RnoINT0039790 @ rn6
Intron Retention
Gene
ENSRNOG00000023972 | Col4a2
Description
collagen type IV alpha 2 chain [Source:RGD Symbol;Acc:1308085]
Coordinates
chr16:83387364-83389686:-
Coord C1 exon
chr16:83389400-83389686
Coord A exon
chr16:83387622-83389399
Coord C2 exon
chr16:83387364-83387621
Length
1778 bp
Sequences
Splice sites
5' ss Seq
ATGGTACGT
5' ss Score
9.89
3' ss Seq
CCTGCTCTCTCTCTCTGCAGCAC
3' ss Score
13.51
Exon sequences
Seq C1 exon
GGCTGGCGGGCTCCTGCCTGGCACGCTTCAGCACCATGCCCTTCCTGTACTGCAATCCGGGTGACGTCTGCTACTACGCCAGCCGCAACGACAAGTCCTACTGGCTCTCCACCACGGCCCCACTGCCCATGATGCCCGTAGCTGAGGAGGAAATCAAACCCTACATCAGCCGCTGTTCGGTGTGTGAGGCTCCGGCCGTGGCCATTGCTGTCCACAGCCAAGATGTCTCTATACCCCACTGCCCCGCTGGGTGGCGGAGTTTGTGGATCGGATATTCATTCCTCATG
Seq A exon
GTACGTATGTGTCCCTCCCCCCCCACCCCCGCTCTGAGCATGGGACCCGGCAGAATGCTCCCCCATCCACCTCCTAGCTGAGGCAAAGAAAGGAGACATTAAATAAACCAGGGCTGCAGACTTGAGCTCCGTGGGTAAAATTTGGATCCCCGGAAACCATGTAAACACCAGCGAGGCAGAGGACGCCTGTGCTGGGAGACAGACAGTGAGACCCCAGTCGTTCCCTTGCCAGCCAGACTATCCAAAAAGCACCAGACTCAAGAGGCAACCCCCTTCTCAAAACATAAGGTGGAAACCCCATTGAAAAGCACCCAGTTTCAGCCCGTGACCTCCAGACAAACACATACACACACACTGATCACGCGTGGCCATTGCTCAAGTCCTGAGTCATACAAGCGCTCCTGGAGCAGGAGCGAAGGGATGTGATTCAGTTTGATCTGGGCTTAGCCATGTGCTGCGTGACGGGGTAGCTTCCCCCAGTATGAGGATCAGTCCGCCACCCCACATTTACATGGGAATTGCAACACGCCTGCCTTAGCACCTAGGTCTACACTTTATGCTTTGCTGCAGCCTAAGTGAGTGGAAGCATTCTATCCCAAGTGCTGAAACTCTCATACAGACTCCTTCTGGAATACAGAATGCTCCTTCCTACACAGCATACGCTGACAGGTTGGTCTCAGAACCCTGGAGTCCAGACTCCATTGCACTCAGAGTCCCAGCTCCTGTGGTACTCACTCCGGATGAGAATCGTCTTTGTTTTGTTTTACTTTTGGCTTTTCTGGAAGAGTCTCATTCTGTAGCCCAATTTATCCTTGAATTCTTGGCAATCCTCCTGCCTCAGCTTACAAACACGAGCTACCTCTGGTGCCTTTAACCCCGGCACTCAGGAGGCAGAAGTGGGCAGATCTCTGAGTTTGTGGTCAGCCTGGTATACAGAGTGAATTCCAGGACAACCAGGGCTACACAGAGAAACCTTGTCAAAAGAGAGAGAGAGAGAGAGAGAGGGGGGGGGAAGGGAAAGGAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAACAACAAAAACTGCGAGACCAGCCTATTTCAAGGGTCGTTTCCTCTACTAGGCATCTTGCATGGATAGTTGATCACCATTTACATTTTGTTTAACAAAAATATAGTCAACCACATCTGCAGACCGAACCCACTTCCTGGTTGCAGCTTTCATTGAACAACCAGTCATGGGTGCTATGGTTTATACCATGCTGCACCTCCAACACCCTCCCCCAACATCAGGACCAGTCCCTTCAGTCACCCTGAAGGCACAGCACACTCCCCAGGGTCTATGTGACAGACAGTCCTGTTATTGACTTAGCAAACAAACAGGGACCAAGCAGGGATGGAGGATGTGGCTTGGTCCGGCATACGAGATGCCCTGAACTTTATCTGCAGCACCAGACAAGCTGGGCACGGGAGCCCACATCTGTAAGCCCTCAGGAAGTGGAGGTGGAAGGCAGCAGGGGCAAGAGTTCAGGGTCATCCTAAGCTCCTAGAGAGTTGGAGGCCAGCCTGGGTAACAGGAAAGACTATAAAAAGTAGGAATGGTGACACGTGCATTTGATCTGAGCTGCTCAGGACCCTAGGAGAGGAGCAATCATTTGAGTCCAGGACATCAACACCAACTAAGGCGTCATAGTGCGTTTCTGCCTTAAAAGTATGTAATTAACACAGTCATCAGAGGTGCCTCAGGCGTGTGGCCCCTAACACACTCCATCTCCTGCTCTCTCTCTCTGCAG
Seq C2 exon
CACACTGCAGCTGGGGACGAAGGCGGTGGCCAGTCACTGGTGTCGCCAGGCAGCTGTCTGGAGGACTTCCGTGCAACACCATTTATCGAGTGTAACGGGGGCCGTGGGACCTGCCATTACTTCGCTAACAAGTACAGCTTCTGGCTGACCACAATTCCTGAGCAGAACTTCCAGAGCACACCATCCGCTGACACGCTCAAGGCCGGCCTCATCCGCACCCACATCAGCCGCTGCCAAGTGTGCATGAAGAATCTGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023972:ENSRNOT00000057461:46
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(26.1=31.2)
A:
NA
C2:
PF0141314=C4=PD(72.2=96.5)
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:
AAGTCCTACTGGCTCTCCACC
R:
GCTCAGGAATTGTGGTCAGCC
Band lengths:
358-2136
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]