGCCCAGCGGTCCTACTGGCCCCATTTTCTCATCGTTACTGTCCTCCTGGCCATTGTGCTCTTGGGAGTGCTCACTCTCCTCCTTGCTTCCCCACTGGGAGTGCTTCGGGCTCGGGGTAAGGTTCAGGGCTGTGGGATGCTGCCCCCCAGGGAAAAGGCCCCACTGAGCAGGGAACAGCACCTCCAGCCTTCCAAGGACCACAGGACCTCTGCCAGCGACGTAGATGCTGACAACAACCATCTGGGCGCTGAAGTGGCTTAAACTGAGACACGGATGGCTGACCATGTTGGCTAGGCCAGGCATGCACGGTGCCACTCTGACCAGGGTAGGAGGCTCTCCTGCTAGTGTGTGCCACCTACAGCACCCAGTAAGGCCTCCCTTGTGGGACTCTCTTATGCAAGCACATGGGCTGTCTCCACACCATGGCAGAGAGACAGACAGGATTCTTTGATTTTGATCGACCCCAAGAGCTCTCCTGCAACAAACATTCTCCAGGACCCTGAAAGGTGTGGCTTTCTGTGGTGACAGACCCAAACATCCAAGTGAGCTGGGGCCATTCCTGCAAACTCCATCCTGAAAGCTGCTGCTTTGAACACCAGCCCTCCCTCCTCCCAGGGTCTCCAAGATTCTTTATGGAGTTGGCCCCTTGTGTTTCCCTTACCAATCATGCCATGTGTTTGGGAAAGTCATTTCTGAAGTCTAACCACCTTCCTTCTTGCTTCAGTTTGGACAGATTGTTATTGTCTCTGCCCTGGCTAGAATGGTGGGCATAATCTGAGCCTTGTTGTTCACTTGTCTAGTGTGGCTGACCCTTGACCTCTTCCTCCTCCCTTTGTTTTGGGATTCACAACTGCTTGTCACAGACAATTTATTTTTTATTAAAAAAGATATAAGCTTTAAACAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019737:ENSRNOT00000056862:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.456 A=NA C2=0.178
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(35.7=58.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGGAAGCAGGACATGGAACG
R:
CTCAGGATCCAGTGCCAGGG
Band lengths:
358-920
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]