RnoINT0107702 @ rn6
Intron Retention
Gene
ENSRNOG00000004410 | Pax6
Description
paired box 6 [Source:RGD Symbol;Acc:3258]
Coordinates
chr3:95711617-95715324:+
Coord C1 exon
chr3:95711617-95711677
Coord A exon
chr3:95711678-95715193
Coord C2 exon
chr3:95715194-95715324
Length
3516 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
TCTCCTCCTCCTTTCCTCAGGTC
3' ss Score
13.04
Exon sequences
Seq C1 exon
AGCCACGTATTCGAGCCCCGTGGGATCCGGAGGCTGCCAACCAGCTCCAGCATGCAGAACA
Seq A exon
GTAAGTGTCTCAGGTCTTTCTCTGGACTGTTGGGCTGGAGGCACGCAGGCCATGGGTTAGGGGAGTGCACTGAGTCGTGGGCCCTGCTGAGCCCAAACCACTGGGAGGGAGGGAGATGACATGGGCTCTCTTCGGGCAGCAAAGAGTGAGCGCCAAGCAGCCCTCGAGGGAAGGCTGGGGGGCGTTTTGCTCTGCTGTGTTCTTGAAGGGCAGAGGCTGGGGCCTTTCAAAACTATTCGCCCGAGTTTTTGAAGCAGCCGTAGAGAAACCCCACTCCCCCCCCCCCAAATCCTGTAACTCATACCCCCTCCCCGCCCCTGCCCGGGCTCTGACCCCAGAGAGAGGGGCTGGGCCGAGCAGGGCGGGGCAAAGCATAGGCTTCTCCTGAGAAGGAGGCCCCTTTGGGCTTGGCCAAGACTAAGCGTCTCCTCCGACCCCAAGGGGTGGGGGGCTTCCCTCCCCTAGTCAATCTCAGTCCAGCTCCTCCCCTCCCCATCCTAGCTACAGGCCTAGATGAGAAGGGGAGTGGAGCACCCCGGGCTGGTACCCTGGTGGAGAAGTAAACCTCACAGGGTGAAGAAAGGAGGATTTACTGGGTCTGGGGAGAGAATGGAAGCTGTACCGTTCAGGAATTGGATAAACCTTGCATTAGCAAGCGCAACTGAGTTGGTTCTGGATAATCCAGGCTCCTGGTGCCTTTGATTCCATAGTCTTTGTGCCTCTCTTCTTACCTTTGCCCAGGCCCTTTGGCTCCAACCTTTGTGCTCAACCAACGGTTGTTGGTATGTGATTGAATTGAATCAGTGAAGCTAGGCCGGGTTAAGGGTGAAGAGTCTACACAGTCTTAATTAAGGCTACAACTATGCTTGGGAGTATGGCGAGGTTTGGGTCTCCTAGAAACTTGCAGCTGTGGAACTGGCCAAGCTTAGAGAGCCCAGCCGCTCATGATGCCACAGGACCAGGGACACTAAGCTCAGGAAAGTGAGCAAAGGTGTGAGCTTTGCAACTGCATTTATGCAGAACCTGTCAGATCCATACCCTGGAGTTCAGACTTCCTAGCCCTAGGTTTTCAGGTGGGCTGAGACGTTCAGTCCTGATCGTTTGCCGCTATGCTATGGTCTGGCTGGCAGGCCCAGAGGAGCACGGGTCGCGGGTTGGCCTGTAGGCTTTGTGCCGTTCGCTGGTTCCCGGGTGTGCACAAGGCGCGGAGCATCCAAATTGACACCATATGTTTTCGTATTAGAAGCTTTGCGGTCGAATTCTAGGCGCATAATCATCGCCACTGGGCGAGAACGCCAGCAGTCCCTAGGGAAGGGACACAATGATTGAGGCTTAACCTCTAAAGGGGAATTTAGAGCTATGTTTTTTCGCTGCCATTTCGATGCTGGCAGAAGCGCCCTGGCCCCGTGTCTCTCGGACCAGCACATGCAGGCTGTAGCTGTGGAAGTGCTGGACACCTTAGTTTTGCAACGAGGGATAGGGAAGGTCTATGATTAAAGGCCTTGTACGCTCTGGAATCTGTAGACTGGGAATTCTCTGGCTTTGCTTTTGAAAAGTTTCCCTTCGTTTCTCTGGGACGGCCTTTCTTTTTTGGGGGGGAAGCTTTTTTCTTTCTTTCCTTTTTTTTTTTTTTTTTTTTGCCCAGAGATGGTCCTCCATACCTGCATGGTAAATGAGATTTAGAAAGCCAAGGTAGATGATAGAGAAAATTTAGGAGAAACCGGAAGCGCAGGGTAGGCCTTGCCCTGTTTAAGAGGCCATCTCTTGCAATGTGCAACGTATCCTCTTGCACTGGCCCGGGACGGCCGGACCCAGATCCCTAAACGCCTGTCACTTCTCATCGAATTGAGGCCCCGCCCCCCCTCGGCGAGCTATAACCCTCCTCCAGCCTCAAGCCTCAAGCTACCCAGAAAACGCAGCTCCCCTTGAAGGGGAGACGAGTGCAGTTCATTCTCGTCTGAGTGATCTACAAATAGGGACGGAAAGGGTCGTTTTATCACGGTCCCGTTTGTCGTGACGATGCAATTTCCCGGAGCGGAGCACTGTCACAAAGTGACAAGGCTGCCACAAGCGCCCCGACTGATCTTTTCAATTAGCCTTCCATGCATGATCCGGAGCGACTTCCGCCTATTTCCAGAAATTAAGCTCAAACTTGACGTGCAGCTAGTTTTATTTTAAAGACAAATGTCAGAGAGGCTCATCATATTTCCCCCCTCTTCTATATTTGGAGCTTATTTATTGCTAAGAAGCACAGGCTCCTGGAGTCAATTTATCAGGAGGCTCCAAGGAGAAGAGAGGAGAAGAGAGGAGAGAAGAGAGGAGCTGAGAACCACATTTCCTGAGAGGGCTTCTGTCTAGACACGGGGCTGCAGGTTGGAGATGTCTGAGGAAGTGGAAAGAGGGGACTGGCTTTATTTTTATTCCTGTGGTTTCTGAGGAGGATAATTCATGGAGGCGCTCCTTCCCTCTCGCCCTAAGTCTCTACGACCAGACAATGGGAAGAGGTTGTGAGACAAGAGTGGAAGGAAGGACCGACCGGTGACACTGTGATGTGGTCTTTTTCTGTTTTGGGTTTCTGTTAATATTTGTATCCTTGGCTGAGGGGGAGGGTGGAGTTCAGCAGGGGAAGTAAAGCGAGTAGTGGCGGGTGGGAAGGCTCCTGGCTTCTGAGCACGACTTGGGGGCAGGCAGATCACTGTGTGAGTTGGGGTTCCAACCCTATTCCTGCTATGGAGGTATGGATTGGGAGTCACTAGCGACAAATTTATCTTTCTGGCTCTTTTACACACACACGTACACACACACACACACACACACACACACACACTCACACACACACTATGCTGTGTGCTGTGCACCTCTGCCAGAGTTAAATCACCATGCTAAGGTTTTATAACATTCTGCCTGGCCGTGCAGGGCTTGGGATTTGCAGCACTATTCTAACACTGCAGAGACTTCTGTGTGGACTCTGGTGACACTCAGAGGTGATGTAGGAAGGAGACTTTAAAAGCTTGATGTTTACCCCTTGTGGGTTCCAAGAAGGGCTGGGAGAGCTTATGAAGGTGGCAGTGGGCTCAGGGAACTACTGTGGTGATGGTGGTACTGGGTGGGTATATTCCTGGGTATTCTCCTGGGTCTGACAACAGTCCAATGGGTAGGTCAATTGTATTTGAAGCTGGGCTCCCCAGTACCCTGCATGGTTGGTGGTTCTGTTGTTGGGTGTTTTTGTTTTTGTTTTTTAAACCAGGACCTAATTGCTAAGGTTCACACAGGTTGGCAGGGAGCTGAGGTTGCATTGTGGTCTTTTCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTTCTTCTCCTTCTCCTCCTCCTCCTCCTCTTCCTCTTCCTCCTCTTCCTCCTCCTTCTCCTCCTCTTCTGCTCTCCTCTCCTCCTCCTTTCCTCAG
Seq C2 exon
GTCACAGCGGAGTGAATCAGCTTGGTGGTGTCTTTGTCAACGGGCGGCCACTGCCGGACTCCACCCGGCAGAAGATCGTAGAGCTAGCTCACAGCGGGGCCCGGCCGTGCGACATTTCCCGAATTCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004410:ENSRNOT00000005882:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (disopred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0029213=PAX=PU(0.1=0.0)
A:
PF0029213=PAX=PU(30.9=97.7)
C2:
PF0029213=PAX=PU(34.4=97.7)
Other Inclusion 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]