RnoINT0068921 @ rn6
Intron Retention
Gene
ENSRNOG00000016659 | Habp2
Description
hyaluronan binding protein 2 [Source:RGD Symbol;Acc:1302979]
Coordinates
chr1:277097905-277099302:+
Coord C1 exon
chr1:277097905-277098160
Coord A exon
chr1:277098161-277099159
Coord C2 exon
chr1:277099160-277099302
Length
999 bp
Sequences
Splice sites
5' ss Seq
CGAGTAGGT
5' ss Score
5.76
3' ss Seq
CATCTCATTTTACCTTGTAGCAT
3' ss Score
8.18
Exon sequences
Seq C1 exon
ATGCTGCTAACCCATTGGGCAGCCTTCAGGAACCTGTGATGGAGCTGCCAGGATTCGACTCCTGCGGGAAGACAGAGATGACTGAACACGCGGTCAAGCGCATCTACGGGGGCTTTAAGAGCACAGCGGGCAAGCACCCGTGGCAGGTGTCCCTGCAGACCTCATTGCCGCTGACCACCTCCATGCCCCAAGGCCACTTCTGTGGGGGTTCCCTGATTCACCCTTGCTGGGTGCTCACTGCAGCCCACTGTACCGA
Seq A exon
GTAGGTACCCATGGGGAAGGGAGAACAACGTGACTGGGATGCAGACATCTTCCCACCAAGTGATACCCACCCAGCCTCGCAGGCCTGGGGCTAAATGCCATGAGGGGAAAGAACAGCGCCTTGAATGAGAGTGGATGTAGCTACCGTGGCTTACCACAGCTGTTCTCTGAAGTTTAACACATATAGCTAACTACCAAGAGAGGGCAGGGTTTGTGTGTTTTGTTAACTGTGAGATCCCTGATGCCTTCAGTACAGAGTTCTTTCCATGTAGCAAGTACTTAGTACTTATGTTGAGGGAAAGACATATAGTTGTTCTCTTTTTATGAGACTTGGGTTTTAGGAAAGTCTTAACTAACGTCTCATGGAAAGAAGGCCGGTGAGTGAAACTGAACTCAGGTCTGTCTTCTTCCTGAGCCTCTTGAGTCTACCCTGAATGGGCAAAATGGCTTATTACCAGTGAACCTCCAGGTCAGGCATTTTCATCTGTATCTCTGGTGACTTCTGGGAGCTGAGAAATCACCACCTCTTCCTTCCAGATCTCTGAGTTCATGGCCAGGGCTGGTCTCATGAGCCCCGGCTTGAGATGCAGCGTGCACATTTTCTAGTCTATCCTATCCTCTGGGGTTCTAGTGTGGTCTCCAAGAGGAACTAGACACATAAACATTAGCACCTACCCACGAATTACAGCAGATTTGCTCGAGCCTTCAATGGCTGACTTCTAGCCAATCCCAGAGAGAAAAGAGATCTCCCAGGTCAAGTGAGTGTGTGCCTGTACTCTCCAGCCACTGATGTAGAAGTCCCCTTGAGTTGTCTTATCTGGAACCGGAACAGATTTTTTGTAAGGGAGCGAAGGACCACAGATAAGGATGCTGAGACTGAAGGTCACATGACTTTACCAAGGTCACATGACTTTACCAAGGTTGAATGGCTTCCTAATCACATAGCTCCTGCCTTTGACATCCCAAGGCAATTTCCTCAGCATCTCATTTTACCTTGTAG
Seq C2 exon
CATGAGCACCAAGCATCTGAAAGTTGTGCTGGGGGACCAGGACCTGAAAAAGACCGAATCCCACGAGCAGACCTTCAGGGTGGAGAAGATACTGAAGTACAGTCAGTATAATGAAAGAGATGAGATTCCCCACAATGACATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016659:ENSRNOT00000022382:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.012 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=PU(21.5=59.3)
A:
NA
C2:
PF0008921=Trypsin=FE(20.3=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:
GATTCGACTCCTGCGGGAAGA
R:
CGATGTCATTGTGGGGAATCTCA
Band lengths:
348-1347
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]