DreINT0090636 @ danRer10
Intron Retention
Gene
ENSDARG00000061517 | lrp1bb
Description
low density lipoprotein receptor-related protein 1Bb [Source:ZFIN;Acc:ZDB-GENE-070912-401]
Coordinates
chr9:36726950-36729633:+
Coord C1 exon
chr9:36726950-36727079
Coord A exon
chr9:36727080-36729506
Coord C2 exon
chr9:36729507-36729633
Length
2427 bp
Sequences
Splice sites
5' ss Seq
AGGGTATGT
5' ss Score
8.34
3' ss Seq
TTTTTTTCCCCAATTAACAGTTA
3' ss Score
7.44
Exon sequences
Seq C1 exon
GTAACCTTTACTGGACAGACCATGGCCTCAACCTCATTGAAATCGCTCGCTTGAATGGACTCTACCGGTCAGTTGTAATATCAGAAGGACTGGATCAGCCAAGAGCCATTGCAGTGCATCCACAAAGAGG
Seq A exon
GTATGTCAAATGCCTCCAAGACAGTGCATGAGTTTAACATTTTTTGCTGTTCAGTAATACATCTTCTGAAAGAGTTTGCAAGTTACAGAGTACATTTTAGGCAACTATGCAAGTGCATTAGACCAGATAATAATGAGCTCTTGGTTAAGAAATGAGATGCAATTTAAATCTTTGAAGGTCAAATATATTTTACGATCTGACTAGGGTGGTTTTGCTGACAAAATTAGCTTTAAAATGTCTTGGCCTCCACTAATGAACCAAATTAAATATTTAAACCCAGCAGATATGCATCTCTATTGAGGCGCAGACCCATTTTGTAGTCCATTACTGTTTTGTTTCAGCAATTAGAGTCAAACTTTGCAGTCTCCATTTGTCTGCGTTTTGTCTGTGCTTGCCTCAAGTTTGATGTTTACACCCTGCAATCAGAATCACACACCGAAAAAAGAGGTTTTCAACATAAGAGTGCTTTAACCCATCTCCCATCTATCTACTGACAGCAGACAGCATCAGGATGGGGATCTTCTAAATCCCAGACATCCAAAAAAAAGCCACCCATTCAAGCCTAAGGCTGTAAAAGCTGTCTTTTCCTGTTCCAGTTGAGTCGAACTTTGAATGATGTTTCTTTGGTAGTGTAACAACCGTTATACACTTTAAAGGAGTAGCTCACCCAAAAATGAAAATTGTGACATCTTTTACTCACCATCTTGTTATTTCAAACCCATAGAGCTTTCTTCTGTGGAGTATAAACTCAGAAATTCTGTGCAGGTTTCTCTTTTCCTTGACGTTTTATAGTGAACGGGGAAGCTTTCAAGCTTCAAAAATGATGTAAACAGTATCATAATAGTACTTTATATCTCTCTTACCAAACAGCTAAAACTCTAAGTAACTTATCAGTTGGATTTGAAATGTATTACCAATTGAATGAGATGATTTAGTGAATGGATTAAATTGTAAAGGGTATTTTGTTCAAGATTTGTAGTTATTTAATTAACAAGATGTTCATGAGTCAATGTCAATATGTCAAGGGATAAGTAGTTTTGACAAAACATGATCAAGACTAGAGATGCATGAGTCATTTGAATCACTCTGGGGTATTTTTTATACCTTGAAATGATTTTTTCTACACAAATAAGAAAAGTCTGGAATGACATTATGGTGAATCAAGGATCCCAGAGGTGTATTCTTCATCTGAACTCTTCATGTAAGGTTGAAGTATGGACATGTGAAGTTTTTAATCAATCAATTCAATGAAAAAGTTCATGTTTCATAGATCTCTAACAAATATGCCAAGGTTTTACTGGGCTGATGTCTAGATGTATTCAGTAATACACCAGTCATAAGCAGACTACTGTACCTTTGGATAGTTAAAACAATCTACACTATTGTACTGTATGTTATATACGTTTAAAATGATATTAGGGTGAATAAACAATTATTCACAATCATAGTAAACAATTGGCCAAATTTATTATTAATTGTTTTTTTTTTTTCAAAACTGTTCTTTAAAGGTCTCTATGAAATGTATGTTTGATTTCAATAAAGTTTAAATCTCAATCTGTAATTATGGGGTTGACCAAAGGAGTTAAATCTAATATGCGGCGCGTTTCTTCAGTTGTTTGTGTTGTGACCCGTTTCAACATTTTTTCTGTCAAATTGATGAAGATCATCTCTTTACTTGCTGGTGTTTTTGGTAACTGCATGTGCTTTCTTAAATTGCAGCACATTAAACTCTCTTGGCTACCATACGAAAGGGTCGATGCAGGTGGAAAACACTCATAAACAAACAAAGGCTCAAAACACAGTGAGGCAATACAAGAACATTTTTAGACCTTAACACTGCAGTGAAACACGACTCAGCACTGGATGAGTGTGTGAGTGTTGTAAATATGGTCCATGTAATTAATCATGTAATCAGCTTCATCTGTGTGTGTGTAATCAGGAGGTAAACTGGAACTGGTGTGTGACTGCAGATCATGATGGGATATGTAGGTCGGTAGAGTGTTTTACAGCGATCCACAAAGGCTACATCAGAATCAGAGAAGTTTTAAGTAAGGGGTAACGTGTGTTGATGACAACCTGCCCATGGCAATATATATTTACTGATGAATGAGTAATTGGAAACTTTTGCCCCTGGGGTATGAATAATTTTGGGATTGACTTCATTATCAGTAATATACAAGTCATATGCAGACTCATTGGATACTTTTGCATCTTTATGGAAGTGAGGTTTAAAAATCAAATCACATGATACATTACAAATAGTCAGTTCAAAAGCATAGTATGTTCACAGTGATTCATGCAGTACTTTTTTAATAAATATGCCAACATGTCATTTTTGCTGAACTGTTTCTTTAAGATCGCTGTTAAATATAGAATTGTTGAATTTGTAACCAGGACCTTTTTTTTTTTTTTTTCCCCAATTAACAG
Seq C2 exon
TTATTTATTCTGGACCGAGTGGGGTAAAAACCCTTGCATAGGCCGCGCTCGATTAGACGGATCAGACCAAGTGACTCTGGTCAGCTCTGGCATCGCCTGGCCGAATGGAATCACCATTGACTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000061517:ENSDART00000139033:34
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=0.000
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=WD(100=93.2),PF0005812=Ldl_recept_b=PU(0.1=0.0)
A:
NA
C2:
PF0005812=Ldl_recept_b=WD(100=97.7)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]