RnoINT0069123 @ rn6
Intron Retention
Gene
ENSRNOG00000049949 | Hapln4
Description
hyaluronan and proteoglycan link protein 4 [Source:RGD Symbol;Acc:1308408]
Coordinates
chr16:21081377-21085681:-
Coord C1 exon
chr16:21085358-21085681
Coord A exon
chr16:21084165-21085357
Coord C2 exon
chr16:21081377-21084164
Length
1193 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
CACACTCTCGGGTCCCGCAGGCC
3' ss Score
9.01
Exon sequences
Seq C1 exon
GGGTGGTCTTCCCCTATCACCCGCGCGGAGGCCGCTACAAGATGACTTTCGCGGAAGCCCAGCGCGCTTGTGCGGAGCAGGACGGCATTCTGGCATCTGCGGAGCAGCTGCACACGGCCTGGCGCGATGGCCTGGACTGGTGCAATGCAGGGTGGCTACGCGATGGCTCCGTGCAGTACCCGGTGAGCCAGGCCCGAGAGGCCTGTGGCGGATCTGGGAGCCCTGGGGCTGGTGGCGGCACCAACGGGGGCGTGCGCAACTATGGATATCGTCACAACGCCGAGGAACGCTACGATGCCTTCTGCTTCACGTCCAACCTCCCCG
Seq A exon
GTGAGTTAAGCGTTTTCTAAAGAAGCGGGTCTCGGGGGTTGGGGATTTAGCTCAGTGGTAGAGCACTTGCCTAGCAAGCGCAAGGCCCTGGGTTCGGTCCCAGCTCAAAAAAAAAAAAAAAAAAGAAGCGGGTCTCCAGCGCTTATTTCCTGCTTTCTTGAAGGAGACCCGCCCCCAAGGGCCTAGGCCCCACCCCTAAATACATAGGCTTCTCCCTGAAGGGGACCCTTCCCTCCCTCCTTCCTCTTTAACATTATGCCTTCTCCCTGGGGAGGAGACTCAGAAAGCCTGGCCCCACTCCAGATGCATACAGTCCCAGTCCCCCAGAATGAGGTCCGCCCCAGGTGCATATGTCCCGCCCTTTAGGGAGAAACTCACCCCAAGTGCCTAGACTCCAACCTTTTGAGGAAGACTGGTCCTAACCGCCTAGCCCTAGGGCCTGGCAAGTGGAGAGAAGTCTGTCTCAGAAACATAGACGAGAGCATAGTCCCCAACCCTCCGGTTCTTCTCTCTTGAGGGAAGACCTCCCCCACGGACTACGCCCCAAGGAGTTAGGCACATTTTAAGCCCAAAGCCTCCCATCCCCGCCTCCCCGAGGAAGAACTGTCCAAAATACAAAGAGCCTACCCTGTGGTCGAAGGTCCGTTTCAAGAGTGTGGACCCGGGGTTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAAGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGGAAAAAAAAAGAACCCCAAAAAAAAAAAAAGAGTGTGGACCCAGCCCCCTAAAAGAACACAGATCCTAAGGACGTCTAAGGACGTAGACACGACGCTAAGGCATAAGGACACTGGCGAAAACCTTCCCCAAACATAGGTCCCGCCCCAAATAGGAAGCCTGCCCAATGGACAGAGATCTCCCTGAATTGCATAGACCCTTCCTCCAAGACCATCGCCCCCTACCAAAGTGAGCAGGCCCCGCCTCCGCCTTGCCCTCCGCTGCTATGAAGACTGTTTTCCAGGGCTGCCACATGGGGGCAGTGAAATGCCAAATGGTACCGGCATCGCATCGGGAAAAAGCGGAGGTCCCAGGTTGCAGGGAATGGGATGGACTAGGAGCAGGAAGCCCCAGGATGCTGGAGCACGCAGCGGGCCCATCCCTGACCCGACTCTGACACACTCTCGGGTCCCGCAG
Seq C2 exon
GCCGCGTGTTTTTCCTGAAGCCGCTGCGACCTGTGGCCTTGGCCGGGGCCGTGCGTGCGTGTGCGGCACGGGGTGCCACAGTGGCCAAGGTCGGGCAGCTCTTCGCTGCGTGGAAGCTGCAGCTCTTGGACCGCTGCACTGCGGGCTGGCTGGCGGATGGCAGCGCGCGCTACCCCATCGTGAATCCGCGAACTCGCTGCGGAGGTCCTCGGCCCGGCGTGCGCAGCCTCGGTTTCCCTGACGCCTCCCGTCGCCTCTTCGGTGTCTACTGCTACCGCGCTCCGGGTGCCCCAGACCCAGCTCCAGGCGGCTGGGGCTGGGGCTGGGCCGGCGGAGGAGGTTGGGCCGGAGGGTCGAGGGATCCGGCTGCCTGGACCCCACTGCGTGTCTAGATCTCGGAGGATGCGCGTTTGGGGGTGTTGATGGCTGATCCAGGGACCTCATGCACCCCCTGGATACCGAGCACGTTTCAGAGTCTCAGAGCTCCCTTGGACAGACCCATGCGGTGCACTGCAGGCTGATTTGGCTACCTGTGGTCTTTGGACATTGACCACACCTAAAGTTTCCTGGCTACGTGACATAACTTTTGCCTGTGGTGAGCTGCAGGCTGACCCACCTGTTGTGGTCCTTGGTCGCTGACTATGATGCCCTCTGAGGATCCCTGGTAGTGGCCAAGCCCACTTCTCTGGATAGTGGGTGACTCATCTTTCATACTTTGTCTAGAAGAGTCATGCTCTCTCCCAACCCCCAGGATCCCAGTAGACCAACAGGACTCTACGGTTTCCTAAAGATGAGCCCCGCCCCCTTTTTGGGCTCCTGAAGAACAGGTGGATGCTTCCTCTCTGTCACCTGGAGGCTGGACCCCCAGGATTAACTGGAGACCTGCCCCCCAACCCCTCTGCATTACTGGGGAGCTTGAAAACTGGTCTTGGAGAGTCAAGGACTTCTCCCCATCACCCGGTGAAGAAATAGAAAACTGTGGTTCACTCACGAGGTGATCATGGCCTGTGTGGGCAGGTGACCAGAGGCTGGGTGTTCCCACTCTTCCAGAGAGTCTCTATGTTTCCGAGGTAACATGCCTTGTCCCTGGGTCACTATGGAGGACAGACCCAACACCTCTGGCTTCATAGGAGAATGTTCCCAGCTGGCTCCCCGGAGCAGTGGCCATGCCTATCCCTCAGGTATTCCCTCTGGCCAGAGAGTAGACTCGCCTGAATGTCCCGTCCCTGGGCTCCTTGGGGAATATCACCAAAGAGATTGTTCCCTCAGACCAGAGACCCCTAAGAATCTGACTTGTAGAGACAAGCTGCTCGGCTCCTTAAGGTCACACAGGCCACCAGTGCAGCCTTACCCGTCTCACCCGCTACACCCACGGAAATGGCACTGTCTGCCTTTCTCTGTAACCATGGTTACCACACATTTCCTTTCTCACTGGCCTAAAGCCCAGACACCTATCACTTCATTTTTGGCTGTCCCTGCCCTGGTGGACCACCGTGGAGACAATCTTCCCCATTGAGTGTCCTCAGGGGAACCCAGCATTCAGTTCTCCAGGACTATTCCGTGGATCAGCTGCCCCTTTCCCAAAGTGCACCTTGTTTCTCTCAGCAGCCCAAGCCCCACCCCTAGACAGTTTGAACCTCCGGACCGTTGTCATGGAGATCAAACTCTGGTGTCCAAGGAAACAGAACACCTGTCCCTTCAAGGCTTTCCCTCCAGGGTCCCATACTGTCCAGCTGTTGCCATAGAGACCGTCAGTGTCTCCATGACAACTGACCTGCAGCACTCAGGAACTTCTTGCTATGGGCAGAGTACCTCTATCTGGAGCTGCCTAATGTGTTCCTCAGGCGCCTGACAAATGTCCCTTCTTCAGACGGGCCTATGCAGGCCTCCGCTTGTGGGCCAGCTGCCTGCCACCACCCGTTTGCATGCTAACTCTACTCTCCACGCAGCAGCCAAGCAGGAACCACCACTGCAGCCCCCTCCAGCATTTTAAATGTTCACCCTGCAGATGAGAGAACTGAGGCTGTGGTGCTGTACAAGCTGACCTTTCCTTCTTGAAGATCAAGGAGGGCAGACTCTCCCTGAAACCACCAATTTCAACCCATTTCTGAGGGCCCATTTCTCAAGGGTCAAGACCAGCCCAAATGCAGGAGCCTCCAGTTCTCAGGTGCTGCTGGGACCAGCAAGTACCCTTGCCCACACACCTTCCTGCCTGACCCATCTATCTCGGTTAACTCCACCCCTAAGTCTGGAAGCTAAGGGGCTGTGGGCTCCAGTCATACCTTTTGTTCTAAAGTATGCAGCCAAAAACTCACCCAGGCTCTTCTCTGGACTAGGATTGTTCTGAGGTTCCTGAAGCCCAGGTTCAATAAACCTTTGTTCCTTCTGATGAATGCGAAACGAGGCTGCCGGTCCCTCTATCAGTGTGGTGGAGTTCTCAGGCCAGGTTCAGAAGCAGCTCCTCTCCCCTTTCAATGCTCACAACCTGAGCATAGAAAAGCGGAACAGTTTACCAGGTGTCAAGACCAGGACCCTTTGAGGTCCTGTCTGACTCCTCATGTGCTCTGTGGCATGAGTGCATACACATAACTCATCATAACATGATTTTAAACATGTTAAATAGGTTCTGGCTGTAAATTGAGGTAGTCATCTAGATTTTTATTTTTCGTTTCTTTGAGACAGGTTTTCACTGTTTAACCCTTGCTGTCATGGAATTTGCTACACAAACCAGTCTTGACCCTGAACTCAGTGATCTGCCTGTCCCAAGTGCTGATTAATGGCGTAAGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000049949:ENSRNOT00000072565:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.092 A=NA C2=0.023
Domain overlap (PFAM):
C1:
PF0768612=V-set=PD(0.1=0.0),PF0019312=Xlink=WD(100=94.5),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=70.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCGTGCGCAACTATGGATAT
R:
CAGTAGACACCGAAGAGGCGA
Band lengths:
347-1540
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]