DreINT0103782 @ danRer10
Intron Retention
Gene
ENSDARG00000035505 | nelfb
Description
negative elongation factor complex member B [Source:ZFIN;Acc:ZDB-GENE-040426-765]
Coordinates
chr5:28955797-28956924:-
Coord C1 exon
chr5:28956825-28956924
Coord A exon
chr5:28956028-28956824
Coord C2 exon
chr5:28955797-28956027
Length
797 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCG
5' ss Score
9.67
3' ss Seq
AGCGTGACCTTCTCTTGCAGGTG
3' ss Score
10.87
Exon sequences
Seq C1 exon
GTACGTAAAGCTGGAGGAACTACTTGAGAAAAGCTTTCCCCTAGTGAAGATGCCATCCATACAGCCGGTTGTCATGCAAGTTCTGAAGCATCTGCCAAAG
Seq A exon
GTACCGATGTGTGCTCTGACCTCTTACTAGTCCCTTCAGGATTTTGTGATCCAGTAATTGCAAAATCAAGCAAATGCAAAAATTCTGCTGATTTGTTCTTTGAGAGGCATCATGTGATGACGTTATTTGCAGAAGTTGGAGTAGGAGAACTGGAAGTTGGCTGGATGTGTAAATTCAGTGGCTACATTTCTGGTTGCTTGAAAACCATGCAGCAGCCATTCAAAGCATTAGACTAAAACATGTCAGAAAAGAGTGTTCTGAGTTGTAATATTACAGTTGATGCATCATGATTTTAATGTCCTGTATGATATATGTAGTGACAATATTGAAATAAGAAAAAAACGGCTCATTTTATTTTGTGGCGTAAAATAACTTTTTTTTACTTACAGCTCTTATCAAATTTAAAAAATGTCATTCATTCATCCATTTTGGTAGTTTTGTATCAAATATGATATAGTAGGCTTTAGGTAAAGTATCTCTTTTTATTGCTATTGCTCTTTTTATTTATCTTTTTTTAAAAGTATGTTGCTACTAATTTTCACAGCAGACCAACAAATGAATGCAAGAAATATTGATGCAAATTTTGAGAGAGAAAAACACTGAGAAAATCAGTCATTCAGAAAAATAATCAGTTAAATATTATAAATACTTTTTCATTGAAATCCTGATTGTATTGTATTGAATGTGGTAGTCAAGTGATCCACTTTTCAAGGTTGCACTACATTTAAATGTACATCAAACCATTTCAAAACAGTTTTAGGTTTGTCTGTCTTTGACAGCGTGACCTTCTCTTGCAG
Seq C2 exon
GTGCCTGAGAAGAAGCTGAAGCAGGTGATGGCGGATAAAGAGCTGTACAAAGTCTGCGCGGTGGAGGTGAAACGGCAAATCTGGCAGGACAATCAGGCTCTTTTTGGAGACGAGGTGTCTCCTCTCTTGAAACAGTATATTGTGGAGAAGGAAGCAGCTCTTTTTAGCAATGACCTCTCTATCCTGCACAACTTTTTCAGCCCTTCACCCAAAACACGGCGACAGGGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035505:ENSDART00000133949:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF062098=COBRA1=PU(3.4=47.1)
A:
NA
C2:
PF062098=COBRA1=FE(16.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGTAAAGCTGGAGGAACTACT
R:
CCCCTGTCGCCGTGTTTTG
Band lengths:
326-1123
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]