DreINT0048867 @ danRer10
Intron Retention
Gene
ENSDARG00000026165 | col11a1a
Description
collagen, type XI, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-070209-167]
Coordinates
chr24:28743154-28747113:-
Coord C1 exon
chr24:28747060-28747113
Coord A exon
chr24:28743208-28747059
Coord C2 exon
chr24:28743154-28743207
Length
3852 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGC
5' ss Score
9.55
3' ss Seq
TCTCTTTCTTTGATTTGCAGGGT
3' ss Score
10.24
Exon sequences
Seq C1 exon
GGCAAACTAGGTGTTCCAGGATTGCCCGGCTATCCAGGACGTCAAGGGCCAAAG
Seq A exon
GTATGCTCTTAAATTGAACATGACACCTGTACCTGCATCACGATCGCTTCACTTATGAGCTAAACAACAACTCGGCTCATTAGCATGAACTAATGCCCTCCTGAGAATGCATTATGCATGCTGCGCTGAGAAAGCGGAGCTCATGCCAGGATTGTTGGCTGTGCTGTTGGTGATTCTGGTCACGCAGGCGGAGAGCAGAACTGAGTACAGATGCCTGTGTCAGACCTCAGAGCCTTTCATCAGCAACAGCATCAGCTGTAACAGCAGAACCCAATCTGGCTCAAGACAGACCCAAACTAGACCTTAAGTGGCCTCCGAGGCCTGGAGACCAGCACTGACGTCATTACAGGCGGATATAGATGAAGACTGAATTTTCAGGTTTTCAGGTCACAATTTTGTGCACTGCTTGGTGAATCTGGAGTGCACTACATGGCCATTTATAATTTATGTGAAATATTTTCCCTTTTTTTGGCAAGCAAAGATATCTAAAAACATGCTTAAACAAGATATACAAAAAAAGCAAAACTGCACAGATCATATTTTTCTGACAATTTTATTTTGTATCTTTATTTTTTCTTTGTGTTTGCTGTGTGCACACCAGTGGCCTCATGTACAAAGACTTGCGTTCATATTTCATACTAAAACATTGCGTACGGACAAAGCTGTAAATGTGTGTACGCAGTTAAAAATTCAGATGTATGAAACAGTGCGTACACGGAATCCCACGCATATTCTCTTTGTACATCTGAATTAAAGTGAAACTGAGTGCACGTGCACAAGTTTTAGTTTAAAAACGCATAAGTTTTGCTACGGTTACGCCAACCGTCCACACTACACCGGAGTTCTCGAGCGCCGAAAACGAAGCGTATCGAAAACGCTGGAGAGGCCGTTTTCATTCTGAAACGCTGCTGCTCCGTCTCAGTGTGGATGATGGAAAACGGAGACATCTGAAAACGGAGGCGGGACTGCAGACATTCGCCTCTCTGATTGGGGCTTTTCCTGAATATTAAGTAGCCTAACACACACAGTTCAGTCCTGCTTTCTCTCCGTGTAAGTTCAGACTTCGCAAGTTTGATTAAGGCTGCAGTCTCTTCTTCTCAGTTTGATATGGAAAGCAGACTATACCGAGGACACGGGTAAATCTTCAAAGGGAACAGTGTACTTTATAACTTCATTCACATCACCCAGGCTGCGTTGTTTCACTTTCTCAACAATAAAATGTAAACATGATTTAAGGAACTGCCTATTTTCATTTTAATATTAGCAACTTAGACAGCAGAAATGTTGAGGCGTCGTGCTGCATGAGCGTCATCTTCACTGTGTGGATATTTATAACAAAACGGAGTCGATAACAACTGCCTCCTTTCAATTTCAGTGAAAAGACGAAACACACCCTCTCTTTTGCTGAATATCAGTTTTAAGAATCGATAATGGCCATTACAAAAGTATAACATACAATAAGTTTATACATTTATAGGAAATAAAGGCAAGCGATCAGTCAATATACAGAATAGGCTGGTTACTCATTAACTTATCTTTGCGCTCAGCCAAAACACGTTACCTGAGAAAAAGTAATAGATTCCAATGACCAAAGTCAGGGAATATGTCGTTAGATAAAGACAACAAGATGAATGAAATATCCCGTTTAATAAATATAGTGAGATTAGATCCAGCGGGAGATGCTTGATGAGCAGTCCGACTAGCACAGCTCTCATCTGGGTAGATGGGCTGCAGCGCTTGCCCGAGAGTGTCTGTGTGGTCACGTGATGTGCGTTTTCAGCGTTTTGGTGTGGACGGAGAGCAGTTAAGAAACGCTGGGTAAAACGGGAGTGTGGACGCGGATCGCTTTCATTCTAAAACGCCGTTTTAAAACTAAAACGCACCAGTGTAAACGGGGCCTCAGCCAGGACTCAACCCAGTGAACTTCTTGCTGTGAGGCGATAGGGCTAACCAATGACACACTAACATTTATTCATTAATTATTAAAAATATTGTTGTATTTAACCGAATTAATGCTTAGACCAACGCCGTGAGGTGTTGTTTTTTAAATCAATGGAAGAATGTTTGGGGAACCTCATTCCCTATTTCTGCATTTATTTTGTTCTGCAGTTTAATTGGAACATTTCACAAGCTTATCTTTAACTGAATTAACATGAAATAAAGTCCAGTCCCAGCACGGTGGCTCAGTGGTTAGCACTGTCACCTCACAGAAAGTAGGTTGCTGGTTCGAGTCCTGGCTGGGCCAGTTGGCATTTCTGTGTTGAGTTTGCATGTTCTCACCGTGCTCATGTGAGTTTCCTCCGGGTGCTCCGGTTTCTCCTACAGTTCAAAGACATGTGGTGCAGGTGAATTGAATAAACTAAATTGCCTGTAGTGTGTGTGAATAAGTGTGTATGGTTGTTTCCCTATAATGGGTTGTGGCTGGAAAGACATCTGCTACGTAATACATATGCTGGAATAATTGGAGGTTCATTCCACTGTGGCGACCTCTGAAATAGAGAGGCTGAAGGAAATGAATGAAAGATTAAAGCCCAGTCCCAGAGCCTAATATAAAAAAAACAAACCTTATCCTTTTCAAGCTACTTCCGATGTCGCTTTCGCGTCCACTGAGCAAGATGTCGGCCGTGAGGCAAAGCATGCCTGACGCTTAGTCGTTAGGTTATAAAATAGAGGGTGTAAACATATTAAAAACACACTGAATAACTTAGGTTTTAGACAGAATTTCACTCGCTTCCCTATAAAGACGGCGCAAAGAAAATGGCGGTGTCTCACGCTGATGTTCCTGGATGTTGACGTGACGTATGTGCTCTCTTTCACATCTGCGTTCCCAACCCAGCACAGCTGGGTTATAGATCAAGAATTTTGACTTAAATTGGGTTAAATCAACCCAACGTTGTTACCCGTCAGTCTCAACCCAGCATTTGGGTTAAAAAAAACACCCCAGCGTTTTTTTAGAGTGTAGGTGTTGGTCTTAGCAGTAGATTTACAGTCTCATAAATCCGCCTCTATTTAGCGACATTAACAGACGGCAGACAAGTGATGTGATTACAAGCACTTTGACATGCCATCATCTCTGGAACGCATTCAAACAGCCTGCCAACTCTCAAATTATCATGAAGTGCACTTTTGGCCATCACCGTCTGAGTGCTTACTGACTAGGGAATTGTGGCCTTTTTTTCCACAGAGTGTCATCGCTTATTCGTCAGTGTCTCACCTTTACAGTTTCATGATATCCTTTGTGGTAAATCAAGCTTGAATTCTATAGGGCTTGACACTTAAGATGAATGTGTAAAACAGTTATTGATTTTCTTTCTTGAATGCTTACACCGCTGCCAGGATTGAGGAACGCCGGTAAGCTGTTTTTAATTTACTGCATTGAGAATGAAAGAAAGGAACGGACGAGAAGTGAGAATGAGAGCGATTAAGACTCATCAGTAGTGACTCTTGTTTGGTTGTTTATCTGACTGAGTAGTCATTTGTTTTCATCCAACGTCTTGTTGTTTCGGGTTGATTATACCGTCCTCGGTCCTTGGTGGACAAAGTTGCATCTCCTCACTGAAAAGCGATCAGCTCCCGATTAATGTTGTGCAAGCCAAACAAGGAAAGTGATCATCGAGATCGGCTTTGTTTATCTTGGGATACATCATCGGCATTCAGAGTTCTTCTAACAATGGGGGACTACGAGCTATTTAAAACTCTTCAGGGGAAGTAGCGACGCCAAAGACGCTAATGCTAGCAGATTGTAATGGCGTTTAACTGCTGGAGAGTCAGGACTCTTGGAGTTCATCCCTCATTTATATGCAGGTCTTGCTTCCTTCCTCCCTCCCTTAAGTCTCTTTCTTTGATTTGCAG
Seq C2 exon
GGTTCGACCGGTTTCCCCGGATTCCCAGGAGCCAATGGAGAGAAAGGAGGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026165:ENSDART00000003503:31
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(27.9=100)
A:
NA
C2:
NO
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]