DreINT0069205 @ danRer10
Intron Retention
Gene
ENSDARG00000006526 | fn1b
Description
fibronectin 1b [Source:ZFIN;Acc:ZDB-GENE-030131-6545]
Coordinates
chr1:4811753-4813426:-
Coord C1 exon
chr1:4813337-4813426
Coord A exon
chr1:4812241-4813336
Coord C2 exon
chr1:4811753-4812240
Length
1096 bp
Sequences
Splice sites
5' ss Seq
CTCGTAAGT
5' ss Score
9.63
3' ss Seq
TAATGCTTTTTCCTGCCTAGAGC
3' ss Score
7.39
Exon sequences
Seq C1 exon
GTCTAAAACCAGGCACTGAATACATTATTAAGATCATTGCCCTTCTGAATAACCAGAGAAGCGCACCACTAGTTGGCACAGCCACAACTC
Seq A exon
GTAAGTATTTACTAATATTCAATTCAATTTCAATTCAGCTTTATTTGTATAGCGCTTTTACAATGTAGATTGTGTCAAAGCAGCTTCACATAAATGGTCATAGTAACTGGAACAGTGTAGTTCAGTTTTTAGTGTTTAAGTTCAGTTTAGCTCAGTTCAGTGTGATTTAATCATTACTGAGAGTTCAAACCCTGAAGAGCAAATTCATCGATGCGTAGCTCTACCATTCCTGAACCATGCGAGCCAGTGGCGACAGCGGAGAGGGAAAAAAAACTTCACCTGATGGGAGTGAAGAAAAAAAACCTTGAGAGAACCAGACTCAGTTGGGCACGACCATTTTAATTTCTCCGCTGGCCAAAAGTCTTGTGCAGAGCTTTAGTCACCGTGGTGGAGGAATGTAAAGAATTCCTTGTTGTAAGCCATATTCTATAAAAATGTCTGCATTATGTAAAACGTTATAGCATACATCGAGATACAAGGAATACTGTTGAATGATACAAGCCAAGGAACAAGGGTTTGGGGTTTGCAAGCATGATGGCTACTGCAGTATAAACAGCACAGCAGCTTGGATTCTTGGAAATCTTGGATTTTGTGAAAGCTTTGATATTGCGCTGGCTTGCATTTCAATTGTACACCTTGCAAAGCCACATATTTTTAAAGCTGCTTAGCTTTTTAGAACTAAATGCAAAAAGAATCTAATGTAAACCGAAGTTAGCTGCATATTTTTGCACCAAGCTGGCAGAACTGCTATCTTACCACTACCTTTTTTAAACTAAAGTGTTCCCTCATCAAAAGATTTGATCAGTGTTTAAGGGGCTGGTCCATCCTGATTACTGTATGACTTTTAATGATTAAAAGTATAATTTTAACTAGTCATCTTTGCCTTAAACTTTATACAGTGTTTAAAATTCAGACTCTTGTTTGGCAAAACCAAATAATGCATTTACTTATTTTAATTGCAAAGCTTTGCAATTTTAAGAAAATTCTTGGATCTACTCCCCTTTTTTATTTGACTGAATCTTCAGTACCTTACTGCTTTGCAACTAGGACTGCTTCCTAACCTGCTGCTTTGCTTTTAATGCTTTTTCCTGCCTAG
Seq C2 exon
AGCTGATATCCGGTCTACCTAGCCTGCCCAGTCATGGTGGCCGAGACAAGCTGGATGTGCCAGAGCCTGACAACAGAATTAATACAGTGGGTCCTACTGGTCATGATTCAACGGATGCGCACGGGCAGCACGTGGAGTACACCGAATACAATAATCAGCCCAAACAACCCAACATAGGTTACCAGCCTCAAAATCGTCAGCCAATCTCTCAACCTAACCAACCTCGACCACAGCCTTATGTGCCTCAAGTTGGAGAGACCCTAGTCTATGTCCCCCAGGTGGGACCCGATGGGGGTCGTGTGCCTCAAATTATTCAGGTTAGTGAGAGGCCTGGCGATGGCCATACTTTTGGTTTTCCAGAGGACAGGACAGGAAGGCCGCAGGAAGCTCAGACCCAGACTACCATCTCATGGCAGCCCTTCCAGCAGAGTTCTGCCTACCTGGTATCATGTCAGCCAATCACCCATCCAGATGAGAAGATGTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000006526:ENSDART00000160791:38
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.226 A=NA C2=0.871
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(27.2=71.0)
A:
NA
C2:
PF0004116=fn3=PU(54.4=26.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATAACCAGAGAAGCGCACCAC
R:
TAATTTGAGGCACACGACCCC
Band lengths:
354-1450
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]