RnoINT0068914 @ rn6
Intron Retention
Gene
ENSRNOG00000016659 | Habp2
Description
hyaluronan binding protein 2 [Source:RGD Symbol;Acc:1302979]
Coordinates
chr1:277102167-277104566:+
Coord C1 exon
chr1:277102167-277102312
Coord A exon
chr1:277102313-277103941
Coord C2 exon
chr1:277103942-277104566
Length
1629 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGA
5' ss Score
7.41
3' ss Seq
CCCTTTTGTTCTTCCTTTAGGGT
3' ss Score
12.68
Exon sequences
Seq C1 exon
GGGAAGGCTCCCGCCAGCTCCTGGATGCTAAAGTCAAGCTGATTGCTAATGCTTTGTGCAACTCCCGCCAACTGTATGACCACACGATCGATGACAGTATGATCTGTGCAGGGAACCTGCAGAAGCCTGGATCGGACACCTGCCAG
Seq A exon
GTCAGAAACTCCACGTGGTGCTGGAGGTAGAGGCTCACTGAAGATCAAGCTGAGTGGAAAGGCCTATGATAGCACTGGGATGGGGACCGGGGTCAACAGGCCACCTGCTTCAGCCTTAAGACATAGGTGGGCATGCCCATCTGAGCCTACATCAAGGTGGGTCAGCATAATAAGTGTAACCGCATGTTGCTGCTTTGTCTCGTCTTACTCTCCCAACATCCTGTGAAGTGGGTGTCACCATCGCGTATTACAAAGGCCTGTAGACATTACCAATGTGAATAGCAGCAGAGTACTAAGCGACAGATAGGACGGAGATCAGAACAACCCAGGGCCTTTACTGCTCTGCTCCGCTCTTATAACAGCACATCCTCAGCTGCTGAGGTCTATGGAGATCCGAATGCGCTCCTGCAGGTGGTGACTCCATCAACTGTAGGCTAAGGGGACCTCAGATCCCTGCCCTGAATCCAAGCCCACACCCCATTTAACTCCAGCCTTGTGTCCCAGGGGATACATTGTCCCTAGACTCCCAGGATGGGCTCTGTTTAGGCTTTCTGCTTGTCCTTACACACTGCCCAACTGTCCTCGAAAACCCCGCATAGCCACACTCTGATCCTGTGCTGTGGTAGAGCCTCCCTGTGAATGGATCCAATGATAATCAGACAACTCAGAGCCTGTCTGGGTTAGGAAGCTGGAGTTTCTCTCTCCACAGACCATGACTCTGTTTTGATCCCCAAGGGCCCATGGATAACCACATACTCAGGATGGAGAAAAGCGTGTGGGTGTGGTTTTCCCTGAGCTCTTGGAAGATAAGCAGGTTCACCAGGATCACAGTGCGCTTGGTTTTCTACGTAATTCAAGGGCTGTGCTGAAAGGAAGCCAGCAGCCACGGTTTTGAAGCCCGACTCTATCTCATATTATAGGACCTCAATCAATCCCTGAAAAGATGTGTCTAACTTCAGTTACTTATAATGTGAACGACCGTAAGGTCACAAGGCATTGGCTATGATTAGGAGAGCAAAGTTACGTGATAAAAGCTGGTGGTTGTGGTGAATAAGCTGTGGTGACTAAGCAGGCTGTTTTCTCTTTGCTTCCCTCCTGCCCATCTCTGCCCTGGCCTACACACTTCAGAAAGAACCCCCATGATTCCCCTCAGGAGCACAATTCCTCTATGGTTCTCCACAGCTCTCCACAGAAAGAGCAAGGCCTCAGGTCACTGGGCAAGAGGCAGTAGGTTAAAGATATAGGCTACTTCTAAGTCTCTGCCTGACTCCCTATAGGTGGGTCCATCCAAACAAACCATCACCTACCTTGGTCAGCTACTGAAAGACGTTGAGGAACCCCGGGAACTGAAAATTCTAGAAGGGAGAGTCAGGAAGCACTACTTGCCCACAGCACTGTGGATGCAGCCCTGGGCTCCCAGCTTTTTCCAAACTCAGGAACTGAAGCTGGGATTAGCTTCTCTCCCTTTGGAGCTGTGCATCATGGGAAACTTGAGAAGACCCTCGGCGCTGGTTTCCAGAGAAGCGCAGGGTAGCTAGCAGGCAACTTTGTTCCACCCTCCCCTTGGAGGCAGTTTGGGTTATGTCTGTATCTAGTTCCCAAGGCTGAACCCTTTTGTTCTTCCTTTAG
Seq C2 exon
GGTGACTCGGGGGGCCCTCTAACCTGTGAGAAGGATGGAACTTACTACGTCTATGGGATTGTAAGCTGGGGCCAGGAATGTGGGAAGAAGCCTGGAGTCTACACTCAAGTCACCAAGTTCCTGAATTGGATAAAAACCACCATGCACAAGGAGGCTGGCCTCTGAGGTGCTGTCTGCAGAGCCTCGAAGCACCTCCTCTTCTGCACTAAACAAGGGGGTGCTTCCTGTGTAGCCAAGGATATCCTGGGTCTATGCTTTAGACAGAGACATTGCTGACCAGCCTGGGTCTTTGCAGACTGGCACTACACCACCTCACGAGGCCCACTCTGTCCTCCTCTCCCTGAGAACCAACAAGAAATACATTACCTCTGCCCCGCTTCTGACAAGTGTGCCTTCGAGAAAACCAGAATTCAGAGATGCTCTCCACCATAAAGACCTGCAGATCTGAGATTTCTCCCTGTCCAGTACCAGAGGAGACTGTTACTCTTCTGCCCACACCATCAGGGTCTTCCGCAGTCTCCATGCAGCCATCAGAGAGAAACCCCCCCCCCCCCCGCCAAGGAAAAAACACAAGTTCTGTTTGCTTTCAGAGTTGTTGTTTTAATAAAGGCAGATGTGGGAATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016659:ENSRNOT00000022382:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.027 A=NA C2=0.005
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(20.3=100)
A:
NA
C2:
PF0008921=Trypsin=PD(18.1=78.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACCTGCAGAAGCCTGGATC
R:
GGTGTAGTGCCAGTCTGCAAA
Band lengths:
343-1972
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]