RnoINT0040025 @ rn6
Intron Retention
Gene
ENSRNOG00000003736 | Col5a2
Description
collagen type V alpha 2 chain [Source:RGD Symbol;Acc:70921]
Coordinates
chr9:52150882-52157189:-
Coord C1 exon
chr9:52156965-52157189
Coord A exon
chr9:52150900-52156964
Coord C2 exon
chr9:52150882-52150899
Length
6065 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGA
5' ss Score
8.85
3' ss Seq
CATTATTTTTCTTTTTGTAGGTA
3' ss Score
10.26
Exon sequences
Seq C1 exon
ATGACTATGATGAAGAAATAGCCTGTACACAACATGGCCAGATGTATTTAAATAGAGACATTTGGAAACCTTCTCCATGCCAGATCTGTGTCTGTGACAATGGTGCTATCCTCTGTGACAAGATAGAGTGCCAAGAAGTGCTCAACTGTGCCAATCCTGTAACACCTCCTGGGGAGTGCTGCCCAGCGTGTCCACAGACATCTGGAGGTGGAGATACAAGTTTTG
Seq A exon
GTAAGACTGCTCAAAGCTGTTTCAGAGGACAGCTAGCAACTCACCTTTATCTTCCAGTGATTGTTGCTTTTCAAGTTTAACAACTCACATGAATAATCATAGCAACTAACTCAGTGACCTCAGGGATTAGTGATTTTGAAATTATTTATATATATATATATATATATATATATATATATATATATATATATGTACACACACACACACACACACACACACACACACACACACAATTCTAAAGTGTGGTGAGCTTCCTGGAGTTAAGTAGGGAACCTTTTTACCCTACTTAGGCCATTAACATTGAAATATAGAGTAATTTTTTGTCTTCTTAATTGTCAGAAGATCTTAGTTTGAAGGGTTGTATGTGCCTTCTAGATGACTGCTATTATTGTGTGTATGAAAGGTGCCTCCATGATATTTAGTTGACTTTCTATTGTATTGCTTTAATGTCCAAGAAACACAGAAAACATTTATTTTCTCTCATACAAGTTTCACTCTAGAGAATGCAATAACTGTTTTTAATATAATTTATTGCTCTAGCAACTTCTCTTACATTGTCTCAACAATCTACGGAATGTGTAATGTGGACCACATAATAGAAGGAAATGGAATCAATTTCTTGGAGGAAAGAATGGTACAAGATTCTGGGTTCAAAAATACTTTTTCAGGAAAAAGTATCTGTGTTTAATTGATATTATACTTTGGATTATGCATCAAATATACAGACATATATATTTATGTTATTTGCATATTTTAATGAGCTAGGTAAGACCAACATTAAGCATTTAGGTTGTTTGCTTCAGTCCTTGTACCAATTGTATCAATTGCCAAAACATTATCAAAGCTTCATTTTTTTCAAATTCCATTGAAAATAGTAATAAATATAATAAAAATATTCAACAGTACACACAGAGAAATATTAGACACATACATCTTTTCATCTTGGAGTTATTTAGCAGAGACTGCATCTAAAATAATTATTTAAACTTAAATTTATAATGTGTGATAAAATTGGGTCATAGTATGATAAAAATAACACACAAAGGCTACTGGAAGCAATAATTTCATAGAATCCCAGGAGTAAATACAATTAATCCTGTGGGGGGATAAACAAATAGCACGTGAGAGTAGTCATCAAATATCAGAAAGCAAAATATATAACTTCCTGCCAGTAAGCAGTGTAGGGGAGCACAACTCATTCAGGGGAAGAGTGATATTGGGCAGCACTAGATTTATAAAAGACATCAACAGAGAAGGGTGATTGAATTCCATTGACTTTACGAGACAAAGGACATACTGGCATATGTCTGGCCACAGATTGGGCAAAATTTCTGGAGATGAGTAGAGTGGCCTATGTATTTAATTCTAGGACTTGACAAGTAACATAGGAGGATCGCCAGTTCAAAGTCAGCCTGAACTACAAAGACCAGCCAGCAGGAGCTCAAAACTAGATATCAAGATCAAACAAAACTAACCCATACCAAACTGAACTAATAGAATATTTAACCAATTATACATCTTCTTATTTTCTTATTTATTTATTTATTTATTTATTTGTCTGTTTGTTTGTTTGTTTACAGACAAGTTCTCATGTATACCAAGCTAGTCTTTAACAAATTTAGCCAAGGATAGCCTTGAATTTTCTAAGTGCTGGGTTCTTTCTATATACATAAGTGGTACTAACTAAGTACTAAGTTGTGCCTTCAGCTCAAAACCTAGTGAAATCATAGATGTGTCTAAGAAAGACGGGTTTTCAGCAGAAACAACATTCAATGAATAGGAAAAAAAGCAAGCCTATGAAAGATGAAAAGGAAGTTAAAGAATGAGGCAATAATGGCCAACTTACAGAAGAGATATAGATGACATCCATGAGAAAAGAAAAATAATAAATTAAAATCAAGAAGAATTAAACACATTACAAGACATAGTACATGCAAAAGATATGTGTATTCTATTAGCTAGTAACATCTATAGTAGGAAACGATCTCCCATGTTCAGTTGAATGGCAGGACTTAAACGATCAGCTGACAAAAGCCGGCCATCTGCTCTTGCAGAAAGCAACTCTCACCGAGACTTCAGGTGCAATGTCCCATTCAACCGAATTCCCCAACTCAATCTCCCTTCTATAATTATATATATATAGGAAACACATCTTGCAATTGCACTTGGAATAACAAAAAAAAAAACCAGGATAGTGAAAACTAATCTTAACAATAAAAACTCTGGGAATCACCCTTCCTGACCTCAGGCTATATTAGCAGAGCAATCATGGTAAAAACTGCATGATATTGGTACAGAGACAGGGAGGTACGATCAGTGAATAAAATTGACAGACTCCAGAAATGAAGCCCCGCACACTATGGTGCCGCCCACTCTTGTGGATTTTCTTTTNNNNNNNNNNNNNNNNNNNNNNNNNTTGAAAAAGTTCCAAAAGACGACAGCTGATGCTGAATAGGAGACCAAGAACCCAAATCATTCAAAAAAAAAAACCACTTCTTAAATTTTTTTGCCTTGGGCATGAATATTTTGTTAGTTGGGGCATTTAGTAGAAATGAATGATTTAAAGGGATTTGTACTTATTTTGTATTACTTGTTTAAATATAGTAGGCAAAGAATCTCCCATGTTCTTGAATTGCAGGATTGACATTATGTTGTCTGAAAAGGGGCCCATCTTGCTCTTGCAGAAAGCACTGAAAAGCAATTTACAGATCAGGTAGCAAATTCCCATCACATTCCAACTCATTCATTCATTGGAGAGTAGAAGGAAACCAATTTGCGTAGAATTCACTTGGCATAACAAAATAAAAAAACCAGGATTGATAGTGAAGCTAAATCTAACAATAAACTTCTGGGGCGAATCACCCTTGCCTGACCTCGGTCTTAATTTATCAGAGCAATCATGGGTAAAAACTGCCATGATATTGGTCAGTATGACAGGGAGGTAGATCGTGGAATAAAAATGAGAGACTTCAGAACAGAACCCCCCACACCTCATGGTCCACCTTGATCTTTGACAAAGAAGCTAAAGCCATGCAATTGGAAAAAGGACAGAGCATATTCCAACGAAGACAAAGAAGCTAAAACCATGCAATGGAAAAAGGACAGCATATTCAACAAATGGTGCTGCTTCATCTGGAGCTCAGCATGTAGAAGAATGCAAATAGATCCATTCTTATCGCCTTTTACACATGGGCACAGGGGAAAATTTCCTGAATTTTCCAGTGGCTTATGCTCTACGATCAAAAATTGACAAATGGTACCTCGTAAAATTGCAAAGTTTCTCTAAGGTAAAGGACACTGTCAATAGGACAAAACAGCAACCAAAAGATTGGGAAAAGGTCTTTACCAATTCTACATCTGATAGAGGGCTAATATCTAGTATGTACAAAGAACTCATGAAGTTAGGATCCAAAGAACCACATAATCCTATTAAAAATTGGGTACACAGCTAATAGTAAAAGTAGAAGTTATATTTTTATGGACCTAGTAATAAAAATATCTTGATTTATTACCCACATTGCCACTTCCAAGCAATTCTGAGCATTTCACATGTCTCTGAGCTGTAATTTTCTTACCCGATAAGTGGGAACAATAATCACCATTTTAGAGACATGTTTCTAAGCTCTGTTTCCCTTCCCTGACACCTAGCAAGCCCTCTAAGCATGCTCTCCAGGAGAGCAAACCAAACATTCACCCATTAACTTGCCCTCATCAGAGGCTACTGGCCATTTAGTTATATTTCTGAGAACTAATAAGTTTCCTCATGCTAGACCTAGCACAATTACTTCATCCTGTATCAAGAGTCAGGTTACTCATTATTCTATTTCTATGGCCTATATACTCTCTTCAGATGATAAATACATACGTACTTCAGAGGATAAGGGCTTTGGAATACTTACATTAATTTATGGGAGTTCCTGTGTTTTTATTTTATCAACTCCATTTGAGAAGAGGCAACATGGCATTGTGGAGAAAGCATACACAATGGAGTGTGGCTATCTGAACTTGGATGCTGTAGGAATATGGCACTGAGAAAACCATTTGACATTTGAACAACTGAATTTTCTCTTTGTGAGAAAGAAAAATGGTGTGCTCTGGAATGTGAATACTCAGTAATATTTCTATAGCATCCCCACTCGTCCTTCCCCATTTCTTTTCTTTCCTTTCTCCTTCCAAGCCTTCTTTACCCTCTATCTGTCATTCTTCCTTCTTGATTCATCAGCCAGTGTTTTTGGTATGAGTTATGACCAGGGCCAATGAATTATTTTGGGAGATGTTTTTATGTAAATAAAATTCCATCTCCTTTGAATGACTTGGGCAATAGTATATCTATGTTGTACACATTATCCCAAAACCTAGCAGTGCTTTATGTGAATTTGGAAGCATTTACCTTTCTATATAGTAATGCTGTATCTCCAGAAAACTGCCTATCCTGTGGAAACAGCTACAGTTTGAATTCTTTTACAAAAAAGTCATCTTTTTTCTACAATGGGGCAAAAGGGGAGCATCGCCAACCCTGTGGCAATGGGCAAACAATGAAGTAGGTATTGCTGCACTTAGCAGAGATCGGGTATCAGATCCGTGAGTGGCTAAGAAATTATGTACGAGTAGTGAGATGAGATGACCTTTCTACATCATTATTATCCATAATAAAAGCACAAATCCAAAAAAATTGGGTACAAAGAATTTTTAACTGAGGAATATCAAATGGCTGAGAAGTGCCTAAAGAAATGTTCAACATCCTTAGTCATCAAGGAAATGCAAATCAAAACAAGCCTGAGTTTCCACCTCGCACCAGTCAGAATGGCTAAGATCAAAAACTCAGGTGACATCAGACTGGCAAGGATGTGGAGAAATACAACACTCATTCATTGTTGGTGGGATTGCAAGCTGTTACAACCACTCTGGAAATCAGTCTGGTGGTTCCTCAGAAAATTGGTCATAGAGCTACCTGAGGACCCAGCTATACCACTCCTAGTCATTACACAAAAGATGCTCCAACAAGGAACAACAACACGTGCTCTACTATGTTCATAGCAGTCTTCTTATAATAGCCAGAGCTGGAAAGAACCCAGATGTCCTTCAACAGAGGAATGAACACAGAAATGTCGTACATTTATACAATGGAGTTCTACTCAGCTCTTAAAAAACAATGACTACATGAATTTTTTAGGCAAATGGATCGAACTAAAAAATATCATTCTGAGTGAGGTAACCTAGTCACAATAGAACACACATGGTATGCACTAACTGAATACCCAAGGAACAATTCACAGACCATATGAAGCTCAAGAAGGAACAACAAAATGTGGATGCTTCATTTCTTAGAAGGGTAACAAAATACTCATGGGAGAAAATACAGGGACAGAGAGTTGAGCAGGAACAGAGACTGCCCCCTTGTGAATCAATCCCACCAAATCAGTCACTATTGCTGATGCCAAGAAGTGCTTGGTGACAGACTGATATGGATGTCTTCTGAGAGGCTCTTCAAGAGCCTTACTGATACCTATGCAGATGCTTGCAGTTAACCATCGGAACTTAAGGGATGTGCAACCCTGTAGGAGGTCATCAATACCAACCAACCAGACTCCCCAGTGCTCCTGGGGTCTAAACCACCAACCAAAGAGTATACATTGAGGGACCCATAATTCCAGCTGCATATGTAGTAGAGGATGGCATTGTCTGTCATCAGTAGAAGGAGAAGCCCTTGGTCCTGTGAAGCCTTGTTTCCACAGTGTAGGAGAATGCCAGGTGTTGAGGTGGGAGCGGGTGGGTGGGAATGGGAGCATCTTCATAGAAGCAAGGGGATAAGGGAGCATGGATGGGAAAGGGAGGACAGTGGATAACATTGAAATGTAAATACATAAAATATCCAATAAAAAAGAATAATGAGAAAGGTAAAAAATATTACAAACAACATTTGTTAAATATAATTCATTAAATATAATTCATTAAATATAATGTAAATAATGCCTAGTGTTTTGCCAATACTAGAACCTCTATGAATGCAGGATGTTTTTCATAGTTGTTTTTCCATATTAATGACATTATTTTTCTTTTTGTAG
Seq C2 exon
GTAGAGGAAGAAAGGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003736:ENSRNOT00000005073:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.105 A=NA C2=0.476
Domain overlap (PFAM):
C1:
PF0009313=VWC=WD(100=73.7)
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]