RnoINT0039038 @ rn6
Intron Retention
Gene
ENSRNOG00000026415 | Col14a1
Description
collagen type XIV alpha 1 chain [Source:RGD Symbol;Acc:1305806]
Coordinates
chr7:95271494-95273298:+
Coord C1 exon
chr7:95271494-95271649
Coord A exon
chr7:95271650-95273218
Coord C2 exon
chr7:95273219-95273298
Length
1569 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
CCCCCACTTTTCCTCTTTAGTGT
3' ss Score
10.38
Exon sequences
Seq C1 exon
GACCTTCAGGGGAAAGTCGTCCTGGCAGTCCTGGGCCACCTGGCTCTCCTGGACCAAGGGGTCCCCCGGGCCACCTGGGAGTACCTGGGCCACAGGGTCCTTCTGGCCAGCCTGGATATTGTGACCCCTCCTCGTGTTCTGCTTACGGCGTTGGAG
Seq A exon
GTAAGTGTCAGAGTTTTGAGGGCTTTGCACAGTTATACAATGGTTACTACTAACCTGTGTGTGGTGGGGGGTTGAAAATTAAACAGTTAGGGAGGGCAGCAGAGCCTGAACCCCCCACTCCTTTTCATCATCTTCTGTAGAATGTAAATTACTGCACAATCTATTCGCATCCCTTAGGAGAGACTTAACACTGCAGCCATGTTTTATTTGCTTCCAAATGTTGATTCCTGGGCTGGGGAAATAGCATAGTGGTAGAACATTGTCAAGTGGCGACCCACAGAGACTTGGCCTCCTACTGGGCCACTTGTCACCTACGGTTTAACATTTAAATATTGTCCGGACTGTTCCTGTTTTGGTGGGGCCATGACATCCTGTGAGGTTTCATTCTCAGTTTTAGATCTCCCCCATAGTAAGCAACACCCCTCCCCCAGATTCCTTCAGGTGACATCTGCCCACCACGTGACAAGAAAGGTCTTAAGATAAAAGTTGTCACACTGTTTTTACCTCATCACTAAGTGATAGGCTGAGATTTTGAGAGATGAAGCTTCCCACACATGGAGGCAGTCTGCCTGCTCACCCTGGGGACTTTCTGAATCATCCAGAGAGAGGTTCAGAGACAGCTATAGGTCTGTCAGGAGATTAATCGGAAATGTGCCTCTTTCCTTTTTAAGAGAATTTTAACCGTCGTTGCCAGAGAAAATGGTCAAAGTTTTGTTGATGTATTTTTTTTTCTGTTCATCCTTTCCCTCCCTGTCCTCTCAAATCTGTCCCCTGTCCCTTAAGATGTCATCCCGTACAATGATTACCAGCACTGAAGTGCCAGTCCTGCTGTTGGTTGCATTGGCCTGGGCATTTGGCTATGGATACAGAACTGGTTCACCACCACTACTAAGCTCCTGCCTCTGATCACGGTCACCTCTTTCCTGCCTCACCTGCTTTGCTGTCTCAGACTTTCAAGTCCCCTGCCTACCCCGCTCCAGACATGCTGGAGTGATAAAATCACAGTGTAACAAAGTAACATGAGACAGCTGTAGTAGAGCTGACTTCCCGGCCAGTCAGAATGGAGGTCTGTGATTGCGCACCAAGACTTTATCCCAAACGCCTCTGGACGGAGTCTCTGTAATGGTTAACTAACTGTACGAGTCTCTTTCCTATCCCACTCATTATGATGAGCATTTTCCTCCTGGCTCTTTTGCTCCGCCTCCCTCCCTTTTCCACTCTCTCCTGGTGATGGACTTGTAAAGAGATTGTTTTTTTAATTTTCTATTTTCTTCTACGATTCTACTGCATTTCAGGGTTTCTTTTGTAATAAATACATCTGGTATTTAAGCGATTGTCATGGTTCCAGTTTTCTAACTCCGTTGTCTAGATTGTCCCTTCTCTTCCTCCTCTTACTAACTATGAAGCCTCATGGGGAAGCCGCATGGTGGGCTGGACAGTGAGTGCTTTCTCCTCACACACCCATGGTTTATTGACCAAATTTGTGTCCCTAAGGACTCAGATAGGGGAGATTATCCACTTATGGTTCCTGGGTCCCATCAAGCCCCCACCCCCACTTTTCCTCTTTAG
Seq C2 exon
TGTCCCATCCAGATCAACCCGAGTTCACACCGGTCCAGGACGAGCAGGAGGCCTTGGATCTGTGGAGCGCAGGCATCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000026415:ENSRNOT00000067649:51
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.991 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(73.7=79.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTTCAGGGGAAAGTCGTCCT
R:
ATGCCTGCGCTCCACAGATC
Band lengths:
230-1799
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]