RnoINT0039775 @ rn6
Intron Retention
Gene
ENSRNOG00000023972 | Col4a2
Description
collagen type IV alpha 2 chain [Source:RGD Symbol;Acc:1308085]
Coordinates
chr16:83397755-83401020:-
Coord C1 exon
chr16:83400877-83401020
Coord A exon
chr16:83397878-83400876
Coord C2 exon
chr16:83397755-83397877
Length
2999 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
AGAATTCTGTTCCCTTCCAGGAA
3' ss Score
9.47
Exon sequences
Seq C1 exon
GCGATCGAGGGTCACCTGGAATGGACGGCTTCCAGGGCATGTTGGGACTTAAGGGAAGACCCGGCTTCCCAGGAATCAAGGGAGAGGCTGGATTCTTCGGAGTCCCTGGTTTGAAGGGCCTGCCTGGCGAGCCAGGTGTTAAAG
Seq A exon
GTATGTCCTTGCTTAAGATCCAGGGGTCTCTGTGTTTGGTAAATAAGCCAGACTTAACAGGGAAAATATCCAAATATCATTATTTCCTCTCATATGTAGAATGAATATGTACATATACATATATATGCATAGGGGTGTGTATGTGCGTGTGTGTGTGTGTGCGCGCGTGAGAGCGTGCATGTGTGTATGTGTGTGCACATACGCCATGAAAATACAAAAAGGACGGGAAGAGAAGAGGACCAACAGGAGGGGAAAGGGAAGACAAGCAACCATGATCAGAGTGTGTCATGTGTGTCCTGATAAGTCCTGCGACCTTGTACAACGCACGCTAATCAACAAGCAAATGAGCCAGGTGTGATGGTGACAGCTGTCACCCTGTCGACTAAGGAGGTGCAGGCAAGAGGCTTGAAAGTTCAAGGCCTGGATGGGCTATAAGGTGTGCCCCAGGCCAGCCTGAAGAACTTAGTGAAACCATGTGTCTAAATAACAATGTCTAAAAAATAAAAGGCATCTGCAGGAGCAGAGCACACAGCGGCTGGGCAGGGAGCACAAGGCTACCAGGTGCAGAGCACAGGGCCAGAGCGCCCAGCAGCTGGCACGGAGTAAATCCCAACGAGCCTGAGGCTGCAGGTTCACCCCAGAAGCATCAAATACACAACAACAAAAGGAGTGCCTCAGGGAACAATGATTCGCCTTCACTGCAGCACAAGTGCTGGGAGAGCTCTCTCTGGCCTCAGCATTCCAAGGCTGGTGCAAACAGCCAATCAGATGGTCCCGGCTACAAGACTCCTCCCATCTCCCCCACACAGACAGTGGATCCCACCACCCTATCCAAAGGGAGGTCTCCAAAGCAAAGTTAATGGCAGTGTTAAGAACTAAGATTGTCACGAAAGTCCATTTGATCAAAACTGTGACATAGCAAGTATGAGCTGCAGAGGTGAGAGTGGGGAGGGGTGTGCTTTGAAACAGAGGCATGGGGGCACACAGCTTTAATCCCAGCAGAAGCAGGTGGGTCTCCACGAGTTCAAGGACAGCCTGGTCAAGAGAGTGAGTTCAAGACAGACAGAATTACCTAGTGAGACCCTACCTCCAAAGACAAGCCAACAAACAAACCACAGACTCACAGAGAAAGAAAGGCTGCGGGGTTGGAGGTGGGATATGCCTTTGGAGAAGGAGGGGACAGCACTCCAAGAGGAAGGACAGGTAAACATGGCGGTACCCAGAAATCCTCCTCGGAAAAGATAGTTAAAAACTTATCTCCGGGCAGACTTTTTTTTACACAAGTGTTCACGGGAGCCTCATTTAGAATATCCAGCAACCCAAACGTCCTCCCACCCTCAGAGACATAAAATGTGGTGTAGACATAGGACGTGCAGAGGTGATCAAACTCCCACAGTTCCCTGTGTGTGAAGTGGCCAGGATAAGCATCCCTCGAGATAAAAGTAGATAAGCAGTTCCCAAGGGTTGGGGCAGGGGACCCGAGGACAGCTGCAAATGAGTCCAGGCTTAGTCAATGGTGAAAGTGTCCTAAGGTTAGATTTGGTGATAGCTGCACAGCTCAATGCACTGAAAACTGTCAAACTCCTCTCTTTAAAACACCGAGCTGCAGCCCAGGGTAATAGCGTGAATCCCAGCACTTGGGAGGCAGAGGCAGTCAGGTCTCTGTGAAGTCAAGGCTAGCCTGGTATACATAGTGAGTTCCAGGACAGCCAGGGCTACGTGGTGAGAGCCTGTCTCAGGAAAACAAACCAACATCCAACAGTGAGTTGTGTGGTACATAAATCTCATCTCACCAAAGATGCCTAAAATGAACAGATAGAAAAGAAAAAGAAAAAAAAACAGAGAAAAGGAAGTCTAGAGACAGGCTCTGTGATTTGGGGGACAGCCTACCAGCCAGGGCTACAGAGCAAGACCCTGCCTCAGAACAATGGAGATAAAATAAGCTCATAGATTAGTGCTGGGTCTATAGCTCAGCCATGTTTATACAGATCGGGGCTCAGTCCCATGCAGAGGGGGAAAAAAAGTTCCCAAAATCCAAGCCTGGTCTTGAACTCCTGGGTTCAAACCTCCAACCTCAGTCCCTAAGTAGCTGGACTAACAGGCTGTCTTAGTCAGGTTTCTATTTCTGCACAAACATCATGACCAAGAAGCAAGCTGGGGAGGAAAGGGTTTATTCAGCTTACACTTCCACATCGATGTTCATCACCAAAGGAAGTCAGGACTGGAACTCAAGCAGGTCAGGAAGCAGGAGCTGATGCAGAGGCCATGGAGGGAAGTTACTTACTGGCTTGCTTCCCCCTGACTTGCTCAACTTGCTCTCTTATAGAACCCAAGATCACCAGCCCAGGGAGGGCACCACCCACAAGGGGTCCTCCCACCTTGATCACTAATAGAGAAAATGCCTTACAGCTGGGTCTCATGAAGGTATTTCCTCATGAAAGGGAAAGAGAAAGGGCGGCTTCTTTCTCTGAGATAACTCCACTTGGGACAAGTTGACACACAAAACCAGCCAGTGCACAGGCCTAATCCCCACTGCACTTCGCTAAAAGCTACAATATTAACAGACTTCCAAGATTTTCACCCACACCTGTTTCCTTAAATAATTTTCACGCCAATTTAGACATTCCAGGCCATGGAGCAGAAGTTGATCTTTTACAATTAAGACTAGGCATGGTGGCGCACACCTGTAATCCCAGGACTTGGAAAGATTCTGTACTGTGAGCTCCAGGGCAGCCGAGACTATGTGGAATTTTAGCTCAAAAGAAAACAGAACAAAAGGGTAAAAGTTACAATGAAATTAAATTAAGAATGCAGCTGCCCTGTGCCCTCCGGTTTTCTCTCCCTCACTGTGGCTCCTGCAGCCTCCCAGGGCTGTGGTTCCTCTGGATGTCCAATTCCAAGATCAGCAGCCTGGGCTCTGAGGACAAGACCCGTTTAGCATTTGATTCCCTCACCATCCCTGGGGTCCCTGGACATGACAGAATTCTGTTCCCTTCCAG
Seq C2 exon
GAAACCGAGGGGATCGGGGCCCCCCAGGACCACCTCCTCTAATCCTGCCGGGGATGAAGGACATCAAGGGAGAAAAGGGAGATGAAGGGCCGATGGGTCTGAAAGGCTACTTGGGCTTAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023972:ENSRNOT00000057461:31
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.980 A=NA C2=0.905
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(18.8=30.6),PF0139113=Collagen=PU(76.3=91.8)
A:
NA
C2:
PF0139113=Collagen=PD(22.0=31.0),PF0139113=Collagen=PU(42.6=61.9)
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]