DreINT0169761 @ danRer10
Intron Retention
Gene
ENSDARG00000002344 | tubb4b
Description
tubulin, beta 4B class IVb [Source:ZFIN;Acc:ZDB-GENE-030131-8625]
Coordinates
chr14:5555980-5558312:+
Coord C1 exon
chr14:5555980-5556090
Coord A exon
chr14:5556091-5557107
Coord C2 exon
chr14:5557108-5558312
Length
1017 bp
Sequences
Splice sites
5' ss Seq
TCGGTATTT
5' ss Score
4.52
3' ss Seq
AACTCCTGAATTTCTTATAGGCC
3' ss Score
6.8
Exon sequences
Seq C1 exon
GTGGAAAGTATGTTCCACGTGCCGTGCTGGTGGATTTGGAGCCTGGTACAATGGACTCCGTGAGGTCTGGTCCATTTGGTCAGATCTTCAGACCAGACAACTTTGTGTTCG
Seq A exon
GTATTTACCTTAATTTTTCACTCTTGTCCTCATTCAGAATCAAGGGTTTTCCCTGCTTAAAGAATTGAGGTTTTCCAATGCCATTAAATTTTGTGCCATCTCTGCCTATTAACAAACGGTCACGCCTACTGACAGACCCCAAGTTATGCTCCTGCACTGGTCGTGTGTTTTAACTATATTCAGTAGTAGCCTTTTTAAAGCCTTTTTTTTTTTTTTTTGTAAGATTACAGTGTTTTAGCTAGCAAATTTATAACTTGTTAACCCAAGGAAAAACCCTTAGTAAAAACCCTTGTTTGTGCTTTGAGGTAAACCAAAGTAGTTAACAGTCGAAGAGAATCTTACATTTTTATTTTTGTACATTTTTCAAAATTGTACTAGGACTAGAATGGGTGTTGAATAATTTTAGGACCAATTTGGTGAGCGGTTATGATCCACTTCAAATGTTGACCGCTATAGAACATCTGATTTGAATACAATGGATCCTGCAGTTGCTCCAAACAAAATTTGAATGGCAGATTGTGACCTGATATAGATCTACAGCAATGATCACATTAAAACCATATTAACTGGATTTTTTTTATTTTTTCATATGAAGTTTTGGCAGTCTATTCATATTAAAACGATCTCTTAGAGACACTTTAGGATATTTTAGATGAGAAAATACCAATATTTAAAAATTAAATCCACATTTGATTAAATTATCCTAATTTAAAACAGATGGAAAATTATTTATTTTTAACGGTTGCATTCTCAAAACAAAAAAAACGTACAAAATCAATAATCTATCAAACCGTCTATAGAACAATACGTGTAATATTTTACACTAATTCCTATCCAGAGAAACAACACCAGGGGCGTAGCAACTGCAAGGGAACGGTGGAAACGTCCCCCTCACTTTTACAGACCGGCCATTTAGAAACCGATTATTTTAAGAATGTAAACTTTTGGATTTCATACAGCTGCACCCCCTGTATATCCTATTTGCATGTATTAACTGAACTCCTGAATTTCTTATAG
Seq C2 exon
GCCAGAGTGGTGCTGGAAACAACTGGGCCAAGGGCCACTACACTGAAGGAGCTGAGCTGGTTGATTCCGTTCTGGATGTGGTCCGAAAAGAGGCTGAGAGCTGCGACTGTCTGCAGGGCTTCCAACTCACTCACTCACTGGGTGGAGGTACAGGGTCTGGTATGGGCACCCTCCTCATTAGCAAAATCCGCGAGGAGTATCCCGACCGCATCATGAACACCTTCAGCGTGGTGCCCTCTCCTAAAGTCTCGGACACTGTGGTCGAGCCCTACAACGCCACACTGTCCGTCCATCAGCTAGTAGAGAACACAGACGAGACCTATTGTATTGATAACGAGGCCCTGTACGATATCTGCTTCCGCACACTCAAACTCACAACCCCCACATACGGAGACCTCAACCATCTCGTCTCCGCCACAATGAGCGGTGTGACCACTTGCTTGAGGTTTCCAGGCCAGTTGAACGCTGATCTCCGTAAATTGGCGGTCAACATGGTGCCCTTCCCCCGACTGCACTTCTTCATGCCTGGCTTCGCGCCTCTGACTAGCAGGGGAAGCCAGCAGTATCGTGCACTTACCGTTCCCGAACTCACCCAGCAGATGTTCGATGCCAAAAACATGATGGCTGCCTGCGACCCACGTCACGGCCGTTATCTGACGGTCGCCGCCGTCTTCCGTGGTCGCATGTCCATGAAGGAGGTGGACGAGCAGATGCTCAACGTCCAGAACAAGAACAGCAGCTACTTCGTTGAATGGATCCCAAACAACGTCAAGACCGCCGTCTGCGACATTCCACCACGAGGCCTCAAGATGGCCGCCACCTTCATCGGCAACAGCACCGCCATCCAGGAGCTCTTCAAGCGCATCTCAGAGCAGTTCACGGCTATGTTCAGGCGCAAGGCTTTCCTGCATTGGTACACCGGAGAGGGCATGGATGAGATGGAGTTCACAGAGGCCGAGAGCAACATGAACGACCTGGTGTCCGAGTACCAGCAGTACCAGGACGCCACCGCTGAAGAGGAAGGGGAGTTTGAGGAGGAGGGAGAGGAGGAGCTCGCTTAAATTAACCAGTCTGTTCCATCTTGTGTTTTCCCTTTCAAATCTTGTCACCTTATGTATTTTTTTTTTTTTTCGTACTGCATATCCTGTCACTTAAAACCTTCAGTTGTTCCTTTTCATGTTAATAAAAGAAACATAAGAACTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002344:ENSDART00000041279:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.099
Domain overlap (PFAM):
C1:
PF0009120=Tubulin=PD(41.9=65.0)
A:
NA
C2:
PF0009120=Tubulin=PD(59.0=37.0),PF0395312=Tubulin_C=WD(100=34.7)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGAGGTCTGGTCCATTTGG
R:
TAGCTGATGGACGGACAGTGT
Band lengths:
352-1369
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]