BtaINT0099709 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001764 | NCAN
Description
Bos taurus neurocan (NCAN), mRNA. [Source:RefSeq mRNA;Acc:NM_001193082]
Coordinates
chr7:3966621-3968627:-
Coord C1 exon
chr7:3968334-3968627
Coord A exon
chr7:3967221-3968333
Coord C2 exon
chr7:3966621-3967220
Length
1113 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGT
5' ss Score
9.81
3' ss Seq
TCTTCTGCTTTCTCCCACAGCTC
3' ss Score
12.4
Exon sequences
Seq C1 exon
GCGAGGTCTTCTACGTAGGCCTGGCCCGCCGCCTGACACTGGCCGGCGCACGTGCCCAGTGCCGACGCCAGGGCGCCGTGCTGGCCTCGGTAGGACAGCTGCACCTGGCCTGGCATGAGGGCCTGGACCAGTGCGACCCGGGCTGGCTGGCCGACGGCAGCGTGCGCTACCCGATCCAGACGCCGCGTCGGCGCTGCGGTGGCCCAGCCCCTGGCGTGCGCACCGTATACCGCTTTGCCAACCGCACCGGCTTCCCGGCACCTGGAGAGCGCTTCGATGCCTACTGCTTCAGAG
Seq A exon
GTATGTGTGAAGCCTCGCCCCTGGAGGGTGGGTCTCCTGGTGACCACGCCCCAAGGGCGTGCGCTTTGCTAAACGGCCACGCCCCTGGAAGTTTGGGTTTCTAGTGGAGGCGGAGGTCAGGTAGGGCAGAAACAGGTTGAAAACTTACTCCGCGGTGAGCCACGCCCCCAGGGAAGGGTGACACCCCCGAGACAAGCTTTCCATAGGAGCCCCGCCCCTCCTTAGGACAAGCCCGAGGCAAGCCAAGCTCTGCGGGGAAGTCCTGTTGAGTGTGTGGTCTAGGTCTTCCAAGGTGGCGCTAGTGGTAAAGAACCCGCCTGCCAATGCAGGAGACGCAAAAGATGCGGGTTTGATCTTTGGATTGGGAAGATCCCCTGGAAAAGGATATGGAAACCCACTCCAGTATTCTTGCCTGGAGAATCTCATGGACAGAGGAGCGTGGGTCGCAAAGAGTCGGACACGACTGAAGCGACTTAGCACGTATGTCTCCTGAGATCTCTAAGAGATGATCTCAGACCTCTGGATGGAAAGCTTCTTGCCTGGAACCTTGCACAGGAGCACCCGCTGGGAAGGGATTAAGGCCTCGGCTAGCCACGCCCCCTAAGCAAGGCCACGGCCCCAGGGACAGGACCAGGGGATGACCCTCGCCCTTGGGTTGGTTCCATACCCTCAGAAGCTGCCAACCTCAAATCCAAAGGAGCTGAGTCTTATGTGAAAGGGCGGGAGTTGGGGGGAATTTCTTCGTAGGGAGGCCATGCCCATTAGGCGCTTTCTCTCCCTGGGGAGGAGCCATGCCCAGGTCTGACCTGCCCCCCTGGGAGTTGGCACTGCCTGAGCTTCACCCACCGGCCAAGATGTCTCTTGACCCTTTATTGCGACCAGTTGACTCTAACTTTGACAGTGGACCTGTCTGAACAATGGGGACGAAAACTTTGCACCTCCATCTCTCAGTCAGGGGGATCCCAGAAACAACCCAGAGAGTCAGAGGGGCACAGAGAGACAGAAATACGTAGAAGATCTGTGCTACAGCATGCTGGAATGTGGGTAGACTTCAGGCAGGACTTCCCAGCTAGGCCCTGGGCCTAGCACAACCTCTTCTGCTTTCTCCCACAG
Seq C2 exon
CTCATCACCCCACATCCCAACATGGAGACCCAGAGACCCCCTCATCTGGAGATGAGGGGGAGATTCTGTCGGCAGAAGGGCCCCCCGCTGGAGAATTGGAGCCCAGTCTGCAGGAGGAGGAGGAGGTAGTCACCCCGGACATCCAGGAGCCTCTGGTGTCTAGTGGGGAAGAAGAGTCTCTGATCTTGGCAGAGAAGCAGGAATCTCAAGCGACCCCCAGCCGTGCCCCTGGGGTCCCCACATTGGCCTCAAGTCCTGCCCTGGAGGCTGAGGAGGTGTGGCTGAGCACAGTGGCCCCCAGCCACAGCAGCGTGGAGGCAGGCACTGTGGTGGGCACGCACACAGACACAGCCCCAGCAAGCACCACGCCCAGGAAGAGGGAGCGCTTTAAAGGGCTGAACGGGCGCCACTTCCAGCAACAGGAGCCCCAGCAAGGGCTGAAGGGGGCACTCGAGGCCAGCATCCAGCCCCCCACACCAGAGGCTGCTGAGAATTATGTGGAGCCTCCCATGACCACTGGAACCACAGACGCCTTGGGGAGCGGCCAGAGCCAAAGCCCCTGGGCTGTGCTGACAAATGAGGTGGAAATGCCCAGAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001764:ENSBTAT00000002312:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.141 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0019312=Xlink=WD(100=98.0)
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGTCTTCTACGTAGGCCTGG
R:
CTCCAGATGAGGGGGTCTCTG
Band lengths:
342-1455
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]