RnoINT0039745 @ rn6
Intron Retention
Gene
ENSRNOG00000016281 | Col4a1
Description
collagen type IV alpha 1 chain [Source:RGD Symbol;Acc:1307148]
Coordinates
chr16:83624118-83627919:+
Coord C1 exon
chr16:83624118-83624295
Coord A exon
chr16:83624296-83627804
Coord C2 exon
chr16:83627805-83627919
Length
3509 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
GCTTGCTTCCTCTCTTCCAGGTG
3' ss Score
12.22
Exon sequences
Seq C1 exon
GTACGGCTGGCAGCTGTCTGCGCAAGTTCAGCACCATGCCCTTCCTCTTCTGCAACATCAACAACGTCTGCAACTTCGCCTCCAGGAACGACTACTCCTACTGGCTGTCCACTCCGGAGCCCATGCCCATGTCCATGGCACCTATCTCTGGGGACAACATCCGGCCCTTCATTAGCAG
Seq A exon
GTGAGCTCAACATTCACAGAGGCAGATGTTAAAAGTAAAGAAGAGAAACTGGGGTTTACTTGCCCTTGAACATAGAGAGAGGTCTGCTTCTGCCTTCCCAGGGCTGAGGTGAAAGGCAGGGTTGAGGTTAAAGGCATGCACCACCGTGCTCTTTTTCTTTAAGAAGAAAAAAAAAAGATTTGTGTGTGTGCGTGTGTGCATGCGTGCATGCATGCATGAGTGTGTGCGTGCATACCTGTGTGTGTGCGTGTGTGCATGAGTACAGGTGTTTTGCAGCCAGAGACATCAGATCCCTCTGGAGCTGGAGTTACATGTAATTGAGAGTCACTTGGTATAGGTGCTGGGAGCTTCTTCTGGGTCCTTTGCATTTTCTTGGCCACACTAATCCATCCCTCCAGCTCCCAAACGTCCTTTTTAAAAGGATGAATCATGACCCACTGAATGGATGCACATTGCATTTCATTTGTCCACACCTCCCCTGCCCTCGGTTATCTGGGTTGGCTGTTCTGACTGAGGGTGCTCAGAATGCGGGTGTTGACACCCAACTTCTTGCCTTCTGTTCTTTCGCTGCATGCAGAATTGGGGTTGCTGAGTCATACGTCGATTCTGTTTTTAAGTTTTTGAGGCACTTCCTTACTGGTTTTTCACAGTGGCCCTGCCCTCGACATTCTGACATCCCCGCCAGCCATGCACAAGGGCGCTCCTCTCCCTTCACATCCTCGCTAACACTGAAAATATAGTTTCTGTTGTATTTTTACAGCAGCCCAGTGGTTGTAAAATGAAGCCTGTGCAACTGTAGTACTCAATATATATCATCTGCTTATGTAGTGTTTGTGCATAAAAACTACACAGACTTATTTCACTCAAAAATGTATGCATGGTCTCCAGTACCACAGAATTAATTGTGCAATAGTAACACATTCCGTGTTCCCTCATTCTATTTAATTTTGCCCCCTTGAGACGCTGTTAGACTGATTGAGAATGCATATGTCTCTGGCTGAGTGATTCCTACATTAAGCTTGTCCTCATTGACATCTGGAGTATTTTCAGTTCAAGAGCTACCCTGGTAGAAGTAAGGCAGGACATTTTATGAGTGAATAATATAAGATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCCCTCTCTCTCTCTGTCACCAATTTCTATCAAAATAGAAATTTGTTGTTCAGTTGTGCTAAGAAGTAACAGAAACATGGAGATGAACAGACTGATTTGGCTAACAGTTTACTTTATGTGTGCAGTATATTAAAGACAGAAAGGATGAGACTGGGAGTTTTCCTTAGGAACTTATGAAAAAGCACCAGGCTTCTCCATACACCCTGGTGAGGCAGCTCTCAATATGCCGCCCAGGTTGGCCTTTAACTTGAGATCCTCACGCCTCCACCTGGACTGTGAGTCTGCTCCACCATGCCTAGATCGTCACAGGTCCTTTAACAACATGAGCATGAAGACGGACAGTCTTGTAGAGCAACTTTACCAGAGGGGGGTAGGAGAACCACAGGTTTGCTGGTGCTCTGGAGTCCTTTGTCACAGCCATTTTTGGGTCATATGATGGAAAATGTCATTTGTTACACTTCAAGACTACAGAGAGCATGCCACACACTGACAGTACACAGAACACACCACACACTGACAGTACACAGAACACACCACACACTGACAGTACAGAGAGCACACCACACACTGACAGTACACAGAACACACCACACACAGACAGTTCACAGAGCACACCACACACAGACAGTACACAGAACACACCACACATAGACAGTACACAGAGCACACCACACATAGACAGTACACAGAACACACCCCACACAGTTCACAGAGCACACCACACACAGACAGTACACAGAGCACACCCCACACAGACAGTACACAGAGCACACCACACACAGACAGTACACAGAACACACCACACACAGACAGTACACAGAGCACACCACACACAGACAGTACGCAGAACACACCACACACAGACAGTATACAGAACATACTACACACAGACAGTATGCAGAGCACACCACACACTGACAGTACACAGAACACACCACACATGGGCAGTACATAGAGCACACCACACACATACATGTGTTCTGTGTGCAGACTTCTGATCAGACACTGTTGAAGGCACTAGAAGGAGAACTAACTTTTCATGGTTTTTCTTTTTAGCTTTCCTTGGAAAACAGGTAGAAAATGATTACTATTTATGTCTCTTGGTTCCTTTTGGACTGGCATCTATGGTGGTCTTCATTTGGTTGAAGACCCAGGCCTGGGGAAACTGTGTGTCTCAGACATCCTTTTCTCGATTCCCTGTTGTAGCAGCATGGCCTTTCTCCTGGGCTGAGGGCGCTTAATACTTTAGCTTGATGGTTTCCAGCAATGTCTCAAGACTTCCAGATCCCTTCTTTCCTGTGGGAGGACCCAAAAGCTTAATTTTAGAAACATTGGCATAAATCTTTCCTTTTGGGTTTTGAACTAAAAAGATGGCAACTGCTTTCTTTACCCTGTTGGCTGTAATTTCTAAGTACTTTCTACAGACAGGAGTGGCTATAAAGTCACAATTCCATCACTTAAAAGAAAGGACTGGTGGTCAAAGAGGAAGGGAATTTTGATGGCCTGGGTTGTGACACCAACCATGGATGTCCTTCTGGAGGGCAGAACTGTCCTCTATTTGGCCATCTATGGCCCTGCCCCCAAGGACCAGAGCAGCCCGGGAAGAAGGGCACTTTGGCAAACTGTCCTATTTCCCATGCCTGAGAGGCAGAAGGCAGCAGATGGGCAGGGCCATTTCAATTTCAGTGGCTGGTGTTTGACGGAACCTCTTAATTCATCTGCATTTGTGAGAATAAAGTAGAGAGAGGGCACACACACACACACACACACACACACACACACACACACACACACGTGTGTGTGTGTGTGAGCGGCACAGAAATTGGAATGACTAACCCAGCCACCCACCTGCCCCCTTTCCGTCCACGCGTGCAGAACTTGTGTAATTACTCACTTGTCTGTACTCATTTAGCAGCGTGGCTAACACTCTCTTCACTCTGTGACTGGAATGTAGTTGTTTGGCTGCTGCTGTTTGTGTGTTTAAGCAATGCGCTCCCCCACCATCCGGAACTCCCTTACATGAGTGAGCTTTAGAACACTGGACTACCCTATGGTTTTCACTCGCCCAGCCAGCAGAGGAGGGGCCTTGTCTTGAGGAGGGGCCAGAACACTGAGTCCCTCTGCCACAGCTATGGTGACCCCATTGTTCCTGTTATACAATAGTTAAAAAGCAAATGCTTTTGAATTAAGTGTTTTAGGAGAAAGAAGGGCTTGGACAACCCATAAAGAGTCCCTGAGCCTGAGTCCCACCACTGGCCATGTTATTCCCATAGAGTTGAGCCAGGAGAACCAGGGAGAGAGGGCAAGGGGTGGGCCATCCCCGGGTCCCATCCACCCTGACTGCTTGCTTCCTCTCTTCCAG
Seq C2 exon
GTGTGCAGTTTGCGAAGCGCCCGCCATGGTGATGGCGGTGCACAGTCAGACCATCCAGATCCCGCAGTGCCCCAACGGTTGGTCCTCACTGTGGATTGGCTATTCCTTTGTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016281:ENSRNOT00000057386:49
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.033 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0141314=C4=FE(53.6=100)
A:
NA
C2:
PF0141314=C4=PD(6.4=17.9),PF0141314=C4=PU(26.3=76.9)
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]