RnoINT0039484 @ rn6
Intron Retention
Gene
ENSRNOG00000050706 | Col25a1
Description
collagen type XXV alpha 1 chain [Source:RGD Symbol;Acc:1590105]
Coordinates
chr2:235705119-235709313:+
Coord C1 exon
chr2:235705119-235705142
Coord A exon
chr2:235705143-235709218
Coord C2 exon
chr2:235709219-235709313
Length
4076 bp
Sequences
Splice sites
5' ss Seq
TAAGTGATT
5' ss Score
-2.29
3' ss Seq
TGGATTAGTAACATTATGAGTTA
3' ss Score
-20.14
Exon sequences
Seq C1 exon
TCAGGGGACTGAAGGGCAGATTAA
Seq A exon
GTGATTTGCCTAGACTCATACAAGTCAGTAAGCATGCCAGGATTCAAATTAATATCCTATGTTCTTTCTCCTACATTTCTTAAGAGAAAAAAACAAAGCAAGAAACCTGTTGTGCATAGCTCATTGAAATGGTAGAAAGTACTATTTCTAAGTATTACTGTTCTTTGTAAGTTTAAAGGTTATTTGACATGTCCGTATTTATATCTGAGTTCAGACCAATGAAATGTTGTTATGTTAGTGGTGTTCGTTGATTTCAGTATGATTTTGCTGCTGTTATGCCAGTAGATATGTTGAGTTTGCTTTTTATCCCCTAGGGCAANNCCTCAACGCGTAATCCTTCCTATGCTGGAAGGTGCCTTGTTTCTAGCTGCTGTAGCCATCTTTATGCCTCTTTGAAGAACTGATTCGCTAGATCAGTCATCTGATATTTTTTTGGAACACAGGACACAGACCACAATGAACAGCCCTTGATGGAGATCCTGAAGGTTCAGGCAGCAGAGCAAGGCAGTGCTGAAACAGCATGAGATGCATGCTGGGAGCTCAGGGTAGCAGAAGCACACGAGATGCTGCTGGGAGCTCTGTTAGTCAGAAACCACGACATGTCTGGGAGCTCTAACTAGGGAGAAAGCACACGAGATGTATGGCCTGGAGCTTTGCTAGAAGAAACACATGAGATGCCATGCTGGCGAGCTCTAACTAGCAGCAACACCACGAGATGCATGTTGGAAAGAAGTCCCTCTTTCTCCCTTTTCTCCGCAGGCTCACGCCCTTCGCTCGCCCATCGAGGACCCAGGGAAGCCTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTAGGATCCTGATAATCCGAAGTAATAATAAGTAGAAAAGAGAGTAAGACCCGGGGTTGCCTTTGTGGCAAGGTACAGCAAGAGCTTGTTGCCAAACCCCACTTACAATTGTTGTCAGGGTTTAGGTAACAGGGAAAAAGACTTCTTATGGGTATAGTTCTTACTTGTTTGGTGAGAGTGAGGGATGTAAACAGCACCGCAGGAGCATGTAAAAATTCAAAGGGTTTTCACGTATAGGACTCTTGGGGAAGGAATGCCAGGTGCTCTGTGATGATGTGAAGTGGGAGCTTGGGATGACCCATGGTATGGGCTCTTACCAATGGGAGGCGAGATAATCTTAAAAAGGATGCAGGTTACCCCAAAAAATATATCATGTGGTACTCAATTTTATTATCTTTAAAGAAGTTAGAAAAATACCACCATTGGCTCAGTGGTACAGTCCTTCGTGAGCATGTGCAAAGCCTTGAGTTCGTTCTTCCAGCGTGGCAAAGAATAAAAGAACGAAGGGTCTAGGGGAAGGGAGAAATTTTCATTTTTGTAGCTTATAATAGCATAAACCCACAAACCCTCCCTCAGATATATGTTAATCACTCGTACAAAAATATTTCCACAATTAGTGCAAATTTTATATTTAGGAAAGTTAGATTGTAAATGTTGAACACTTTGTTTATCTTTTCCATTGATATAAGAAATAAAAATTGACAACTGTCACATTTCGACTGCTCATACGCACGATGGCACATAACTTTGAGGAATATAGATAATCACTTCATTTTACAACATGATGTTGATGTAATAGCGTTAACATACCATTCCTCATAGTGGCTCTTTTCTGTAAAGTTTGCTGTCCACTTAAATTTCAACACAAAATCACTGCCTGTCGCAGTAATTCAAGTAAACCCATTTAAGCCCATTTGCCAATAAAGCAATGAATGCCACTTAACCAACACACTTGGTCTTGGTTAGACCTGCTCCAAGATAGGTCTACTGACCTCAGGGAGGGCAGAGCACAAGTGAAAAGGATCAGTTCATGGCACGGCATTGAAGCTACCTGCTGAGGGGGCTGCTGATTCTTCATGAGTGAGTGCTTGCTTCTAAAGGCATCGTCCACTTCATTTCCTGTCTCACCTGCTCCTCCTTCACTCTCCCTGCTACAACTTTGCCTTCAAATGCTCATGTTCATGCTCAAGCAAACCACACCAGTTTTCTACGTCCTGTATTCAAGAAGCCCCAGTGGTTCTGATTCCAAGCCTTCTGCCACAGTGTTCTTGGCACACAGGAGGTGAACAAGATGGAGCTTCCGCCCATGCTGTCAGAGTGAACGTATTAATTTGAATGAGTGTCTCATACGTTTCTTGAGTGTATGTTGTTCTGTCTTTTCCCTTTGAATATTCATGTTGTTTGGTTCAGTTTTATTGTAACCGCCATCCAGATTGCAGGATGAATGCTCCCGTTTATGCATGTATCTATGTATGGTCTTTTGCATTCTGTACAGCACCAACTCCCTGTCTATACGTTTGCAGATGTCTATGTTAATGTGGACCAGCTGGGGTGCATTCCTGCCTTCCTCTCCTTTTGCCTCCTTTCCTTAATTCCTCCGTCCCTAGGATCCACGCAGACGTCCCACAAACCTTGACCTTGATCCCCAAATACTAATTTCCACGGCTACATTCCCACTACGTAATTATCCTGCCTACCTCATTTTAATGAGCCCAGACTGCTTTTCCTAGCTGCAGCGTTGCAAGCTGGAAACTCATTTACCATTGTGAACAGCAAAGATGGAGGAAGACTGCCTAGGCTTATCCAACTGTCCCTCCAGTTGGCATTGCCACCGAGTGTTAGTTAGCACCTGAAATGTGTGTTTAACTCAATAAGTCAAGGGTTCGTTTTTATATTTGCTGGCGAGGAAAAGTTAAACACAGCAGAAGCACATTTTAATTCTGGAATGTTTTTACTGGGAGCTGCAAGATAGAATATGACTGGACAGCCTTGGGAGAGAGCAAAGTTGCTGCCTTTTCCTCTGAGTCTGTACAGCTATCATGTGTTAAAGAAAAAGGAGTGGAAAGGCAAAGTTAAAGTAATCAAAATCGGACGGAGTCTCCGTTACCCAAAGCCAAGCTCCCCCTGATACTGACTGGCTTCAGTGTAACTTGTCCGCCATCTTTGCCTGGTCCAAAGAACAAAACCCAATTCACTGTTGACTCCAATATTTTGGCAGTCGGCACTGATCTGCCTTTCTAATGCATCAGCCCCTTTGGTATCCTTCTTTCTTCTTGTCTATTGTCATAAGTAAATAAATAAATCCTGCTTCCAGAATCCACTGTCAACATGGCAGTCTAAGTTATTTTTTATAGCATCGCCGCGTCTTATGTGCATCGTCAGTAAACAATGGTAAATGCCTTCCAGACTATTTTTAGCTAAGCCATATTTTGGATCATTTTTTATTCTACACCCCCTCAAAATAAAACCTGTCTTCTATTTAAACCCTTGTATCCACAGGGGGAAAAGGGAAAGAAAGGCAAAAAAGGGCCTAAAGGGGAGAAAGGAGAACAGGGCGCTCCTGGATTAGATGCACCCTGCCCGTTGGTATGTCTAACTGATGCAACCGTCTCCAGATGTCTTGTGTTGGGATGAGGATGAGATGGGAGAGGAGCAGACCAGAGGGACCAGTAACAGCAGGTTCCTGAGAGGATCATTTAGCACAGACCTTCAGACAGGTGTTCAGAAGTACAAGGTTGCACTTGCTGTCCTTGACATCTCGTTGCCAGCCACTCAACTCCACTCAGTTTCTAAACTCCCAAGCGGTGCTGGCTGATTGGAACCTAGCTGTAGGATGTGAAGAAGGGCCAACAACATCCCATATCCCTCCAAAGAGGAGGCCATGGTTTCCTGACAAAGGCCTCGTCATGAGAATGTGAAGCTTCTCTATGTGTTACTGTCCCTTCTAAGTTGTTCCTCTCCCAGCTCTTTTCTTCTAGTTGTTTCTTTAGCACATTTTTGCTTTCAATGAATTCTTGGATTAGTAACATTATGAG
Seq C2 exon
TTAATCTTTACAAACAGGGATTCCGTGGCGTTAAGGGGGAAAAGGGGGAGCCGGGCCAGCCTGGCCTGGATGGGCTGGATGCTCCTTGCCAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000050706:ENSRNOT00000071463:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.593 A=NA C2=0.894
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(7.6=55.6),PF0139113=Collagen=FE(12.9=100)
A:
NA
C2:
PF0139113=Collagen=PD(46.8=90.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
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]