RnoINT0122917 @ rn6
Intron Retention
Gene
ENSRNOG00000033215 | RT1-Db1
Description
RT1 class II, locus Db1 [Source:RGD Symbol;Acc:1593282]
Coordinates
chr20:4091556-4095331:+
Coord C1 exon
chr20:4091556-4091825
Coord A exon
chr20:4091826-4095049
Coord C2 exon
chr20:4095050-4095331
Length
3224 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CACCTCTCTTTCTCCTCTAGTTG
3' ss Score
10.48
Exon sequences
Seq C1 exon
CACGGTTTTTGGAACAGTATAAATCCGAGTGTTATTTTTACAACGGGACGCAGCGCGTACGGCTTCTGGTCAGATACATCTACAACCGGGAGGAGTACACGCGCTTCGACAGCGACGTGGGCGAGTTCCGCGCGGTGACCGAGCTGGGGCGGCGGGACACCGAGTACTATAACAAACAGAAGGAGTACATAGAGCGGGAGAGGGCCGCGGTGGACACGATCTGCAGACACAACTACGAGATCTCTGATAGATTCCTTGTGCCGCGGACAG
Seq A exon
GTGAGACAGCACAGGGGCGGGTGAGGGGCGGAACCACGCCCAGGTGGGACTGGGAGGGCGGGGCAGGGCGGGGGTGCGCGTGTGCGCAGGAGCTGCAGGGGATGCTGGGTTCCCTGCCGCTGGGGACACAGGTGATTTAGGCGGCCTCTTGTCAGAGGGAACAAAACTCATCCTCTGCGCGCTGCTAACCGCTGGTCATCCCTCCGGCCCGGAGAAAAGTCAAGACGGCCCAGGACAGTGACGCGGGGGTGGAAACTGTCCCAAACGTTCTTTCACCTTAAGCAGAAGGGTTAGGACAAGGGGTGGACAGAGGAAAGTAAAGTCGCACCCGAACTGAGGGAGACCAGCTCGGTACCTAATACATGTGACAAGTACAGTGGTTGAATCTCAGGTTGCGACTCAATTTTTTTTTTCCCTAAAAATTTACTTTTCTTTCCTCTCTCTCGAGATACACACAGGCTGGTTCTGCAGGTGCCTTGGACGGATGTTACCCTTGCATTTTAAAATTGTCATTAACGACTTAGAATAATTCAGTAGCTTTCTTAAGACTAGCAGTTTAGGTTTCATATCTGTAAGGTTTGGGCCTTAAAAAAATCATGCTTTAAAATGAAGCTTTTGCTATTAAAATTGTTTTAATCATAGTGCAGTTCACAGAGAGACTGGCAATTTTGCTGATCCTACCGTATTATAGTACATTATTAAATCATTAGAGACCATTGTAGAGTAAGATATGTGTGTATATATATATATATACATATATTAGTTTATCCAAAGGAGCTATAGCAAGGTACTGAAAACACCTGGCAGCCCTCAGTAAAGATGGCGGTGAGGGGGCTGGGGATTTAGCTCAGTGGTAGAGCGCTTACCTAGGAAGCGCAAGGCCCTGGGTTCTGTCCCCAGCTCCGAAAAAAAGAACCAAAAAAAAAAAAAAAAAAAAAAAAAAGATGGCGGTGAGGACATGACTTTCCCATAACACAGACGGCACAGTCATGTGACTGCCCTTTCCCAAGATGGCTGACATTCATGGACCGCTCTTAGCCTCTTAACCAAGATGGCTGACATTCATGGCCTGCCCTTAACCAAGATGGCGACGAAGCTGTGGTTTGTTGTTGTTGTTGTTTGTTTTTGTTTTTTCCCACAACAAAGATGGCGACCAGTCATGTCTTTATGCTTTCCTTGCGGATTTTCATTGTTCTCCTAGGATATACGAGGTTGAGTAGCGGGTAGCATAGTCACCGTTTGCTTGCACCTTAAGGCCACCTCCTGCGTCTACATTTGCTCCGGCTCATGACTGTTGCTGGCAGATAGCTGTGGACAGGGGTAGCAGCCATGCCCAGTGCAGTGTTCTATTCCACTGCAGTGCTCTGCTGCTGTCCACCAGGGATGCACACATGCTGACGTACAGGGTCTGGGACAGGCACAGGGAAGCCAATGGCAGTTTCTGCCACTGCGACTGCCACTTAGTGCTGCTAATGCTGCATAAGTACAGGAGGGAGGTCGCATGGGGGGGGGTGGCGCCTGTATCCACATATGTGGAGCCACTGAAGCTGGAACAGAGGTGTTGCTGTGGGCAAAGGAAGGGACTGCCAGAGCTTGGTTCCCAAAAACCTAGATTTAGGGAAGTTCAAACTGAAGTCTGTGTGTGTCAACAGTTTTTAGAAAATCTGGCGTTTTGAATGAAAGCAATGTCCGAAACCAACTCAATTTATATAAATGTTGCTGTGACATCCCTTGGGCATCTGGACACCTTGTATTCATTTTCTCAGCCTTCATCAGACCCGTGGGTGGGGTGGCCTCCTGCCTGCTAGCCTGGGGTAGAACTGTGGTAGATGGTGGGTTAGACTCAAGTCAAAGGTGTTTGAACTCTCCCTTGGTGAGAAGAAAACACCCGATCTTTGTTCAGGTCCTTGGTGGCCCTTTGTTCAGGTCCTTGGTGGCCAAGGCTCTTGGTAGAGTGCCTGATGAGTGGGGTTGACCCTAGCGGAGGACACAGTACTCCTAGGCAGAGGCTGGGACCGAGTTGGACTTCCTAAGTCTAAAGTCCAAGGTTGGGATGTTGTAGGTTACTTAGCTCACACTTCTATATGCTTTTCATGATTAAAGGAAGTCAAGATAGGAACTCTGGCAGGGCAGGAACTTGGAAGCAGGAGCTGACTCAGAGGCCGCTGAGAGTGGCTTGCTCCTCATAGCCTGCTCAGCCCGCTTTCTTATAAAGCCCAGGACCACCAGGCCAGGGAGAGCACCGCCCACAGTGGGCGGGGCCCTTCCCCATCAATCACTAATTAAGAAAATGCTCTACAGGCTTGCCCACAGCCCAGTCTTATGCAGGCATTTTCTCAATTGAGGTTCCCTCCTCTCAAGTGACGTTTAGCGGTGTCAATTCAACATAAAACCACCCGGGACAGTTTGTGATGTTGAAACCCGCAGCCCTGATTGTACAACTCAAGGTGGGGTGGCAGCTTCTTCACTCAGCTTCGGAAGATTGTAGGGAGGTGAACTGAAAATAAGCAAAGACAATGAAGGCGTCCATAAACGAATTTGAAGGGACGGAGAGATTACTTACAATAATGAGCCATGTGAATGGCTGTTACATTGTGTTGTCTAGACCCCCCCCCCCCCCCAAAGGCCACCCCACTAGGAAAGTGGCCTAGTCTCTTCAGTTGGGACAGGATCCTCCCCCAGCACTGCCATCTGCCGCTTGTTCACTGCTCTGCATGGGTCAGGGTACACACTGTAGCTCAGCCCACAATCCCGGAAGCTCACACTGCCTGGCCCCTGCTGATGTGACTATGAGTCCCTGTGTATCAGACATTATGAGAGTAATGGCAACGTTGATTTATTTATAGTCTTGCCAAAACAGATGAGAAAAGAGTAACTCTCAGTAAGTCTTCCTGCCTCACACACAGAACCATCACCATCTACAGACAAGAGACAGAACCCACGTGCCACAGAACATATGGGTGCCACTTAGCTGTTGGTAAAATTACCACAGCTGAGAGGTAAGCCTGTCTCTCCCTGCCTGGAGCTTCACCTCCAGCTGGCGATTCCTCCTGAGAGTGGAGCTGACAGTAAATCGTGAAAACAGAACCTAAGTCCTGGATGACTATGTGGTAGAACCTTAGTCCTGCCTGGACTTCAGCCTGGGTGGATGGAGGCAGGCAGGCAGCCCACGGGGAAGACAGGTCTGCCCTCATGGCTCCTCCTCACCTCTCTTTCTCCTCTAG
Seq C2 exon
TTGAACCCAAGGTGACTGTGTACCCTTCAAAGACGCAGCCCCTGAAACACCACAACCTCCTGGTCTGCTCTGTGAGTGACTTCTACCCTGGCAGCGTTGAAGTCAGATGGTTCCGGAATGGCGAGGAAGAAAAGGATGGACTCGTGTCCACTGGCCTGATCCCAAATGGAGACTGGACCTTCCAGTTGTTGGTGATGCTGGAGATGGTTCCTCAAGGTGGAGAGGTTTATACCTGCCAGGTGGAGCATCCCAGCCTGACCAGCCCTGTCAGAGTCGAGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000033215:ENSRNOT00000000522:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.011
Domain overlap (PFAM):
C1:
PF0096914=MHC_II_beta=PU(93.5=82.7)
A:
NA
C2:
PF0765410=C1-set=WD(100=87.4)
Main Inclusion Isoform:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
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]