DreINT0076421 @ danRer10
Intron Retention
Gene
ENSDARG00000003903 | hapln2
Description
hyaluronan and proteoglycan link protein 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8089]
Coordinates
chr16:29372332-29374324:+
Coord C1 exon
chr16:29372332-29372514
Coord A exon
chr16:29372515-29374046
Coord C2 exon
chr16:29374047-29374324
Length
1532 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAG
5' ss Score
5.73
3' ss Seq
CCCTACTTTTGCTTTCCCAGGCT
3' ss Score
8.6
Exon sequences
Seq C1 exon
CCTGGACTGAAGGATTAGACTGGTGTAATGCTGGATGGCTGATTGACGGGACGGTCAGTTACCCTGTCTTGCACCCACGGCCGGCTTGTGGAGGGGATCTTCTGTCAGGCATCAGGAGTTATGGGCCTCGTCACAAAACACGGGAGAACTATGATGCTTTCTGCTTCACCTCCACCACTAAAG
Seq A exon
GTGAAGTAAAAAATGAATGGAGATTCTGTTTTGATGGGCTTCAGACAATGACAACACCTGTTTCACATTTACATGTTCTTAATGTTAAAACACAGTAATGTTAGAAGTCTATGAACTGTACATTGAACTGTTTATACCAGGGGTGCCTAGAGGGCCAGTGTCCTGCAGATTTTAGGTCCAACTTGCTTCAGCACGTGTGCATGGATGTTCCTAGAAAGCCTAGTAAGAGCTTGATTAACTAGCCCAGCTCAGGTGTATCTGATTGGGGTTGGAACTACACTTTGCAGGACAGAGACCTTCCAGGGCCGAGTTTGAGCACCCCTGGTTTATACAGTACCACCCAAACATTTTGGGCGCCAGTAAGATTTTTCTCTAAAGAAATGATCCAGTGACAAAAGTGTAATGATTTCGGAAGTATCATGAGACATAAAACAATAATTCAAATATCAAACACTTTAAGCCTTGGTGATCCAAATATCTTTTAAAAAAAAAAAAAAAAAAAAAAAAAACACTCACACTTACACACACACACAAACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACTCACACACAGATTTACAGGTGAGATTTACTAAACTGTTTCTCTTTACAACAAAAAACGATTAAAAACACAGCTACTATTTGTCCCCCCAACAGACTAGAAGAGAAAAAGCCAATCAGCGCTGTTGTTTTTGTATTTAGGAAAGACAAAGAGTCTCTTACTCTGAGTGACATCTCCCACTTTGCCCACATGAGTCTGTTGATCATGGCATTGGAGAAATCAATGTCAAAAACAAAGATTCAGGAATTTAGGTTTAAAGTGGTTTATTGTGCATATCAGTTCTTTTTAGGATATTTTACACTGTCCACTTTATTAGGTACATGCTTTCAACTGCTTGTTAACACAAATATCTAATCATCTAATACATGACAGCATCTCAATAAATTTAAATTTGTGGTCAAGTATGGTGACCTATACTCGGGTTATGTGCTCTACATTTAACCCATCCAAGTGCGCACACATTTGTGAACACACCCAGAGAAGTGGTGGAATCAGTGCCTTGCTTAATGGACTCACCCCAGCCCTGGTGTTCACTCTCACCACCAACAATCCCTGCTGGATCCGAAACTTAAACCTGCAAATCTTCCAATTCTTCCAAGTCCAACTGTCTAACCATTAGGCCACAGCTGCCCCAATTTAGGCTTGTTGATTTGAACAAGATGATCTTTCGAAGTTTAAACCAAGGATCAAAATGTAGAAGAGAAGACCATTTACATGAATTTGAACATGGCATATTTTATGGTACAGTATGGGCTGGTCTGAGTATTTGAAAAACTGCTGATCTGATACTGGAATTTCCATGTGGAATAGTGCAAAAAATGGTCCACCGGGTTGAATCAGAAGTAAAATGTGGTCCGGCCAAAAAAAAGTATGAATGTAAATGCATAAAAGTTAAAACAATACCCTACTTTTGCTTTCCCAG
Seq C2 exon
GCTCTGTATTCTTCATTGAGGGCCAGCTGAATTTTGCAGAGGCTGAACGAGCCTGCAGACGGGATGGTGCTGGACTAGCCAAGACTGGTCAGATCTACTCATCTTGGAGGTTTCAACAGCTGGACCGCTGTGATGGAGGCTGGTTGGAGGATGGCAGTGTACGATTCCCCATTATCAACCCAAGAGAACACTGTGGAGGGATTGCAGAACCGGGGGTTCGTAGCTTTGGGTTTCCTAGCAAAAGCATGCGTCTCTATGGGGCTTACTGCTACAGGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000003903:ENSDART00000087149:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0019312=Xlink=PD(57.9=88.7),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=97.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGTCAGTTACCCTGTCTTGC
R:
GGTTCTGCAATCCCTCCACAG
Band lengths:
343-1875
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]