RnoINT0039468 @ rn6
Intron Retention
Gene
ENSRNOG00000050706 | Col25a1
Description
collagen type XXV alpha 1 chain [Source:RGD Symbol;Acc:1590105]
Coordinates
chr2:235660892-235663720:+
Coord C1 exon
chr2:235660892-235660954
Coord A exon
chr2:235660955-235663651
Coord C2 exon
chr2:235663652-235663720
Length
2697 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TGTTTTGCAATTTATGACAGGGC
3' ss Score
6.28
Exon sequences
Seq C1 exon
GGAGAACCAGGCTTCATTGGTCCTCAAGGAGAACCAGGCTTACCAGGGTTACCAGGAACAAAA
Seq A exon
GTAAGTAGACCTTTATTCCCCCTTACTTTCCTGTGAAAATTGTGTGATGTCTGTCAAAAGAAAAGGGCGATGACTCTACTATTTAGGTGACTGGATGTTTCTGCCTTGGAACCGAGGCAGCCTGACCCACCCAGGCATGCAACTGGAACTTATATCTAAGACTTCAGCCTTTGCTGCTGGTGGGTGGAAAATAGCAGTTGTCAAAGATTGCCCTCTAGATTCCTCAGGAAGTGTTGAGATGCTTCCTAGCTACCTGGAGAGGTGACTAAGCAGAAAGGAGGGCTGGAGGTCGCCATCCCCTGCTCTGTCACATCTATCTTAGGATACATTCGTAAATTGGACGCTAATCCCATGCCCACGGATGTCACAGAGATTTCTAAATACTCCACTCCACAAGGATCTACCCTGAATGGTGTTTTCAGAAGTGTTCTATAATGAAAACCATCTCTTAGTGTTCTATTTGGCAACCATAAAGAGGACCCTAAAACAGAAACTGTATGCTGCCTCTCAAAAAGAACACAGTGCTGCAGATATTGTCAGACCTGGCGGTCTTGCTTTATCTACCCATTAGACATAAAAAGAGAGGACTCTGATGATAGCGCTGCACTCGTGACAGACTCATGAATCAAAGAGACAAAGTGACATCAGCATACAGTCATTTGTTTTTAAACCATGGCAGACTCTGGTTCGGTGAGTTCTGCGTTCACCAGAAATGAGCCAAGGGTGATTTCCAATAGTTAAAGGACTATGTCATGGTCTATTCAGACAGACTAGTCCTCATTTCTGCCTTGGTCAAGTGAAAATGACTCTAATCCTAGTGAGTAGAAACTATCCATTGCCTAAGGGGACTGGAACTCGGTAGGGTTATGCAATGGTTGTTTTCCAAGGAAATCTCATTTTCGCATAATGAGCTATCAGGCCCGTTAGCAAAATATGGAAAATTTCTGCTTAAGCCTGAACAGATTCACACGAGATAAACCTTTCTGAGAGAAAAAATACATTGTCTGTTGATATGAAAACTGTTGCATCTATTGGAGCTTGGAGCTTTAAAGCCAGGGGAGGAGAGGAGGGGTCCAGGCAGAGAAGACTCTCCACCACCACAGGAGGAGAGAGTCTCAGAGGAGGAAGCCATCGGGATCTCCTGTAGATTTTTGCTATACAGAGGAAGGTAGACAAACCCAGCTGGCACAGATTCTTATCCGTAAATACCCTGTTTATAGATAATGGCTATACCATTCCACAGTTTCCGAGAGAGGGAGATCCAGACATCGAAGTGGGAAGTTGGCAGTAATTGCCCTTAGGAAGGAACTCGGCATGATTGTGAAGAACAGAGACTTTCTCTACACCCCTAGGAGAGGAAAGGGATGTGATGTGCCTGTGTGGTGTTTCTACAAGCCAGTGTATGCGAAGAAAGCCATTGTTAGCAGTATTCCCAATGTACTTGCCTCTCTTAACAAGAGTTGTATCCTAAGGGGAAATTCCCAATTTGAAAATCTATTCTGACCCAGCAATGGTCTTTTACAATTTTTGTACATGGTCTGGATTTGTATTCCTAATAGTAGATCTAAAAATAAACAAATATGGGCAGTGAAAATAGATCTAGATATCTGTAGAATGGATGGCAGGTCCCCAAGCACTGTCCCTGTGCCTTTGTCTAAGCCACATCCGCCTAGAAGACTTAAGTTTCTGTCAGAGTAGAAGAAAACAGGGCATCACAGTACAAAGTGTGGAACTTCACCACTGTGCTGTATACATTTTTGCTAGAATTACTTAAAATTTGTTATAGAATGTGAATGGATGTCCATTGTACAACAACAACAACAACAACAATAGTAATAAAGTTAGTAATAGACCATATTGATACCTTCAAAGGTTCTTACATTTCTTCACACAGCTGCATAATAGACATTTAACAAACCATTTCCGTGTTTATAAAGTGGAGAGTAGAAGGAAGAGTCGCATTAGTACTTGGAGTGTTCTAGAGACACAGAAGGAACAGCAGTGAGTGAATGGGTAGGAGGGTCAGTGGCTAGGTAGGTAAACATGTATGTATATACATGAATGCATACATAAATAGACATGGCTAAGGAGAGGGTTTGTTAGGAGAATTGACTCGTGTGGTTATGGAGGCAAAGATGTCCCACGTAAGCCAGTTACCCACAGACTGGAAGGATGCTAGTAATGTGGTTCTACCCGGGCCTGAGGGTTTCAGAATCCTGGAAGCTGATACTGAATCTCCCAGGCAGCAGTTAAAGGTCTGAGATGTGGTGCGCGGTGCTAGTCTTGCCATCCAGGCACAAGACTAGAGTTGTGGTGTCATGGAGCTCCGAGGGAGAGACGGCGTGTCTGTCCTCTGCCTTTTGTTCTATCCATCCCAGGCCAAATGGGTATTTTAAGGGTGAGCCTTCCCCACTCAGCCCACTGACCGAGGTGCAGTCCCCTCATAGAAACAATAAGAGTGTTTTAGCCGTTCCATAGGAACTCACTGACCCAGTCAAGATGGCACTAGAAATTAACAACTTCGGATTGGTTTGTGCATGAAATGGGATCAGTCGTGTCCAGAGATTAACACAGTGCTGGCACACTGTGCATAGCAGTGACCTTCTGTTAACCTTGGTTTTATTGAACTCCTGTATTCCTCGCCAGAGAACAACCATGGGGAGGCTACTATTCTATCTGTTTTGCAATTTATGACAG
Seq C2 exon
GGCGAACGTGGGGAGGCAGGGCCTCCTGGAAGAGGTGAACGAGGGGATCCTGGAGCCCCGGGGCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000050706:ENSRNOT00000071463:12
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=FE(31.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(15.6=43.5),PF0139113=Collagen=PU(22.8=56.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
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]