RnoINT0132939 @ rn6
Intron Retention
Gene
ENSRNOG00000025167 | Sema4b
Description
semaphorin 4B [Source:RGD Symbol;Acc:1307872]
Coordinates
chr1:142004892-142007108:+
Coord C1 exon
chr1:142004892-142005043
Coord A exon
chr1:142005044-142006926
Coord C2 exon
chr1:142006927-142007108
Length
1883 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
GTGCCCCTCTTCTCCTCTAGGGC
3' ss Score
12.5
Exon sequences
Seq C1 exon
ACCCTGCCTTTGTGGCCTCAGCCTATGTTCCTGAGAGCCTGGGCAGCCCAATAGGTGATGATGATAAGATCTACTTCTTCTTCAGCGAGACGGGCCAGGAGTTTGAGTTCTTTGAGAACACCATTGTCTCCAGAGTTGCCCGAGTCTGTAAG
Seq A exon
GTGAGTGCGAGGGGAGCACCCCCATCTGTGACCTTCCAGAATTATCCTCCAGGGAGCAGCAGCTCAACCAGCAATCAGTCTGTCTCTCCTCTTCCTCCTCATCCTTGTCCTGAATCTGGGTGTCTGGGCTCAGGGCAGTGTGCCTCCCAGGGCTGAGCTGGTGTCTCTATGCTGTGCGGTAACCCCTTTTATTTTTTGGTTTGTTTTGTTTTTTTAAAAAAATTCTTTTTTACATTAAATTTATTTAATGTATATAAGTACACTGTCACTGTCTTCAGACACACCAGAGGAGGGCGTCGGGTCTCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCGGTGCTCTTAACCACTGAGCCATCTCTCCAGCCCTTGTTTTGTTTTTTTAAGATAGTGTTTCTCTGTGTAGCCCTATCCATCCTGGAACTCACTCTGTAGACTAGGCTGGCCTCAAGCTCAGAGATCCTCCTGCTCCTGCCTTCTGAGGGCTGGGAGTAAAGGCTTGTACCACCACTGCTGGTTTCTTTTGGTTTTTGAGCTAAGGTTACACTACGTAGCTTTGGCCATTGTGGGACTCACTCTGTAAGTCAGGCTGGCCCCAAACTCACAGACATCCATGTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGAGAGTGCCACCACTCCTAGTTGGCCTCTGTTCTTTTAATTGAGAAAATCTTACATTAAAAGTAGGTATGAAGGTGTGTACCCAAAATCCTGACATTCAGGGAGCCGGGGAGTGGTAAATCTCAAGTTTAAGGCTATCCTGGACAACTTAACAAGGTCCTGTCTGTCTGTTTTCCAAGACAGGGTTCCTCTGTGTAGTCCTGGCTATCCTGGAACTTTCTCTGTAGACCAGGCTAGCTCCACTCAGAGATTCACCTGCCTCAGCCCACAGATTCTACCTTAACATTTTAAATAGTCATTCCTCTTTTAGGGTCTCTTGAGTAATCCAGCTGCCCTCAAATTTCCTGTGTAACTCAGGCTAACCTTGAACTTTTGATGGTCCTGCACGTGTTATCCCACCCTATTTACATGGGGCTAGGGATAAGCTATTTGGAAAAGAAGTCCTTGGCTTTCTCATGAGCTGGAAACCCAGGAACGTGCACCTAGAAGTGATCTATAGGAAACAGACAACAGCCAGATTCTTGAGTTGGAACTTCCAGGTTCCAGCCCCACTCCTTAACTGTTAAATGGCAGGGATGGTGTCACTAGCTGTCACATGAATTAAGTTCTGTGGTGTAAAGCTCTTAGGGTCCCGGCTATCCTCACAAGGAGGAGCCACTGTGTTTTCTACTGATCCATTTAAACTAATGCATCTGTATTAACTTAGTTACAAACCTGAGTTATGCTATTTCTCCCTGTTTGCTCAATAACCTGTCAATCATGGACACCTTCCCTATTATTCATTTATGTGTTCATTGTGTTGAAGTCCTTCCTACTTCACTCCCTGGCTGGGTGCAAACTCCTAGACTCTAGCAATCCTCCTGCCTTATCCTCCTGAGTAAGCTGAAGCGGCCAGTGGTGCTAGCATGCCAGATAGCAAGCATTGGCCCCTGAGTTCCCTCCTGTCCCTTCCCTCTTTAGATGGTTTCCCCTCTGTCCTTGTTTGCTCATCGTCCACAGTAGGGAGTATACTTTTGTGATGGAAAGCATACCTTCCTCCCTAAGTTTTCTCTGTTTAGATGCATATTTGTCCTGGTTCTCTCTCTGTCTCCATTCCTGTGTGTCTCAGTTATGCTGAGGAGGGCTGGCAAGGCAACACTGGAGTCTGAGAATGGCCCTCCCTCAGCTTGTGACTAAGCTGTGCCCCTCTTCTCCTCTAG
Seq C2 exon
GGCGATGAGGGTGGAGAGCGGGTGTTGCAGCAGCGCTGGACTTCCTTCCTCAAGGCTCAGCTCCTGTGCTCCCGGCCCGATGATGGCTTTCCCTTTAACGTGCTACAAGATGTCTTCACCCTGAACCCCAACCCTCAGGACTGGCGCAAGACCCTTTTCTATGGGGTCTTTACCTCCCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025167:ENSRNOT00000030914:7
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=FE(11.4=100)
A:
NA
C2:
PF0140314=Sema=FE(13.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTCAGCCTATGTTCCTGAG
R:
GGTAAAGACCCCATAGAAAAGGGT
Band lengths:
312-2195
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]