DreINT0076428 @ danRer10
Intron Retention
Gene
ENSDARG00000018542 | hapln4
Description
hyaluronan and proteoglycan link protein 4 [Source:ZFIN;Acc:ZDB-GENE-060503-243]
Coordinates
chr22:17804057-17806275:+
Coord C1 exon
chr22:17804057-17804359
Coord A exon
chr22:17804360-17805227
Coord C2 exon
chr22:17805228-17806275
Length
868 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
TTGTTGTGTTTCCTTTGCAGGAC
3' ss Score
12.93
Exon sequences
Seq C1 exon
GTGTTGTGTTCCCATACTACCCTCCATCGGGACGATACAAGCTGAACTACCATCAGGCTGAGGAAGTGTGTCGAGAACAAGATGCAATCCTGGCCTCCCATCCACAACTACACAAGGCTTGGCTTGAGGGTTTAGATTGGTGCAATGCTGGCTGGTTAGAGGACGGCTCAGTCCAGTATCCCATCTCCCACCCCAGAGACCAGTGTGGCCGCAAAGACAGCCCTCCAGGTGTCCGCAACTATGGCTACAGGCACAAAGACGACGAACGCTATGATGCTTTTTGCTTTACCTCCAACCTCAACG
Seq A exon
GTGAGTGTTTGTCTTTTCCAGCCTGAGGCTGTTGGACTACATTCCTGTTGAGAAGGTCTTTCTTTCAAAGACTTATTTTTGATACTTGTCCAACAAATGTTTCCAGAGCCACAAATGAAGGAGTCTTAACTTAGCAATACATCAGTTCCTGTAAGAATTGGTCAAATCAAATCCAGTCTCAGAGAAACTATGACTTAGTACAGCTTCTGGGGTGCAGACTCACTTTGTGACGATGTAGGAATAATAGGCCTTTGTACAGTTGAAAGTTGAATTGATTTTATCTTCAGGAAGAAATCTATTTTTTGGCCCAAATTCAGACCATTTGTCAGTAAGTGCTGTATGATCCAGTGGGTACACAAGACTTGCCCAGTTCTTCAGACCCACTTGCAGTCAAGTCACTGAGAGCCAAAAGGCTTTTCTTTTCAGCCCCAAGTGGGCTATTAGAGAGGACAGTTTGTCCTGAAATCTTTATAGCTAGGGCAATTTTCAATAATACCCCTACACTGACCAGCTGCTGGAAATTTACAGAATGGCCCAGTGGGAAATATGAGACGATGTGCCACCCTAACAGTCAGCAGTCACATAAACAAACAGAAAATCAATGAATGACTTCTAAAAAAAAAAAACAGGTGGCAGTCTGAAAGATTTCTTTCCTTTTTTTCCGCTTTTCACCTCACTCAGCCAGGCCTGAACAAAAACACATTTATAGTTCATCATGAACAAGGCAGGCTATGAAATCACAATCCAGATTTAGAGATTTTATGCAGTGAAATGTCTTCCTTTAATAAGGATTTCACAAACAGACTGCAGTGTTCAGAAATTTGTGGTGAGCTAATCTTTTCACAGTTTTGTTGTGTTTCCTTTGCAG
Seq C2 exon
GACGTGTTTACTTTCTCAAGCGTTTTAAGAAGGTTAACTACCTTGAGGCGGTAAAGGCATGCCAACGTGATGGCGCATTCATAGCCAAAGTTGGACAACTGTACGCTGCTTGGAAGATCCAACTCTTGGACCGTTGTGAGGCAGGGTGGGTAGAAGATGGTAGCATCCGTTACCCCATTGTCAATCCTCGAGCCCGCTGTGGAGGCCCAGATCCTGGTGTCCGAAACCTGGGTTTTCCTGATAAGAAGTTCCGCCTCTACGGAGTCTACTGCTTCCGCAAAAACACCGACATCCAGTCAACACAGACACCAACTGAAACCACATCCAAAATGGCTAACAGCACCAGAAGTATCTGAAAGTTCAAAAACTAGTTATTAGCTTTACTAGCATTTGAAAAACAAGGCTTTTTTGCACACATGCTAGGCTATTAAGCTAGCGCTCAACTCGGGGCATAATTGAGCTTCTATAATTTCACTTACTTGATTGAAATGTTTAAATTTCTCTAAATTGAGAAACCCTTGAAGCATATTTCCTCAGAGACAGTGCTAAGGAAGAATATGGCACAATGCATTAGCTTAACTGTTTCGCTGTACACCCTGCATGCTGAAAAAAACGAGAATTTTGCCGTGAGGTTTTCAATTTGGCTTATTTTTACTGTTTCACAGGGAAGACAAAAGCAACTTTAAATAGTGCTAAGAAAATATGAACGCAAATTTAGCCTCAACATGAGCGTAGCACATTAGCAATAGCCCTCACTCACTAGAAGATGAGAAACTGCTAGCATGAACTGGGCTTAGCTTTGCCAATTACTATGCACATAACTCTAGAAACACAATTTTTTGATACATTTGGATTGACCTGGCAAGCAATAACAAAAAGCATGCCTTTTCTTTGATGATCATTACAGTGATAAAGCTAAAATGTTGTGAATGACAGAATTACATAGGCTGCTTTACTACCTCTTAGCGGTTGACAATTGCACTGTCTGTTCAGTATTGCACAATAAAGTCTATGATGATGCATTTTAGATTAAAGTTATTTACCTGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000018542:ENSDART00000136016:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.078 A=NA C2=0.144
Domain overlap (PFAM):
C1:
PF0768612=V-set=PD(0.1=0.0),PF0019312=Xlink=WD(100=94.1),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=77.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCAATGCTGGCTGGTTAGAG
R:
GCTCGAGGATTGACAATGGGG
Band lengths:
356-1224
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]