RnoINT0068922 @ rn6
Intron Retention
Gene
ENSRNOG00000016659 | Habp2
Description
hyaluronan binding protein 2 [Source:RGD Symbol;Acc:1302979]
Coordinates
chr1:277099160-277100766:+
Coord C1 exon
chr1:277099160-277099302
Coord A exon
chr1:277099303-277100631
Coord C2 exon
chr1:277100632-277100766
Length
1329 bp
Sequences
Splice sites
5' ss Seq
TCGGCAAGT
5' ss Score
4.02
3' ss Seq
CCCTTCTGTCTCTCATCCAGCTT
3' ss Score
9.47
Exon sequences
Seq C1 exon
CATGAGCACCAAGCATCTGAAAGTTGTGCTGGGGGACCAGGACCTGAAAAAGACCGAATCCCACGAGCAGACCTTCAGGGTGGAGAAGATACTGAAGTACAGTCAGTATAATGAAAGAGATGAGATTCCCCACAATGACATCG
Seq A exon
GCAAGTATCGTCCCCCCACACCTCCTCCTCTGGGTCTTATCCTGGGTGGATTTCTCCACAGATAGGAATCTGGGGTTTGACTTTAGGAAGTGCCCTGGAAAAGTTTGGTTTTTAATCCCTCGGGGATCCTGTAATGTAGATAATTTATTTCAAAGCTTGTATGACTTGGGAGTATATGAGAGTGTCTTAGTTAGGGTTTTACTGCTGTGAACAGACACCATGACCAAGGCAAGTCTTATAAGGACAACCTTTAACTGGGGCTGGCTTACAGGTTCAGAGGTTCAGTCCATTGTCATCAAGGCAGGAACATGATATCCAGGCAGGCATGGTGCTGGAGAAGTTCTACATCTTCAACTGAAGGGTGCTAGCATAATACTGGCTTCCAGGCAGCAAGGATGAGGGTTTCTTAAGCTCATACCCACATTGACACACCTACTCCAACAGGACCACACCTTCTAATAGTGCCACTCCCTGGGCTAGCATATGCAAACCATCACAGCAGCACTGTTGATAATTGCGTGAAACTTTTCCATGGAAGGGAAGAGATGTGAAGAATATGACATCATGGAAAGCACCCGGCCTTGAATCCCAACTCCCCTGCTTAATAGCTAGGATTCAGGTTATCTTCCTCACCCTTAGTTTTCTGTTCCATAAAATGGGGGTGCTGTTACACAGCTTCCAGTTGACTATGTGTTGTGACACAATGTGCATGTGCACATGTGTGGTACCTACTAGGTGCTTGTGTTGTGACACAATGTGTATGTGCATTCGTGTAACACCTACTATGTGCTTGGGTGCAGAGGCTGTGCTGTTTTCAGCTGTTGAGTGTTCAATTCTGTGGTTCCCTGACCCAGTCACTTTATGGGTCTTCTCTCTTTCATGTTCTCTTTCTCTCTCTGCCTTCCTCCTCCTCTTCCTTCTCTTCTTCCTCCTCTTCCTCTTCCTCTTCCTCCTCTTCCTCTTCCACTTCCTCCTCTTCTTCCTCCTCTTCCTCCTCTTCTTCCTCTTCTTCCTCCTCTTCCTCCTTCTCTTCCTCCTCCTCTTCCTCCTCTTCTTCAATAGCCCCTCCCACACAGCCTGCTTTTGAAAAGTGAATCAAGAATGATTTTGAATCCAAATAGTTACATTGACTGTTAATATTCTTTTTGTGTTGAGTTGCCCCTTTCTGGAAGTTTTAAAACACAAAATGTGGATGAAAACGTTTCTCAGTTGTGGAAGGAGTAATATGGCTTGCTAACTCACTTTCTAATGCAACACAAAGTCAATGATTCCCTGATCAAGGGATGACATCACACCCAGTCCTCCCCACCCCTTCTGTCTCTCATCCAG
Seq C2 exon
CTTTGCTCAAGTTAAAGCCAGTGGGCGGTCACTGTGCTCTGGAATCCAAATACGTGAAGACTGTATGCTTGCCTAGTGACCCCTTTCCCTCTGGGACTGAGTGCCACATCTCTGGCTGGGGCGTAACGGAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016659:ENSRNOT00000022382:9
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=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(20.3=100)
A:
NA
C2:
PF0008921=Trypsin=FE(19.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCAAGCATCTGAAAGTTGTGC
R:
CTGTTTCCGTTACGCCCCAG
Band lengths:
271-1600
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]