RnoINT0126304 @ rn6
Intron Retention
Gene
ENSRNOG00000011321 | Rftn1
Description
raftlin lipid raft linker 1 [Source:RGD Symbol;Acc:1563347]
Coordinates
chr9:12934403-12942358:+
Coord C1 exon
chr9:12934403-12934484
Coord A exon
chr9:12934485-12941027
Coord C2 exon
chr9:12941028-12942358
Length
6543 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
CCACTCTCTGTGCCTTCTAGTTC
3' ss Score
8.34
Exon sequences
Seq C1 exon
GGAAGGGAACGTGTGCACCAAGCAGATTGTGTTTCTCCAGAGACCATGTCTACCTCAGAAAACCAAGAAGAGGGAGTCCAAG
Seq A exon
GTAAGAGACATGAGAGCTCTTTTCTCTTCCTCCCTGGGTTTATGTCTGCACACCTTGGCTTCAGTGGGGTCTGTGCCAGCTGGGCCTCTCCAATTTCCAAACCAAACGCTCTGTGGGCTCAATGAAGACCTGGGTCCACACGGGTCATAGTAGGGATGCTAGGATGGGCTGTTAAGGAGCTGGAAACTGGTCCTCAGGCTCCCTGCTGGCCTGACCACCGAGCAGATGGCAGATGCGTTTCTCCTCATCAGTGTGTGCTAGAGAATCCCACAAGGCTAAACTCGGGATTCCACAAAGTCAGCCGCAGTTTGACAGAGGCCTGAGAAGGGCTGAGATCATGGTCAATGCCCTTCCTGAGCTCACGGAATTTGGCTGGAGGTCAGGCCTGGCTATTCGACCTCTCGGGACATTGGGGTTTGCAGACCCTGGCCTGGTGTATTAGTGTAAGTCTGTAATCCTGCACTCATTGCAGGAAGATGAGTTTGAGGCCAGCCTCTGCTATCTGTGTGAGGGCCCTGCCTTATAGCATAAACCAGCCGTTTGCTAATCTTAGCAGAGGCACTCCCTGCTTCTTCTTGCTGGAACCTGAGCCAAAGGTCTTTGTCTGACAGTGATGGAGACTGAGGCCAGCATAGCCTGTGGTAGTAGTCATCCCCATGCAGGCCTGGGCTGGAGTGCGTCGCCAGGTCTCTCTCCTCCTTGGAGGACTTCTTGTCTATATAGTATAAACTTAAAGATTTACATGGCAGGCAGAGTGGAAAAGAGCCTAGGCCGTGGGGAAGGGGTGTGCTCTTGAAGGGGATATTGGAACTTGTGCCATTTCTCTTTTGGTTTCTGGGTCACCATGGGTGAACACTGTCTATCGCCCACTCCCTACGGTCATGTGCTGTCTCACCTCAGGTCCAAAGGCAACGGGATCAACAGACTACAGACCAAACCCTCTGAGCCAAGCTAGACCTTCCCTTCTTTCAAGTTGACTTTCCTATGATGTTCAATATTGATTTTTATTTTATGTGTACATGGGTATGCCTGCATGCATACTTGTGTGCCAGTGCCTGTGGAGGCCAGAAAAGGGTGTTAGAGTGCATGAATCAGTTACGGGTGTTTGTGAGCTGCTTGGTGTGGGTGCTGGAATTGAACCTGTGTCCTCTGAAAGAGCACCTAATGCTGAGCCATCTCCTTCCCTCCCTCCCTCCCTTCTTCCCTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGTCTTTCTGTGTCTCTCTGTCTCTCTCTGTGTCTCTGTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCAGCCTCCTTTAGTTTCTTATTCTATTAGAGCAAAATACATGGAGTAGCCTGTTGTAGGTGTACACTAGCTTTTCAGGAAGAGACCAGCATGTCGATGGAGTCTACCAAAGCCCAGTTAGGTGTCACCTGGATCTACCGTAGTCCACCTTGACCGCCCTACCCACACTTTGGCGGAAGCTCTGCACAGTTGGCACCTCCCCCATATACCCTACTCTCTGCTCACGAGTCCCAGTAGGAACATCCAGCCAGTGAACAGATTGCAGTAGCTCCCTGTCAGCCAACAAACACTGTGGGTTGCCCATTTATTGGAGGAATGCCAGTTTGGTGAGGACAAGAAGCCAGATGGGCTGGAGTGCAAAGGAAGGCCACTCTCTAGGCTCTGGGATAGGAATGTGACAGGTGACACCAGAGGTGGACCAGAAGGCAGCTGCCAGTCATCATTAACCACCAGGAGCAGTCAGCCACCACCTGGAAGATGGATGGCCGTGGACTGATATCAGATAGTGCTCAGTCACGTGCTCTCAGGACGCCACCAGCCACAGAGAGCAACACTGAAGGTCTGCTAACAGACACGGAGAGATTGGGCTTTCGCCCTTTGGTGGAAACGGCTCTAGACCCCCTTGCCAGCTGTCTCTGTGGGGCTCCTTGGTTTTCACACGAAGACCTTGGCATTCCACAGAGAGGACACGAAAGTCGAACTGGCTTTCCTCAGGAAAGGACAGAAGCCATGTTTTCTTAGTGGGCGAGCCAACCCTCACTGGCTAGGCTGATGCGGACAGACTGCTCTCTCTTCTTCAGTGTCCTGCGTCAATGTGGTGCTCAGCAGTTTCTTGTTTTCCGGGAGGCAGCCCTCCCTCCACCCCCTGCCAGGAAAGGAAGCTTCCAGAAAGAGTTGTGTGCATTCCGTATCCCACTCTCTTCGTCCGTCCCCACCCTTCCCACCTCTGCTGCCACCTCCTGGGTCTGTGTCCTGTCATGACCCTGTCAGCCCCTGATTTTTGTTTGTGAGGTACCTGGGTTTTAGGTGATGCTCAGGAGATACCTGCTGAGTCGCTGACTGATTAATCAGACCTCTCAGCCCTGAACACAGTGTGCTAGCACTGGAATTTAAAGGACGGGACTGCAGGATTGACAGATGTGACCTAGTGTGTCCTGTCAATCATTCTAGTCGACTGTGCTAGAGGAGTGTTCCTTCCTTCTCCTTCCTCCCTCCTTCTTCCTCCCTCCTTTCTCCTCCTCCTCCCTCCTTCCTCCTGCTCCTTCCTTCTTCCTTCCTCCCTTCCTCCTTCCTTCATAAGATTTTATTTTTAACCACATATGAGTGTGTGTCTGTGAGAGTGTGGGTTTGTGCATGTGCGTGCAGTGGCCATGGAGACCAGATGTATCAGATGGCCCTGGAGCTGGACTCTGGTAATGGTGAGCATCCTGACAAGGGTGCTGGGAACCAAACCTGCAGAGCCGTCCTCTGCTCCCAGCTCAGCTTCCTGAAGCAAGCGCGTACAAGCTTCTGAAAGGCACTCATTAGACCCACCAGCCCCTGCTCTACAACCTAACTGTAAGGTGAAGGCTCTCTGCCCTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCCTACGGGTTCTCGCCCATTTGTCCTTTTCCTTTTGGAACTACAAAACCTAAGGTCTTGTGGGTGCTAGGCAACTGTTGTTAGAGTGAGCTACATCCCCAGCTGTGTGTGTGTGTGTCTGTCTGTCTGTCTGTCTGTGTGCTTATATATGTATACATATATAAACACATATATACATACACACATATATAAACACATGCACATGCATAATTTTTTTTTGAGACAGGCCTAAATAGGGTGCCCAAGTTGGATCTAAGCTCACTCTAGCCCAGAAGACCTTAGCTTGTGACTTCCTGCTTTCACCTCTCCGGTAGCTGCCTTACAGGCCCAGCCCCCACACCTAATTCTGAGTTCGGTAGGTGAAGCCGGATTAAGCAGTCTCAGTGCCACTGTGTGGCAGCTGAGAAGAGCCCTGTTTCCGTTGTCCTGACAGTCATGGTACTTGACCGTACAGACTCCCTGCCACTCCTCCAGCTGCAGAACTGCTCTCTTCAGTTGGGAGAGCCCTGAGGTTGTGTTCCAGACCTGAGGCAGGCTGTGCTCCTGGCCTCTTCCCAGTTTCTGTCCTCTTTTGGAGGCTCGGGATCTGAAGCTGGTACTGTTTATCACATGGGGCAACTGCCCCATTCCTACAGGAGGCCTGCCTCAGAGTGCAGAGCGGGAGAGGCTGAGGAAACCCTTTCCTGTGGACGGCCTGAGAACCACCAGCAGCCGCAGTCGGACTTGAGAGTCGAGTCAGTTCCCATCCTGCTTGCCCACTGAGCTGCTTCCTCTGGAACCAGGGCCTGTAGCTGGGTTTTCCAGAGACTTCCGTGATGACGTTGCTCCCCAAGGGCCTGGGTCTCAACTGAGTAGTCTGGCCCCTTTCTGGACTCACCTGTGATCTTCCACTCACACTCTCTCATAATTAATGCTTTATCGTATGTGATGTCAGGGAGCCTACAAAACAGGAAGCTCTTTGTTTTTGATAAGCCAAACCAAAGTATCATTCACTGCCACTAAGTCTGGACTTCATTAGTTGGTGCCTTAGGTATAAGGGCCCCCGTGACCTGACCACTTCATTCTGACCTCTGAATGCCCGAAGTGCTTATGCTCAGAGGTGAGCCATTCCAAAGGTGCCCTTATCCCCTAGAAAAAAGATTGTTTTGTTTGTATTTTGTTTTGTTTATTTGTTTTTGCTCAGAAAGGAAGGCTGGGAAAGTAGTTCTGAAGAAATCAGGTCAAACTCAAGCCCTGGAGTTTCCTAACTGTGTGACTTGGGACAAGTTATCCAATATCTCTGAACTTCTCTGTACTATGTATAAAATAACACTAATAATGCTTTTGGGGGGGGCTTACCTGGGGAAATGAGGGAGTCGTGAGCTCCTGTCAGACATGAGACATAGTAGGTTCTCATATTCTTAGGCAGTGTGCCTTGGAAACTCTGAATGTGGACCACTGTCCCATACCCAGGCCCAGACTACCCTGCCAAAGAGAAAGTGGGAAGGCCTGAGCCACACCTCCCTGGGGATCTGGCTCTGTGATTGCTGGAAGATCCAGGCAGCAGCAACAGAAGTCCCAAGGTCACCTCAAATCCATATGAGAACACAGAAATAGTATAGTCCTAAAGGCCTGTGTTTGCCTGGGCAGGTCCCTCTGTGATGACCCAGAAGGGTAGAAGGTGGCTGAAATGGGTCTTACGTAGCCCATGGTGACAGGCCAAACTCTCCTGGAGAAAGTGCTGGAGGAGAGCAGCTTCTGTGCCCACCTCACACCCCTAGAGCTCTTAATCTTTTCCAGGTCAACAAAAGGTGGCCTAGAGGACACTCTGTGGCAAGAGAGCTGGACATTTCCTGGTGTGTTAGCAAGGGCAGATACTGAGCCCATGGTGGAAAGTGGTCCTCTCAAGGCTGGCAGAACTGTCCTTGATAGGACACTGTGTGCCCACAGGAGGCATTACTCAATGCCAGCTACAGTGTATGGGGCTATAAGAGGGACTTCACAGAGATAAGGGTTTGCTTGGGGACAGCCATTCTATCCCAGGGCCAGGATATGGACTCAGCAGCCTTGGGGTGCTTTGGGGTAGCTACAGGCCACCTCTTACTTGAGGCAGTCTTGCCATTCTTTCAGCAAAGGCACAGCTTCCTGACCTCCCCCAAAAGCTGACTGCTCCAAGGATAAAATACAGGCTAACTTAACCAACGTCTCACAAATCCATGGGAGAGGTCGTTGTTGTTGGTGTTTGTTTTGCTCTCTGACTTCTTTAAGAATTGAGGCCACTATTTTTTTGGGGTAGAACGCTCTGACAAGACCAGGCAAGCTTTGAAAGTAGTTTGTATAGCATGTTTTTGTTCTGCCCTCACAAAGCACTCAATCTTTAAGGAGGTGCCTGCCATGTTTCTCGCTGATGGTGCAGCTGCATTCTTAGGCTTTCCCCTGAGTGTGCTGGGAACATTGATATTCTGTCCCTGCCCCTGCAGGGCAGTCCACAATCAAAAGGTTGTGGCTTTGTTTCCTTGTTCCTCAGCTGGTGGAACTCTTCTGGTGAGGATCGGGAGGTGTGGCCTGGTTGGAGGAAGTGTGCCATTGGGATGGGCTTTGAGGTTTAAAAAGCCCCTCCCATTCCCAACTAGCTCTCTCTGTCTCGTGCTTATAGATCAGATGTAAGTCTCAGCTATTGCTCTAGTGCCATGCCTGCCTTCTGCAATATTCCCCACCATAGTGGTCATGGACTCTAACCCTTTGAAGCTATGAGCCCCCAAATTAAACTCGAAATAAATGCTTTTTCTTTTAAGTTGATTTAGTTACATTGTCTCATCACAACTGTAGAAAAGTAGGACACCCAGGCCTCCTGAGCACAGGGTGACATTCATGTTTCTCCTAGCTTTTTTCCTCGAATACGTAAGTGTATGTTTGCCATAATTACCCCGGTGCAACTGAAATGGAAGACGGAGACTAGTGAGAACTTAGAAGCGAAAGTCCCAATATGTCTCATGATCACAAAGGAGGCAGAGAAATCTGGCCACTGAGTGTTCACGCCGGATTCTCTCAGCAGCCCCACCCCCGCCCCGCTCATCAGAACTACCTTAAGATCAAATCCTCTCACAGGTATATGGCCTCAAAACTCCCAGCCTCTGTTGATTTCCTTTCACACAAGCGAATGCTTAGTTGTAGTAATGTCTGCAAAGCAGGCTCAAGGATGGATTTGGGTGGCGGAGGCCTTCAGAGAAGGTACCCTAGTAGGGAGGAGCAGAGGGAGAAGCTGGGGTGAGCTGCGTTCCGGTCGGTCTCCGGGTGACTGTGAGCTGGGCTAGCTTTCAACAATCTTAAAACAAAATGGTCTGTTATGAACCAGCCACACCAGTTGTAGGTTTGCAGGTTGCCGGGAGACCTTCTCCTCCTCCTTCCACAGCTCCCCAAATCTAGAACACACATGGAAGGTGTCGAGCAGGTACCAAGGGTGGGAGAGAATGGGTTGGATTAGATTTAGCTTGGTGGTGCCCCAGGAATCTGGGAACCGGGTTGGTGATGTGAAGCAGAAGAATCGGCTTCTGAGATCTGTACCCGTCTCCACTCTCTGTGCCTTCTAG
Seq C2 exon
TTCCAGTGGCGGTTCTCCCGGAACGACATCCACAGCAGGCAGACAAGGAAATCCAAAGGGAAACCCAGCGCCGGAGACAAGCAGCAAGCGGAAGAGAACGAGAAGAATCTAGACGACCAGTTCTCCAGGGCTGGAGATGCGGGAAACTGTGTGCTGGGGGCACAGCAGTGGGGCAGAGCCTCTGAGGTCAGGGAGCAAAGGCCGGGCTCAGCCGCCGTGCAGAACGGCCCCGCTGGCCACAACAGGGACTCGGTGACCCTTAGGCACTCGAATCCCAGAGCAGAGGCTGAGCTGGTTCCAGGCCCCGCTCCAACAGAAGCAAATTGAGTCAGTAGTTTGTGCCAGGCCTGCATTGTGATTGCAAACCTTGGGAAGCTTGCTAGCAGCTGGTTTGTTCTGTGTTGTTACCGTTTGGCTTGACCTCCCATTGTTAGCCCAATGGCCCTGTGAGGGCGGGTCTCCGAAGGTGGTGTTTTCTGCACATCCACTGGAAAGCTGTCTTAATGACCCACTTATATTAGAGGGCAAGGTTGGGCCGTTCCTCCTAGACCTCAGGGCTGGAGGCCTGGCTCCGGTCCCGCCCCTTCCACAAGGGAAGGTATGGGCCACAGTGCCTGCGCTGCCCCACAGGGCGCCAGAGCACATCTGGGTCAACTTCTGGGACATCCTTCGCTACAAACCAAGGTTTTTCTGCTCACTCCTACGTGCTGCTGCTCTGGGCAAGAACTTAGTGACTTTAACCCTGCAGCCTGCCGGCTGGCCTCTCCACCTGAACTCTGGAGACCCTGCTGATGTGGAAGGCAGAGATGTTGGAGAGGAAGCCTCCTGCCTGTCTTAAGATAGTTATAAATAGGGGTTGGGGATTTGGCTCAGTGGTAGAGCACTTGCCTAGCAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCAGAAAAAAAAAAAAAAAGAAGAAGAAAAAGATAGTTATAAATACTGGCGATCTGGAAGCAAACAGGTAATTCCCTACGGCCCGGCTCTTGTTCAAGAAAGTATTCTGTGTTAATGTTAATGCCAAAAAAAATGTTTTTAAATTTTGTCTTCAACACATGTACGAATATGTTGTCATTTTTGAGCAGTTGGTAACTGGGTGCCCTCGTGTGCTATTTCTGTTGACGTGTCATTGACTGAGTTGTACGCCGTGCCTGTCACATGTTTAAACTGTCCATAAAGTGTTGTTAAGGCTTTAAGTAGAAGCATCTGGCAAACCGTGGAGAGAGAACACCAGTTGTCTCAATGGAAACAGCCCTGTCTCTTTCTTGTTTAGTTATTTAAAGCAATAAAATGACCTGAGTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000011321:ENSRNOT00000015210:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.907
Domain overlap (PFAM):
C1:
PF152501=Raftlin=FE(5.6=100)
A:
NA
C2:
PF152501=Raftlin=PD(7.8=34.9)
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]