RnoINT0068913 @ rn6
Intron Retention
Gene
ENSRNOG00000016659 | Habp2
Description
hyaluronan binding protein 2 [Source:RGD Symbol;Acc:1302979]
Coordinates
chr1:277100632-277102312:+
Coord C1 exon
chr1:277100632-277100766
Coord A exon
chr1:277100767-277102166
Coord C2 exon
chr1:277102167-277102312
Length
1400 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
GACTGTTTTCTGTCCTACAGGGG
3' ss Score
10.46
Exon sequences
Seq C1 exon
CTTTGCTCAAGTTAAAGCCAGTGGGCGGTCACTGTGCTCTGGAATCCAAATACGTGAAGACTGTATGCTTGCCTAGTGACCCCTTTCCCTCTGGGACTGAGTGCCACATCTCTGGCTGGGGCGTAACGGAAACAG
Seq A exon
GTGAGTCTGCCTCATGCTCCCCATACACACAGGAGAGCTGCACCATCCAGAGAATAAAGGGCCAACGGCATCTGCCCTCCTGCTCTTGAAACACATTCAAGATGCGTCATCAGAGAACGCATCTGCCTCATTGCTCAGGTCCCAGTTGAATGCAACCATTTATATGGGGCATGCTCTGTAGGTCTCTGGTCTCCACAGTGGCCCCTGGCCTCCTGTTCTAGACATGTGACCTTTCTCAAGCACTGGCTGCACACCAGGGAAGACCACTCCCCTTCTCTAAGGAGATTGCAGAGACGCTGGGCACGTTGCACCTGTGGGCACCTGTGGTGCCGGGCAGGTACTCAAGGGCAAAGATAATGCCGTTGTGAGCTACTAGCCTTGGACCCCTCTTCAATGTCAGTCCTTCTTGTAGAAGAGTCTGGGTTGTTTCTCAAGCCGCTCCATTTTACTTTCTCAGTTGTCATTTTTACCTGCGGGGCTTGGATTATGTGCACCGGATTATGTGTATATCTTGAATACAAAGAAGTCCATAAGAATATTTTCAAGTTTTTACCAAACACTCAAAATATGTCACCTCTTAGTAGTATCCTTAATAACGGACAGAGGAAAAAAAATCACTTCGAAGAGGTTTAGTTTCATAAAGAAAGGGAAATAGAATGTATGGGACACATCTGCCAGAGGCTCAGGGGGAAGAAAATCTCTGACTAATTGGACTCAAGGTCAACCAGGAAGGTTTCTGTGGCTCTTTGTTGTAGCCTGTCTAAACCCCTCCACTTTCGCTCTCCTCAATGGGGTCTGCTCAGCATGGTGATGTCTCAGTTGGGAAGCCGGTAGGGCCTCAGATTAGAATGCTTTTATTTTTCCACAAATAGCTCTTAAGATTACATTTTCAAAGTCAATGATACTTTGAGCAATTTCATTATCTTTAAGAAGGGGAAATATCTCTCTAGGAAGCAGATAGTTTAATGTATCGGGGCACCTCAGCCCACTCGTGTATGTATGCATGAGTCCATCTGTCCATCTATCCTCATCTATCCATGCATTCATCCATTCATTTTTCCAGAACCTACTATGTGTTGGCTCTTCTGGTAGATACAGGAAATTTAAAGGTGGTTACGAGCCAACCCCACTTTCCAGAATTCATGAACGGGTTAAAAAGGCAGAGAACAGAGCAGATGATTTGCCCAACTGTGATCAGAACGGCTTAGAAAGTGCCCAAGCATAGGGAGGGGAGGATGCAGAAAGGTTGACTCTAGTGTTGGTAAATTCATTTCTCCCCATCCTCCATAAAAACACCCTTTTCCCTGAACTGAGAGTCAGTGGTTTCTTACTAATGGTGACTTCTAGTAGGGTGGGTATCATTCCGGTCTCCGTGGTAGTGACTGTTTTCTGTCCTACAG
Seq C2 exon
GGGAAGGCTCCCGCCAGCTCCTGGATGCTAAAGTCAAGCTGATTGCTAATGCTTTGTGCAACTCCCGCCAACTGTATGACCACACGATCGATGACAGTATGATCTGTGCAGGGAACCTGCAGAAGCCTGGATCGGACACCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016659:ENSRNOT00000022382:10
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=0.027
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(19.0=100)
A:
NA
C2:
PF0008921=Trypsin=FE(20.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTCAAGTTAAAGCCAGTGGG
R:
CTGGCAGGTGTCCGATCCAG
Band lengths:
278-1678
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]