GgaINT0014717 @ galGal3
Intron Retention
Gene
ENSGALG00000006500 | NDE1_CHICK
Description
NA
Coordinates
chr14:7618978-7620885:+
Coord C1 exon
chr14:7618978-7619114
Coord A exon
chr14:7619115-7620209
Coord C2 exon
chr14:7620210-7620885
Length
1095 bp
Sequences
Splice sites
5' ss Seq
AGGGTTAGT
5' ss Score
5.02
3' ss Seq
ATTCTGCTTTGTATTTGCAGGTT
3' ss Score
9.85
Exon sequences
Seq C1 exon
GCTTTGGAGTCCAAACTTGCCTCCTGCCGAAACTTTGTGTATGACCAGTCTCCAGACAGAACCACAGTGTCCATGTACATGAATAGAGATGCCCTTGAAACACGCATGAGTCCTCACCAGCCTCTCTGTGATACAGG
Seq A exon
GTTAGTGCCATTCTCAGCTGTTTTGTCTTAGAACCCTTTGACTGGTACTGTTCTGTTTCTTGTTTGTTCTTTATTTTGGTAGAGCAAGACCTGTTTCCGAAAGGTAGGAAACTTAGTTATTCAAGATTGATTTCCATGTTTCAGATCAGTTTAAAAATTGTAATCACAAGCTGTTGAAATCTGAAGACTAGCTGTGATCAAGTTCAAATTCAAAGCAATTGTAACACATTATAATAAAACCAGTGTTTAAATGTGAGCAAGTACAACTGAGGAAGTTCGTGCTTATTGGCTTGGTTTGGTTATGCTTTGTTCTTGTGCAATGATGAATCAGCAACATTTTGGCATATGGGGATTTCTCTTATCACAGTTAGGATTTTTATCCATATGAGAGTTGGGGGGTGGGAGGAAGCGAATAATGAATTGACTCATTTGAATGCTTTATGGTTGCTAAGATGTATTTCCAGGGAGCAACTGTCAAAAGCTATTACCTACTGAACTGGTCATCTCTTTCCTCCCACTCCCAAATACGAAAAATTTATAAGTTTATTGCAAATTAGAGTTCAGTACCTAAGCCATGAAATCTTGTATGGGGTGGGTTTTTTTTTTTTTTTTCCCAAGTTTCCTGGCTGTTTATAGTACAGATTATTGCAGATGCAACTGTTCAGCCAGACCCTTAATCTGGGAATACGCGCTTGTCCTGTTAAACAATGCCCAAAGTTGTCACGTGGAAAGAATGTTCCATGTAGTACTTGCTATTGCAGCCTGGGGAGAAACCTACAAGAAAGCCTCAAGGGCCATACATTTGCATATTCCTATAGGTGATTACATATCCATTACTGTAATATAAGAACTGAAATTCTAACTCCTGTAAAATCTAGCCTCTCACTACTCAAAGGGAAATGGAACCTTGTTTTACAGTGGACAACTTAGCCTAGTGAAGTAACAAGCTCACTTGATATTCAGACCATTGTTTTGTTTTTTTTTAATCTGTTGGCTTTTCTGGCTTAGTGTTGCATTCTTGCAAATGATCAGTTACTGTGATTGAGATGGTAAAACTGAGCAAGAAGTGCTCTAAATTCTGCTTTGTATTTGCAG
Seq C2 exon
GTTAGTGAAACGCCTGGAGTTTGGAACAAGACCTTCAAGTACTCCAGGACCAATGAGCCATCCTTCACAAAGTGTTGTTAAGATGCTGCTATGAAAAGGAAAAATAAAATCTTATGTACATATAACTTGAATATCAATAGGCAACCAGACAGAAGTGTAAGAGTAGTTGAGGCCTGAAAAAGGAACTACTGTTGATAATGGCATCTTATGGCTTTGCCCTTCTGGCTTCTATGCTGAGTTGTGTGCGTGGTGTGATGAAGCAATGTTGCCTAGCAGCACAGGACATAAAATTGCTTCCTGTATTCACTGCTGTGAATAACTCCTGCTTTGACACTGCCAGTTAAAGCTATCGTCGCTTTACCTACAGCAGGTTCCCAGTGCAACTCTTTAGGTTTTGGCTTTTGGTGTTAATAAAATTGCCCATGATTTCTGGCTTTCTGGTGCAGTCACTGAAGTTAGAGAAGTGGTTGTAGGTAGAAACAGGTGTATTTCTGTGGAGAAACAGTTTAGTTCTTTGTAGGTTGCTTGCTGGTCAGAATCTCGTGGTGAAGCTCTGTAAGCAATGATTTACCTTGTAGAGCAGATAACAGTTAAAAGGTGAGGAATGCTTAATACTTCTGGTACTCAGGAGATCCCAGATGGTAGAGAACTTTGCCCTGGATTAGCCTGTAGATAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006500:ENSGALT00000040196:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.391 A=NA C2=0.677
Domain overlap (PFAM):
C1:
PF048808=NUDE_C=FE(22.7=100)
A:
NA
C2:
PF048808=NUDE_C=PD(10.1=62.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg19)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGACAGAACCACAGTGTCC
R:
TTCATCACACCACGCACACAA
Band lengths:
345-1440
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]