RnoINT0101369 @ rn6
Intron Retention
Gene
ENSRNOG00000020747 | Nkx2-5
Description
NK2 homeobox 5 [Source:RGD Symbol;Acc:620520]
Coordinates
chr10:16635989-16638764:+
Coord C1 exon
chr10:16635989-16636412
Coord A exon
chr10:16636413-16637844
Coord C2 exon
chr10:16637845-16638764
Length
1432 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
CTGCCTCTCCTTCCCTTCAGAGC
3' ss Score
12.39
Exon sequences
Seq C1 exon
GGACAGCGGGCACCATGCGGGAAGGCTATCCCCGGGGGTGGGCAGTGCCACTCTCTGCCACCCACCTGGCGCTGTGAGACCGGCGTCGCCACCATGTTCCCCAGCCCTGCGCTCACACACACGCCCTTCTCAGTCAAAGACATCCTGAACCTGGAGCAGCAGCAGCGCAGCCTGGCGGCTGGGGACCTGTCTGCGCGCCTCGAGGCCACCCTGGCGCCCGCCTCCTGCATGCTGGCCGCCTTCAAGCCGGAGGCCTACTCAGGCCCCGAGGCGGCAGCGCCCGGCCTGGCAGAGCTGCGCGCGGAGCTGGGCCCCGCGCCTTCGCCCCCCAAGTGCTCTCCTGCTTTCCCAACCGCCCCTACATTTTATCCGCGAGCCTACGGTGACCCTGACCCCGCCAAGGACCCTCGGGCGGATAAGAAAG
Seq A exon
GTAAGGAGAACCCCAAGTCCTTCCCTTCTGAAGTCGCTTCATGCCCAAAACCCTGAGTCAGGAAACCCAAGCCTGACAGTAGCTCGTCTGGGGTGAAGGCTGCGCGCGGGGAGATTGGAGTGTAAGATTCCAGGTTGTCCAGGATCTTCTCACCCCGCTGTCAATCGGAAGTTTAGAGGAAACACTGAATTTCGAGGATCAGAAAAAGGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATTAAAAATTGTTTTCGGCCTACAAAACTCCAGTAGGTTAGGGCCTTGCTCTTGGATCTGTTACCAAGTTAAGCTACCTAACAACTCTCGGTAGAATAAATCTTCTTATTGGAGAGTTAAAATCTCTTTCAGAATTGGGGGTATTTTTGAGAAACTCAGAATCGCTGAACCGAAAGCTTAGCCCCCGCAGATCTTGGGCCTTGTGTAGCCCATCCTGCCTTTCTGGGCCTTGCCTCCTTTGTGACAAAAGAGAAGAGTCTGGGGACAGTGTCGTGATTTTGAGACGCGATGCTGTGGATCCCAGGAGCTGGTGTTGGCTTTGTTTTTCCAGTACAATTTCCCAGCAGGATCAGGCAGAGATTTCTTTCTGGGGAATGTTGGAAAATATGGAACGAATAAAGAAAGACACAGAAGTGAACAACAGGCTTCCGAAGGTGGCTGAATACAAAATATCTCAGAGTAGGGAGTGGGACTCCTGGCCAGCTCACAGAAGGAACAGGGAAGACCCAGGCCCACCTCCGGGTCTGAGCAAAACCACAGAGGCCCAATAGCTTCTGCGAGTTAGAAAAGCATTCCCAAGTTTCTCTAGGAGTCAAGAGAAGGTCCAGTAACATCGGAGGAGGACTAGAGGAAGACTAGAACTGATTGCTACCAACTGGAATCCTGCAGGGCCGGTGTAGAGGCCTCCGTCCTCCCACGGTTACTGGGAACCGCACAAACATCAGCTGGCAGCCGTGCGGGAGACGCCAAGCTTTGGGCCTTCTAGTTCTTTAACTGCTTGTTTAAAGACAAGCTGACCACCCGAGGGTCAAACCGGAGTATTCCTAGCACAATTCACTCCCAGCATCCTTATGGTTATATTTTCTTTGCAGCCAGAAAATCTAAAACACAGACTGCCTTGAGAACGCGAACTATCCTGGGAAGGGGTTTGGGACGGGGCGCCTGAGATTTCTCTTGTTTTGTTTTGTCCTGAAACACAAGGTGTCCAAGCCACTTATGGTTTTCCCAGCTGCGCAGTTGCGCCAACCTCGAACCGTGCGAGCCCCGCGCACTCGGCGAGGAGCCTAAGCGGAGCTGTGCGTCCCGCACAGGACAAGGGTGACACCGCCACCGCCTCCCCACGAGGGCCCTGAACTCCCGGGCCCGCCGCTCTAACACACCGTCTCTCTGCCTCTCCTTCCCTTCAG
Seq C2 exon
AGCTGTGCGCGCTGCAGAAGGCGGTGGAGCTGGACAAAGCCGAGACAGACGGCGCCGAGCGACCACGCGCGCGGCGGCGACGGAAGCCACGCGTGCTCTTCTCGCAGGCGCAGGTCTATGAGCTGGAGCGGCGCTTCAAGCAACAGCGGTACCTGTCGGCGCCTGAGCGCGACCAACTGGCCAGCGTGCTGAAGCTCACGTCCACGCAGGTCAAGATCTGGTTCCAGAACCGCCGCTACAAGTGTAAGCGACAGCGGCAGGACCAGACTCTGGAGCTGCTGGGGCCGCCGCCGCCGCCCGCGCGCAGGATCGCGGTGCCGGTGTTGGTGCGCGACGGGAAGCCCTGCCTGGGGGACTCGGCGGCCTACGCTCCCGCCTACGGCGTGGGTCTCAACGCCTACGGCTACAACGCCTACCCCTATCCCGGCTACGGTGGCGCGGCCTGCAGTCCCGCCTACAGCTGCGCAGCCGCGTACCCCGCCGCGCCCCCCGCCGCGCAGCCCCCAGCCGCAGCGGCCAACAGCAACTTCGTGAACTTCGGCGTCGGGGACTTGAACACGGTGCAGAGTCCCGGGATGCCACAGGGCAATTCGGGCGTCTCCACGCTGCACGGCATCCGAGCCTGGTAGGGAAAGGGCCCGTCTGGGGCACCCCGGACCGACTCCCACCTTTAGGAGAAGGGCGATGACTCCGGGGATGGAAAGGCTCCCACTGTGTCCTGTCCCTCGGATTTCACACCCACACTTGCGCAGGCCTGGGACCTTTCTCCGATCCATCCCCTTTTGTTGACCTAACCTGATGCCTCGGTCCTGGGAAAGCCCTTCCAGGGCCAAGGCACCCTCCACGGATTCCCATACTAGGACCCGGAGCCTGGGCCGGGCGCCCGGGCCCTGGGTGCCTTGCCGCCACCCACCCACCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020747:ENSRNOT00000028155:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.532 A=NA C2=0.201
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=27.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACACGCCCTTCTCAGTCAAA
R:
GTCTGTCTCGGCTTTGTCCAG
Band lengths:
357-1789
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]