DreINT0049522 @ danRer10
Intron Retention
Gene
ENSDARG00000099930 | col27a1b
Description
collagen, type XXVII, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-100119-2]
Coordinates
chr5:64555343-64558949:-
Coord C1 exon
chr5:64558905-64558949
Coord A exon
chr5:64555397-64558904
Coord C2 exon
chr5:64555343-64555396
Length
3508 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAAG
5' ss Score
6.84
3' ss Seq
TCTCACATTTGTGTGCTTAGGGC
3' ss Score
9.14
Exon sequences
Seq C1 exon
GGTTTACCTGGTGTTCCTGGGAAGAAGGGCAAGATGGGTAGGCCG
Seq A exon
GTAAAGTTTTCTCTCACCATCCTCTCTATAGAAAATCTGTGAATGACTGATCTCTTTGTTCAATGATTTGTGACCAGTGGTGGAAAGAGCTTTTTTTTTTCAATTCAATTCAATTCAATTCAATTCAATTCAGCTTTATTTGTATAGCGCTTTTACAATGTAGATTGTGTCAAAGCAGCTTCACATAAATGGTCATAGTAACTGGATCAGGGTAGTTTAGTTTTAGTGTTTGAGTTCAGTTCAGTTTAGCTCAGTTCAGTGTGGTTTGGTTAACTAATTGTTAAACTAATTACTTACTAATAGTTACTTTACTTTTACCCAAGTACAAATCAAACCACAGGTCTAGAGCAACCAAACGTAGACCCTTACAGTTTATGAAATCAAATAAATTGTTGGTGGATTTTTTGTACACCACTTTTTACAACTCCCCTAGAGTTAAGGAGTTGAGTTTTACCATTTTGAAATCCATTCATCTGACCTCTGATGGGAGCATTTTTAGCTTAGCTTAGCATAAATCACTGAATCGGATTAGACCATTAGCATCTCGCTCAAAAAATTGTTTTAATTTAAAGCTTGGCTCTGCTGTAGTTACAAAGTGTACTAGGACAGATTTAAAATGAAAAGTTGCTATTTTCTATGCCGATATGTCTAGGAACTATATTCTCATTCTGGCGTAACAGTCAAGGAACTTTGCTGCTGCATCATGGCTGTAGTAGGGGCAATTATACTACACAGCACTGTTATTTTGTTACCTATCTGGGTTCTTTTTGCTGCCTCATTGCTGCCTACTCTTTTTTTATACATGTTTGAATGAGATCCTAAAGGGCTTATCTGATTCAAATAAAAGCTAAGCTAAAAGTGCTACCGCCAGACCCGGACATAGACTGAATGGATGGAGTTGTAAAATGAGCCTATTACCAAAACGTTTTGTGTTATTTTTAGGTTGTATTAAAGCTAGTGCAGTTTAGTAGATGGATGAATGGATAGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGACGGACGAACGGATGGATGGATGGATGGACGGACAGACGGACGGATAGACAGATAGACGGATGAAAGTATGAATGGATATATGGATTAATAGAGAGACAGACGTATGGATGGATGGATGGATGGATGGATGGATGGATGGATTGATTGATTGAGGGTCAGACGGATGGACAGACAGATAGATGAATGAAAGTATGAAGGATATATGGATTAATAGATGGACGGACGGATGGATGGACGGTTGGACGGACGGATGGATTGATGGATGGATGGATGGATTGATTGACAGACAGACAGACAGACAGACGGATGGATAGATGGATGGACGGAAAGACAGACAGACAGTCAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATGAATGGAAGTATAAATGGATAAATGTATTAATAGACAGAGGAATAGAGAGAGAGGCATGCAGACCGTCAGAAAGAACTGTTTTGCATTACGCCCTTTATATAAGTAATAATGCAACTGTTATTTGTCAATGTTCCCAGACAGTCTGATCTGACAGTAGACAGAGCTATTCTTTCATTTTGCTTGGATAAATAATGCAAAATCACCACTAATTATTAGCAAAAACTCTTTACCATCTGTGCGCCCATAATCATTTCCTATTTACCAAAATGACACTGGCGCTCTGAGTCCGTTTGTTTTTCAAAAGAACTAGACATTAAGAATTCAAGCTCATCTTTTTTCCAAAACAACTACCAATTATGCGCAGTCCTCTCTGGAGCACAAACGCCGGTGCCAAGCACAGATTCATCTGTTCCTAATAAACGATTCTTGATTCTTGAGTTCTCTGATAGGCAGCACTCTTTTTGATAGGCAGCCGTAACTTACTGTTTGCCTTGCTGAAGGACAAATAAAGATCTCCACACAGCAACAAGTGTTGACTTTGGCCTTAAGACAAGCACACTTTTAGCACACCGTGGAGCGCAGCGTCATTGCTCTTGTCTTCTTATATAACTTAACAGTAGATGGAAGGGAAACAGCGCTGTCAGCGAATCCCTTTTCTCGCTGCTCCTGGTCGTTGCCAGTGTAAGGAAACACTCAGCCATGGAATTTCCTGCAGGGCTGACAGAGACGAGAACTGCGCTTGTTTCTGTGACTCGGCACCAGGCTCTGTTTTCACAACAACAACAAAAAAGCAGCCATACTCTCAAACAATAAAGATTGCTGTTTGTTCAAACTACTTATTAAAATGAGTTGAAACAACACAATTCTTGAGGGGATTTTTTTTGTACTACTTAATTGTTTTATGTTTATTCATTCATTCATTTTCTTTTCGGCTTAGTCCCTTTATTAATATGGGGTCGCCAAAGCGGAATAAACCACCAACTTATCCAGCACGTTTTTACACAGCGGATGCCCTTCCAGCCGCAACCCATCTCAAGGGCGGACTGGGACAAAAATTCAGCCCTGGCACTGTAGCCACATCAGCCCACATTACCACACCGACACAGCCCCACCCACGGACACGCACATTCACTATTTACTTTGGTGTACAGATATATATAAGACATTCTTGCCAGATTTTGATTACGTCCGGGTAACCTTGGATTGGGTCGGCCCATCTTGAAATTAGACGGCCGTCGCCGATTGGGCCAAATGCATTTATTATTATTTATTAATAATAACATTTATTATTATTCTTTTTTATTTATTTTTATTATTTATGTTTTTTATTTATCATCATCATAATATCACATCTAGCAAGAGATAAAAGCTGCCTGCACGTAAAAACAATAAAAAAAATGTAAATAATAATTAAAAAAAACTGACCGGCTCACATTTAAAAATTGGTCCGGCCCTTCTGGCATTTGCCAGAATTGCCAGATGGCCAGTCCGCCCCTGACCCATCTCTAACCAAACACATTAAAGTATTTGAATGCAAGTACATTTTAGTTAAGGCCACCTAATATAAAGTGGGAGCCTTTCGTTCACACACACCCAAACTGTAAAAAATGCAATAATATACAAAAACCATACATTTTAGCTTGATTTCCACATACTTAAATACTACAAATTTGGCCTCTAATGTATCCCTCTAAACCACTTTAGTGAAATGAACTACACTACAGGGTCTTCTACATTGTGTTTTGGCTTTGTAAGACAAATAGTTTAAGGTTAAAAACTACTCTGTCTTATTGCTACTTTCCTGTTTGAAATCCAGTTTTTCAATATCCCGTGATTATGGAGTGGTTCTGGTGTAACAGAGCTTTGCACAGGGATTAGAGCGAAGAGACAGTGTTTACTATGTGGGCAACTGGAAAGAGCAATGTAAAAAAACTGGTATCTGCCCTTAGTTTAAGTGCGGTTTCTCCGTGTTTTGCTCTGCTAAGCTCTGCTGTCTCTCACATTTGTGTGCTTAG
Seq C2 exon
GGCTTTCCAGGAGATTTTGGGGAGCGAGGACCACCAGGACCTGATGGAAACCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000099930:ENSDART00000167886:5
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(18.2=100),PF0139113=Collagen=FE(16.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(5.2=22.2),PF0139113=Collagen=FE(19.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
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]