RnoINT0039696 @ rn6
Intron Retention
Gene
ENSRNOG00000003357 | Col3a1
Description
collagen type III alpha 1 chain [Source:RGD Symbol;Acc:71029]
Coordinates
chr9:52034685-52036376:+
Coord C1 exon
chr9:52034685-52034759
Coord A exon
chr9:52034760-52036322
Coord C2 exon
chr9:52036323-52036376
Length
1563 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
3' ss Seq
CATTCAAATTTATATTCCAGGGT
3' ss Score
7.54
Exon sequences
Seq C1 exon
AATTATTCTCCCCAATTCGACTCATATGATGTCAAGTCTGGAGTCGGAGGAATGGGTGGCTATCCTGGACCAGCT
Seq A exon
GTAAGTACTAATTTTTCTGATCATTTTCAAGTATCACACTGCCTTTACTTCTGGAAACACAATATTACAATGCAATTGTACAAAAATGTTCATTGACTACCAAGGTTGGAAGAGAAAACAGCAACCTATCTGTGATTCTTCTATCCTAACTCATTCCCTCCCTGTGGTGATTTGTCCTTCCATATTGCTTCTTCCTAAGGTCCACCTGCATCAGGACCTATCACACCACCATGCTCTGGTCCATACTTTTCTTGTCTACTGTGCAACTGGGTGTACTTTTGTTAGTGCTTCTACTTCTCATCTTCTCACCAAGTTACTCAGCATCTTCCATTCCTTCTTGTTCAGTGACTTTACATTCTAAACGATAGTTTAAGTAATGAATGCTCAATATTACAGTCCATTTTTCCTCAAGGTTTAAATTTATTATTAATGTTTTCAGAACGCATTCATATTTTATGTTCCACTACCTTAGACAATACCTATTTACCTTTTCAGTAAAGGATTTTCAAAATGGTTTAAATGGGCTAGATATTTAATAACACAAAAAAAGAGCAAAAAGCATTGAAAGCTGGATTTAAAGCCACCTATGTTGGTGACTTTTGCTTTGGAATTAGCTCTCAGAAAGTACAACACTATTGAAGCCTATAATTCACTTCACATACTAGAAGTATCAGCATAAATAAACACAATGTGGCAATATATTTGTGGCTCTCAAAATTAAGAACTTTTATGAGTAGATCCAAGGTGTCTATAGAAGACTATTGTTATTGGTATAAAAGAAGTTGAAATATATATACTTATATTTTTCTAAAGAATATTTTTAAACAATGTGAAAACCAATTGGAGAACCAATTACTTTTTGGAATATTGGTTATTATTACACTCATGTTATCAACCCTCCTTTGTAAGATTACCAAAACTAAATAGAACTACAATTTATTGACATTTCAGAAAGATAATTTAAAATTAAGTAAAAATATTGTTATCAGAATATAAAAATAGGATAAATCTGTTTTTCTAGTTTGGTGTGAATTTCTGAATAATCAATTTGTTTTAAATTGTGAGTGTCCCACGAATAATGATACATGTTTGTATCTAAATCTTCATATCAACATGACTGTGGTATATCAACATAGCTATGAGGTCTAGAGTTGACTGACAGGGTTAGTTTAGAAACTTGTATCATAAGATCTATAGTATGAAGATATTTTCCCATTATGCTTAGCCAAAAAATGTTTATAACCCAGAGATGTATCAATGAAATATTATAAAGCTTATTATCACATTTTACACTGACCTCTGAATTTTCTTAAGTGTTAAAGCTAACATTTAATATCAATTGGTAATCTAGACTGACTCTCTAATTTCATCTGAAGTAAAGTTTTCGTGCAAAAATCTTTATTGAAAATATCTCAGAAGTAAACATACTCAGGTGTGTTATCAGATAACAAGATATAAAGTTGTATATGTTTTAGTACATATTGGCGTCATGTGTAAATAGACATCACTCTGCAATGTGTGCATCTGTCTATTCTGTGTTTATCATTCAAATTTATATTCCAG
Seq C2 exon
GGTCCACCAGGCCCTCCAGGACCCCCTGGTTCCTCTGGACATCCTGGATCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003357:ENSRNOT00000004956:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.960 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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]