RnoINT0133041 @ rn6
Intron Retention
Gene
ENSRNOG00000004033 | Sema6a
Description
semaphorin 6A [Source:RGD Symbol;Acc:1305493]
Coordinates
chr18:41387219-41389510:-
Coord C1 exon
chr18:41389411-41389510
Coord A exon
chr18:41387337-41389410
Coord C2 exon
chr18:41387219-41387336
Length
2074 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
CCCATCTCCTCTTTTCACAGATA
3' ss Score
10.77
Exon sequences
Seq C1 exon
ATGAGGCCAGCAGCCTTACTGCTGTGTCTCACACTGCTACGCTGCGCTGGGGCTGGTTTCCCAGAAGATTCTGAGCCGATCAGTATTTCGCATGGCAACT
Seq A exon
GTAAGTATCACACTCTCACTCCCCGTGGCTTTTGAGGGCATCTTAGCCTGCATCGGCCTAGCCAAAAGCTAAAAGGAATTAGAAGAGACACAGTCATTTCAAACTCGATGTATGACAAGGATTCATGTCAGGTTGGTTGGATGGAGTTGGATGGATAGGGAGACTGTTAATAGCTTCATCAAGTGTTGTAGCAACACCAACAAGTCTTTGAAAGGTCTCTTGAGCCTACTGATGAAATTTTACTCTACACACAGAGGCATGCTCCTGCCTTCACACCAGCCACAGGGGAGAATATTGCTGACATTTGAGGACTGAGAGTGTTATGTTTTTATTTGTGACCCGTATGTACAAAATAATGGGTGTTTTTGAAATACTTAAGAGGAAAAAATGTAACTTTTCAAAAAAGCCTTAGAAGCTTGCTGGTCTCAGCAAGGGGCTGGCCTTGGACCTGTAGAAGGTTCATCCATTTATAACTTTATTTTGATACCTGCTTTTTGTCAGAGGTAGATACTGACATAATTAGAATTTCCGGTGACTCCCTAAAAGAAGAAAGTCTTACCTCTGTTTTGGAAAGAACATCCGATTCCCTCTTTTATTGTCTGCCCTCCAAAAGACAATTGTTCAAGAACATTTTTGTCAAGTACCACTTTCTATGTAATTATCCCCAAACACCGAGTGAACCATACCAAAAGATGTCCAGGATATTTCACAGAAAGCAGATGCACCAGTGCCGAGCTTCCAGCTGGAGTCTCTGGAGGAGGAGATGATTTTATATACAAAGATGAGGAGCCAACTTGGCCTGAATTATATAACAGCAGAGGGTCAGAAGGTCAAAGTCGATGCTATCACTTCTGAAGTAGTCAAGTTCTCTTCCCTTGGGATTAAACATTAAATAACCCTATATTTATCTCCATCTACATAAGATTTCTATCTTTGATATTCTACTTCAACCCAAATATGCTATTGACAATCATTAATGGTCACGTAACCCCGTGATAAAGGGTATAGAGAAGTTGCCATAGCAACCCCATATGATGACCAGATACATGAAATTAAAGAATCATGGAAGAAAAAGCTTAGAATAATTATATGACAAGCTTATTTGGGAATGAAGTATATTGACACTCTCTAGTAACATACTGCCATGAGGAAGCCCAGAGACCATGGGGTTAGAGTGTAGTCATCCAGGGATGAATCTGTGAGTGGTTCCCTACTCACAGTTGCATCACCACAACTCCCCAGAAAACATAGCCTTTTGAGTATGACTCATCTTTCTGCCTTTTGGAGGGTTGCCAATGCTCTGGAGACTATCAGTTTAGAAACAGAGAGATGTGGAGATGCAGGTATTTCTAAAGGTCAGATATTATTACACATCACAGACTCAGCCAAAGAGCACTAAAGGGAAAAAAATGGGCTCATGGACTCTGCCTGATCGCCCGACTGGCTACACTCACTTTGACCCTGTCCTGTCAAAGCCCACTTCTCTGTGAGATTAGCCAATTGCTTAGCTCCAGAGTGTACTTCCCACAGTTCCTAGAATGTCAACCAATCTAGCAGGGCTGCCCCTCAATGGTAGATTATTCCACCCGGACGCCTGTGGAGACTGTATTTTTCTTCTGGCTCCTGGATGAAGGCTCTCGCCTCCAGACCACATTGCCTTTGTGGTGATTGATGGGGAAGGCAGCTTTGAAATAGTTTTGTCCGGAGACAAGATCTTTGGCAGCCTGCCCCCTCAGGCTTAGCACTCCACAGAAGATGAAAAGAAAACTAGGGAAGAAAAGAGCACCTTCGTGCAAAGGGTTGACCGGCAAGTTTAACCCTCAGAAACTATGACACTTAGAGATGTTAAGCCTGGGCTAATTATCATCTGGAATTGAAGTGTAACTCGATCATCCTCAAGGAGCCCTCTCATCATGTTTCCTGAAGTAACAGCTTTACTGGAGAAGGGAAATGGTGGCATGGTCTGAATTAAAACATGTGTTTTGTTCTGGGGCCCGCCTCCTCCTCACACTGGCCCGTTGATTCTTGGCTTGATCTGCATTTCCCTCTCTTACCCCATCTCCTCTTTTCACAG
Seq C2 exon
ATACAAAACAGTATCCGGTGTTTGTGGGCCACAAGCCAGGACGGAACACCACGCAGAGGCACAGGCTGGACATCCAGATGATCATGATCATGAACAGAACCCTCTACATTGCTGCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004033:ENSRNOT00000005446:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.025
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(3.9=42.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
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]