RnoINT0039257 @ rn6
Intron Retention
Gene
ENSRNOG00000003897 | Col1a1
Description
collagen type I alpha 1 chain [Source:RGD Symbol;Acc:61817]
Coordinates
chr10:82745801-82747646:+
Coord C1 exon
chr10:82745801-82745987
Coord A exon
chr10:82745988-82747451
Coord C2 exon
chr10:82747452-82747646
Length
1464 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
GTCTCTTCCCATTTGCTCAGTCC
3' ss Score
6.62
Exon sequences
Seq C1 exon
CGGGAGTTTCACCTCCGGACGGAGCAGGAGGCACACGGAGTGAGGCCACGCATGAGCCGAAGCTAACCCCCCACCCCAGCCGCAAAGAGTCTACATGTCTAGGGTCTAGACATGTTCAGCTTTGTGGACCTCCGGCTCCTGCTCCTCTTAGGGGCCACTGCCCTCCTGACGCATGGCCAAGAAGACA
Seq A exon
GTAAGTTCCAAACTCTGGGGAGGTTATGGTTTCTTGCTATCGCGTTCTGCATAGGGGTCCTAGCAATAAAGACTTAAACGGAAGCGCGGGGTGCTCCAGAGTTAGGAGGGATGAGAAGGTGATGGAGAGGAACTGGGAAGAGAGAGGTCACCCTCGCGAGCAGAGGAGAGTGAGCAGATCTCAGAAGTGGAGCCCTGGTTGAGATGGCACGGCAGGAAATTTCAAGCATCTATCTGTAGCGCGACGGGAAAAGTGGGAATCTGGGCAGGGGTTGGGTCAGAGTACGTCGAAGATCAAATAAGACCTCTGGAATAGAGATTCGAAGCTCAAGATGTAAAAGCAATCAAAAAGGCTGCGGGATGATTCATAAGGAAAGATTGTTTGCCCTCTCTGCAGGCTAGACAGTGTTGCTGGGGCCTCCGGGGTGCTGGGCTCTGGGAGTGGGGTGGGGGGAGGAAGGGACGCACGGAGAGGGCGGGTTGCTGGATGAGAAAGTTTGGCTAAGACTTGACTGGGCGCGGTCCCTGTGCCTCCTGCTGGTCAACCTTGAGCACTACGAGTCCTGGTACAGTACTTTACAGCGCGCGGGCTTAAGAGGGAAAACCTGGGCTATTGCCGGGCCTGGACCCTCATCTCCAGACTAGGAAAATAAAAGCACAGATGGATATGATAGCCTTGGTCTTTGAAAGTGACCCAGGCCAGTAAAATTGGGTCCGCCCCGTGCATTGCTTAGCGTTGCCCGCCACCTAGTGGTTGCTTTGATCCGGTGCTAGAGAGGTGGGCGTGGTTAACTAATCATTGCTATTTGTAGACTTGAGTTCTTTCTTTGGCTAAGGAGTGACCCCAAAGCTCTACTGGCTTTGAAGGAAGGACCGGGAAAGCTTTGATTCCTGGGAGCGGAGAGTTAGGGTGTATCTAACTTTAGGGATATATTTTACTACTCTGGACAAGGCTCCACGGAAGTCACCCTCCTCCATTTTAGCCCCGCCCATTCCGTCCCACCTGCCCAAGGAAAGGAGGTGGGACCAGGGCTGGAATTTCCCTTCTCTCCTCCCACCCCCGCCTCCGGTCTCCCCGCAAACCACGTCCCACAAACCTCCACCTACTTTGTAGGAGCCCTCCTACTCTCCGTCAGGAGGACTTCTATTTCATTTGGTTCCCGCGCGCGTGGGCTGAAGTTGAGTTTGGAAGCAACCCCAGCCTAAAGCTTTGTTTAAATTCCTGGGAACTTGGAAGTTACAGCCCTGGCCAGGCTTCTTGGTGCTGTCACTGAACGCCGTTACAGAGCAGACCTGCATTTAAGGATTTAAGGGAAGAAAATAGGGGTTGGGGGAAAGATGTGGGAAGTGGAAAATCTACGTGCACCTCTTAGACAGGGGAAAGGGTGAGTAAGGCTGGGATCCCTGGTGCATCAGGTAAGGTTTCAGAGCCGCTCATGTCCTGTGTCTCTTCCCATTTGCTCAG
Seq C2 exon
TCCCTGAAGTCAGCTGCATACACAATGGCCTAAGGGTCCCTAATGGTGAGACGTGGAAACCTGATGTATGCTTGATCTGTATCTGCCACAATGGCACGGCTGTGTGCGATGGCGTGCTATGCAAAGAAGACTTGGACTGTCCCAACCCCCAAAAACGGGAGGGCGAGTGCTGTCCTTTCTGCCCAGAAGAATATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003897:ENSRNOT00000005311:1
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009313=VWC=WD(100=84.8)
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:
GAGTTTCACCTCCGGACGGA
R:
CCGTTTTTGGGGGTTGGGAC
Band lengths:
342-1806
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]