RnoINT0039480 @ rn6
Intron Retention
Gene
ENSRNOG00000050706 | Col25a1
Description
collagen type XXV alpha 1 chain [Source:RGD Symbol;Acc:1590105]
Coordinates
chr2:235690068-235691841:+
Coord C1 exon
chr2:235690068-235690103
Coord A exon
chr2:235690104-235691787
Coord C2 exon
chr2:235691788-235691841
Length
1684 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
TGTCTTTTTTTTTTTTTTAGGGT
3' ss Score
12.96
Exon sequences
Seq C1 exon
GGAGCATCTGGCTTAGACGGAAAGCCAGGATCCCGG
Seq A exon
GTGAGTCGGCCCCGCGTCCTGCTCTGATGTGCTTCCTGGATGTGAATCACGTGCTCGTGGGAAGACCCCATCATTCTTTGCGGTCTTTCCAGATGATGAGGCATCACTTAGGGCCAGAATCAGAGGGGAAGGTAGATGAGGACCGTGGAAAGGGAGAGAGAAGGACAGAGGAGGGGTCGCAACTCCAAAGTTTAGCCTGAGCTGCCAGGACATTTTCAGAAGCCGAAGTTTGAGTCTACATAATTTACTCAGTGAGAAAATGACCCGTCCAGTTGTGTCTCAGTAACCTACAACAATTCATAAAAGCCTTCCCGGAATCCCCTGAGGCCCTGAAGTGGCAGAAAGAAGAAATTTATTTTAACTTACTTTTCCTTTTCATTTATGTCTGGCTTAGAAATGTAATTTCTTCTATAAAACTGACTTCCACGTCTCTATTTGTGGAAATGAATCGTGTGTCTTCTGTCATTTTTATCACTTTTGTTTTTTGGCAGTTCCACATCTTAAATTTTAGCCATGGTCACTCTTGTATTTAGAAGCCCTGTAGAGGTGAACCTTGAATTGGGGCAGTAAGAGCATGGCTAAGATTATCACCCACATGAGGATGAGTTTGAAACTCTGAACTCTTCCCTATCCTGAGATTTTAACAGACTCCCCCAAACAGCTAGACTAGCAATGGGGAGTCCATAGACAAGCTGAAATAACAGTATATCCGCAAATACGACTTTGCACTCTTTGCTTCTTTAAGCAAAGTCTTCCTGACAATTGAGTGACTATATTTGAAATCCTCACCTTGTTTTTAAGAATCTAAATCTGAAATTTTTCAACTCTAAGGACCATCAAGTAGTTTTTTTCCCCACCAGACCCCAGAGTTCTTACATTCTTTCATGTATTACCTTATCTGCCACAGAAAACAATAAGGTATGCGCGCTGTAGGCAGAGCCTAGAAGAGCAGTCCCGCCATCATGTGAACCCTACTGTCATAATAGAGCTACAAAAAGTTGTTCTAAAAGTCAGCACTATTCTTTTTCACATATCTTCCATTTAAATGGCTAAAAAAACAAAGTTTGAGGACTTTGACCATAATTGTCAATGGCTATGGTGATAGGATCTGGGGAAAGGGTGATAGAAAGAAAGGACAGTTACTTTCCTTGTTAAGATTATGGAGACAAGGGGACAGAGAGAGAGAGATGGCTCTGCAGTTAAGAGCACTGGCTGTTCTTGCAGATCACGGAGGTTCAGTTCCCAGAACCCATGTGGTAGCTCGCTAGGAGCTCCAACTCCACTTCAAGGGGATCTGGCGCCCTCTTCTGGCATCTATGTGCACTGCACACACATTATATCCATACATACGTGCAAAGCACTCACGCATACATATAAAACAAAAATAAATCTGGAAGGAACAAAAAGGGATGAGGATGAAATGAAGATGCTTCATCTGAAAAGAATCAGTAAATATGAAGTATAGCTTTTGTGTAGACGCTTCACCCCCTTGCATGAATTTCTCAGAAACAAGTGGCATGAAAAACTGTTAAGAATAAAGTGCTTTAGAATCGGATGATGCTAAGACATCAGCAGGCATCGTTCTCCCAGGCAAGTCAGAGTAAATCACAGAGTAAACCTCTTCTTGCCACCCCAGTCTCTCGCCTGTCTCAGTATTTTATTTTTGTCTTTTTTTTTTTTTTAG
Seq C2 exon
GGTGCAGATGGTCCTATAGGACCCCATGGCCCTGCAGGTCCCAAAGGAGAAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000050706:ENSRNOT00000071463:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(12.3=66.7),PF0139113=Collagen=PU(16.4=91.7)
A:
NA
C2:
PF0139113=Collagen=FE(25.4=100),PF0139113=Collagen=PU(3.2=11.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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]