RnoINT0133079 @ rn6
Intron Retention
Gene
ENSRNOG00000021101 | Sema6c
Description
semaphorin 6C [Source:RGD Symbol;Acc:3659]
Coordinates
chr2:196341891-196343987:+
Coord C1 exon
chr2:196341891-196341935
Coord A exon
chr2:196341936-196342601
Coord C2 exon
chr2:196342602-196343987
Length
666 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
CCCTCCTTCTCGGTCGGCAGGCG
3' ss Score
8.25
Exon sequences
Seq C1 exon
ATGGAGCGACTGGGAGTCAGTCTGGCCCTGGAGATTCTGCCTATG
Seq A exon
GTGAGTCTTGTGGCCTCAGTGTTCTTTTCCCTTAGCCCACACAACCAGATCTGTTTGGGCTATCAGCAGACCAGCACCATGAACAGTCAGATGCGACACTGGAATTCGGACTCCTGGGTTCCAAAGGGGGTGGGGGACTCTTGGTGGTATCATGGGTGGAGAGCATATGTCTCACTGGCTCTGACCTGGTCTCTGTTACCAGTGCTTCTGGGTCCTGGCCCTTCCCCTGAGACCCCCAGTTCCCCCAGTGATGCCCACCCAGGGCCCCAGTCTTCCACTCTTGGAGCTCACACTCAGGGTAAGGGGGTCACCTGGGAGGGACAGTATTGCAGCGTGGAACTGCTGAGTCTCAGAGTTCTAAGCCGGGTACTGATTGGTGTTTGATGCCCACTAACACCTGTTTGGAACCTCCCTTCACCACAGCTGGACATCCCAGCCAGTGTCCTGCACGGGCAATTTGGCAGTTGTTCTTGGCATGGCTACAGGGGCTACAACTGGTATCGGGATACCCCAGACCAGTGCTCTAACCTGTGTGTTTAGGGATCCTGAGACTGTGTGGAGTGAAGCTGAAAGGCAGCATGAAAACTTGCTGTTAGCCCCACCTGTGCCTGTTCTGTGCACCAACTACCCTAAAGCTGAGCCTCCCCCCTCCTTCTCGGTCGGCAG
Seq C2 exon
GCGTGCGCAGGGACCTTTCCCCAGCCTCAGCCTCCCGATCCATCCCCATCCCACTCCTCCTGGCCTGTGTGGCGGCGGCCTTCGCTTTGGGCGCCTCAGTCTCCGGCCTCTTGGTGTCCTGTGCTTGTCGTCGCGCGAACCGCCGTCGGAGCAAGGACATCGAGACCCCGGGGCTGCCGCGCCCCCTCTCCCTTCGCAGTCTGGCGAGGCTGCACGGTGGCGGTCCTGAGCCCCCGCCTCCGCCCAAGGATGGTGATGCAGCGCAAACGCCCCAGCTCTACACTACCTTCCTGCCTCCGCCCGAGGGCGGATCCCCACCGGAGCTGGCCTGCCTGCCCACCCCGGAGACCACGCCCGAGCTGCCGGTGAAGCACCTCCGTGCCTCCGGGGGTCCCTGGGAGTGGAACCAGAACGGGAACAACGCTTCGGAGGGCCCAGGCCGCCCACGGGGCTGCAGCGCGGCGGGCGGGCCCGCCCCGCGCGTGCTGGTGAGGCCACCGCCCCCTGGCTGCCCCGGGCAGGAGGTGGAGGTGACCACGCTGGAGGAACTGCTGCGCTACCTGCACGGCCCGCAGCCGCCCAGGAAGGGCAGCGAACCTCTCGCCTCCGCCCCGTTCACCTCCCGGCCGCCTGCCTCGGAGCCCGGCGCCGCCTTGTTCGTGGACTCCAGCCCGATGCCTCGTGATTGCGTGCCGCCGCTGAGGCTCGACGTACCGCCCGACGGCAAGCGCGCGGCCCCGAGCGGGCGGCCTGCTCTCTCGGCCCCGGCTCCACGCCTGGGCGTCAGCGGCAGCCGAAGATTGCCCTTCCCCACGCACCGGGCGCCCCCGGGCCTGCTCACCCGAGTCCCCTCGGGAGGCCCGTCCAGGTACTCCGGGGGGCCCGGGAGGCACCTCCTGTACCTGGGCCGGCCCGACGGCCACCGCGGCCGCTCCCTGAAGAGGGTGGACGTGAAGTCTCCACTGTCGCCCAAACCGCCCCTCGCCACACCGCCGCAGCCCGCCCCGCACGGCAGCCATTTTAACTTCTGACAGAAGCTGCTAGCGCCCGTCGAGGCGCTGGAGGCCTAGGCCTGCGGAGGCCGCTGGCCTTCCCGGACTCCAAGAGTCTCCCGGGGTCCCCTCTCGCCTCGGTTTATTTATTGACTGTCTTTCCCCCTGTCCTTTGGCGAGGAGCTCGCCGCTCGGAGCGCCAGCATTTCAGGGGACCTGGCCGACTCCCACTCCCCGCTCCCTTCCAGCCACGCTGCCTTAACTCGTCGCTCCGGACTCCCGCGGACTGGGCCCCGGGCGGGCCGGCCGGGGCTGGAGCCGCGCGCTGTGTACAGAGTCCTCCGGCCTCCTGGGGCCGGGACGTGCCTCCTCCTACTGTGTAGGAGCCCCCACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021101:ENSRNOT00000028645:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.875 A=NA C2=0.882
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(11.3=43.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
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:
TCAGTCTGGCCCTGGAGATTC
R:
CAGCTCCGGTGGGGATCC
Band lengths:
355-1021
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]