DreINT0052197 @ danRer10
Intron Retention
Gene
ENSDARG00000102517 | crtac1b
Description
cartilage acidic protein 1b [Source:ZFIN;Acc:ZDB-GENE-090312-28]
Coordinates
chr13:39969846-39971862:-
Coord C1 exon
chr13:39971694-39971862
Coord A exon
chr13:39969992-39971693
Coord C2 exon
chr13:39969846-39969991
Length
1702 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGA
5' ss Score
5.24
3' ss Seq
CTGCTTTGCCACCCTGACAGGGA
3' ss Score
6.8
Exon sequences
Seq C1 exon
GGCTCATCTAATAAATGGCTTCGTGTAATTCCACGCACACAGTTTGGGGCTTTTGCCCGTGGAGCAAAGGTGATTGTCTACACCAAGCGAAATGGCCCTCACACACGCATTATAGATGGAGGATCAGGATACCTGTGCGAGATGGAGCCAGTAGCTCACTTTGGATTTG
Seq A exon
GTATGAATTAATTTTTTTACTGTCTCTCCTTAAAACATCTTTGTAAGAAATTCATATTAGGAAAAGAACAGCTATGAAATTGACCAAGTCTGTACAATATCTATTTCATAAGTGCATTCACCATCTCGGAAATGTTAAGGCTCGTCGAGTAGCCGGAAAACAAGTATTCGCTCTGCTAACTCATTACAAAGAAACAATTATGATGTAACTCCAGGTCATGTTCAGTGGGGGGCTTTGGGTCTCAGTAATATAATCCTCTGTGTGGAGGTCATTTCCTTCAATATCTTCATAGACTGGAAGCCCTTAAAGAAGACTGCAGGTGCAGCAGCCGGTGGCATCGGACCGGGACCTTTTCCCCATGGCTTGGCCATATTACAGGTGCTCGAAGGCACATGGCTTCATTTGGGAGCTTTTGGATGGATTTGTGTCAGGAATCGGTTGCCAGCTGGAACTTGAGTTGTTCTGAATGTGCTGTGAAAAACAAAATGATAGCCATCAATGGTCACATGATCACCCTGAGGGCTTGTAAATATGTGCATACGTGCTTGACCACCACTCATCAATGTTTCTATCAGTAAGAGTGTTTGGAAAACGGATGTAAAATGTCAACCCTAGAAGTCTGATTGAATTGATTTTTTGAAATGTCAACCTTTTCTCACCATGTGATACTGTTTGGGATTAGTTTTACTTATACTGTGGCACTTTTTGTCAGATAATTATTTATTACTTTGTGTAGTAATGTGTGCAGTTGGCCAAAACATTTTCCACATGCATAATTTGAAGCTTACCTTTATGAAATAAAACCCTCACAGATGCTAAACTATAACTTTCAATAACTACTGGTAAAATGTCATGCTTTTTGCCTCAAGAGGCACCTGTGCCAGTCAGGCTTTGCCAGGAGCCCCTGTGGATCTGTTTACCTAAGAAATGTTTCTTTAATTAAGGACTGGGAAGGCGATCAGCCTCTCTCCTGCTTGACTAAAGGCTATAATGGAAGGAAAATCTAGCGGCCACCCTGTCCTTTCTAATTTCTGCTCCTTTGAACTTCTGTCTTCCTCCTCCACCACATTCATTTCCAATGGATGATTTCTCCATTCGTGATCACTATGACAGTCTCGCTTAACGGCTATGTTAATTACCATCCCGATGTCTGTGAGAAAGTGTTTCTGACAATCAGATTGAAGTCACTAAATGGATGCTGCTGTAAAGCTTCTTAAATGAAGTGCTTTCCAACCACCGTGCCATTTATATGGCTCCTTATTTCAGCCACTGAACAACAGACAGATTTCATCGGTCTGGCATACGAGAACCTCATTGCTTTAATGCCTCACTGACTGCTATGCCAGAAACTCTCTGGCCCATGAACCCCACACACCGGCAGTCATGAGAAACCGGTTCTGCCGACATCAAATGAGACGTGTTCAAGCCTCGCTGCTCACGACGCTGCCCGCAGCTGAGACTGAACACATTCTTGTGCATTTGTTCAAGCACTTTGTGTGCCAAACCAGAGCCTATATTCCAACCTGGCTTTTGCCTAGAAACATCTTGGGAGGGCCCTTTTTCTCCACAATGGTATTTTTCCATGGAGAGCTGTACATTAAGAAAAGAAATCATTCATTATGTCTTTTAAGCCTGAGGGGAAGCTATAAAGACAAAGTGTTGGTGAAGTACTGAAAGCACTGCTGCTTTGCCACCCTGACAG
Seq C2 exon
GGAAAGATGTGGCCACCAGTGTAGAAGTCTTCTGGCCAGATGGACGCTCTGTGGCCAGGCCTCTGGAACCCAGTGATATGAACAAAGTGATGGAGATCCATTACCCAGAGAATGAGGAAGAGGCAACCCCAGCGCTGGAGATCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000102517:ENSDART00000157852:7
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=0.378
Domain overlap (PFAM):
C1:
PF0183918=FG-GAP=PD(5.0=3.5),PF075937=UnbV_ASPIC=PU(60.9=68.4)
A:
NA
C2:
PF075937=UnbV_ASPIC=PD(37.5=49.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTCATCTAATAAATGGCTTCGTG
R:
GCTGGGGTTGCCTCTTCCTC
Band lengths:
302-2004
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]