DreINT0048935 @ danRer10
Intron Retention
Gene
ENSDARG00000009014 | col11a1b
Description
collagen, type XI, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-070912-607]
Coordinates
chr2:15775682-15778695:-
Coord C1 exon
chr2:15778606-15778695
Coord A exon
chr2:15775736-15778605
Coord C2 exon
chr2:15775682-15775735
Length
2870 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGA
5' ss Score
9.63
3' ss Seq
TTCTGTCACTTTTTTTGCAGGGT
3' ss Score
9.78
Exon sequences
Seq C1 exon
GGTGATCCAGGTCCTCAGGGAATTTCTGGGAAACCTGGCCCTGCTGGATTGAAAGGGTTTCCAGGACAAAGGGGGCTTCCTGGCGCAGCG
Seq A exon
GTAAGAACAAATGAGTTAATGTCATGTGTCCCACCAAATGGCCATTAGCTACTTAACCGCCTGCTGTTCATGCAAATGCTGCGGCCTCAGGAGAGGGTACAGTCCTCACTGTAAGACTGAGCCTCATGGAGATTAACTGGCACATTTAAGGGCCATTAAGACATTCAGTAAGCATTCGAATCACTGCTGAGAATTTCCAGTAAAGGACATTGCAGTACACAATATCACCAGGAGAAGAATACGCAATACATGCAGAAGAGTTATAGACAGAAATACATTTGTTTTACATTAGTTTCATGGAAAAAAAGTGTAAAATGTGCTCAACAATATGAAAACCTAAACTTTATTTAAAAAGCAGAATACATAAATTAAATAATTTTTACAGTTCACCTTTATTTCTATAGCGCTTTTACTATGTAAATGGTGTAAAAGCAGCAGAACATAAAAGATACTGAATGGTTATCATAAGTCAAATGACATCTGTTCAACAAAATCTTTGAATTTACATATATGCACAATATTGAAAAAATCTGATATCACGATATTTCATTTTTTGTGATAGATATTGTAATATAAATACAGTTTCACAAGATGGTTTGATTAGCACTATTTAAGTTTTCTGGTCGTAAAGTATTCAGGTACAGAAATTGAATAATAATAACGATGTAAAAAAAAAAAAATACTTTTTTCTAATTTATAGTCCAAATATCTCAAAGTTTTGATTTCACCTTCAGAAGAAATAACTCCAAATGAGTATTTTTTCCTTAAAACAAGCTAAATTATCTGCCTTTGGTGTAAGTAAAATAAGCTTGTTTTTGCTTTGAATTGTAGATATTTGGACTAGAAATAAAACAAAAATAAAGTAAGATGTTTAGACATAAATCATATAAACTCTGTATGAATAATTAAATACAATAAATCTTTGTTTCACCTCCAAATATCATATATTTTTTTGTTTGTAAATGTTCAAAACTTTCTTGAAAGACTCAATACCAGGCCTTAAAAAAACATGCAAATGATAAACCCTTACTGTATTATGGTTAAACTTAGCAGTGACTCTACAAATCATGTTCAGACACAATTAAGACTCAACATTGCATATCTTGCGATGTAACTATTGCGATATCAACCAAAAAATCATGAAATTTCTGTATTATTATGGAATTTTAAAAAGGTATAATCTAGACTTTAAATGTCAGCGATTTAATTTATTTATTTTTTTGTCCTGCTCATAGTATATCAGGGATTTTTGTTTGCTTTGTCACTTATCAAAATGTAATTTTTCTATACCGTATTTTTTATATCATGATGATTTGACCACTATTGGGATGGTTAGGCTATATGCAGCTCCGTTTTATTTCTTAAACAAACTGGTAGTCACTTAAGTCAAATGCCGTCACTAGAGGTTAACTAAGGCAAACATGTCAGCATAATAAACAATTTATGAGCTTTTGCTTCAAAATACGCACTTCAAAGACTAGGTGTTAAAAGTAGACCACAGAAAAGCTAAATATAAAACTACTATTGAGCTATCAAATACGGAAGAGGGAGCACTTCACAGCCAACAATAAGTAATACATATAAATCTTTAAGAATCATTCCCATAATGGCTACTAATGTTGTGCAAAATTATATTTAAGCTAAAACCATATTATTGTTTTATTATATTAAAAAAAAAAATACTTTATTAATATATATAAGCACAAAAGCAGCCTGTTTGTCCTTCCAAACAATTCCTTCATGTTGTCCCAACTCAAATCAATCAAGTTAACCTAATCATTCTTACAAATTTAAGTAGATCAAACATAAAACAATTAGGTTGTCCCAAAAAATTTTCATGAGTTGTGTTGTTTCAACTCCTTTTAAATAAATTGTCATTTTTTGAGTGCCCTAAGCTTTTTAGTCAGTGAAAATGAATTTGATATTTGACTTAAAGTGGGAACCCTGAATTTATTTGTATTAATAAACTTTAAACTGTACATTGGTATAGTGTATCAGAGTGAATCCTGATACAGAAAGTGTATGTTACACTTCCAGTAGAAAGATTACATAATTTAGTAAAAAAAATAAAGATCAGTCTCTGCAAAGCATTGTAGCATAAAAAATAAAGAGAATGTATCAATGTTTTCAAATATGATTTGATCTAAACACCTTCATGGTAGCCCTGTTGACAGAAATAAACATGAATAGGCATGATTCAATATATCTTCTATGTACATTAATGATAAATACAATATTACGATGATTAATTGTGCCCAAAGCTTGCAGTTGAAGGTTAACTGGCATCTAATAGTTTCTGACTGGCATTTAACTATATAAATAAAACTTAACTGGGTCAAAGCAGGGCCCCTTATTGGACAGGAGCCCATGGGCTCCAGTTCAAACAATTAGGCTACTCAAAGGACATGTAAGTGAAAAGGGCGTCTCTACTCATTTTTCTACATTAACAAGATTTAGGCTGTGGGACCGAATATAATCAATTACTGTTTTGTTTTTAGTTTCTATTGTGAGTTGATGCTGAAAGTCACATTTAAAACACGAGCCAATAAGATCTCAATAAACAACTGTTGATTTTACAGTCACTCATTGTTTTATGTTGACTTTCAGTTGGCTCATATGTTTTTTTATGACTCAAATTATGACTTGATGGGGAGGAAAATGACGCATTATTGGTGTCACATGACACCTGCGCTGCCAGCATTTGGATTCTGATGTAGTAAATTGGGAAAGTGCCAGTTTGCTAAACACTCTGGGCTGTATTTCCAGTAGGCATAGAGTACAAACAGCTGGCACAACTACATGCAGATGCCACTTTGACAGCAGCTCTCATTACAGCTCTCATTATTCTCTTTCTGTCACTTTTTTTGCAG
Seq C2 exon
GGTCTGTCAGGTCTGAAGGGAGGCGAGGGTCCACAGGGTCCACAAGGCCCTAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000009014:ENSDART00000049589:40
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(36.2=100)
A:
NA
C2:
PF0139113=Collagen=FE(21.2=100),PF0139113=Collagen=PU(20.2=94.4)
Main Inclusion Isoform:
NA
Other Inclusion 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]