BtaINT0103601 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003650 | NR4A2
Description
Bos taurus nuclear receptor subfamily 4, group A, member 2 (NR4A2), mRNA. [Source:RefSeq mRNA;Acc:NM_001076208]
Coordinates
chr2:40011973-40013752:+
Coord C1 exon
chr2:40011973-40012838
Coord A exon
chr2:40012839-40013622
Coord C2 exon
chr2:40013623-40013752
Length
784 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TATATTGTCTCCTTTTGCAGCGC
3' ss Score
10.74
Exon sequences
Seq C1 exon
CCATGCCTTGTGTTCAGGCGCAGTATGGGTCCTCGCCTCAAGGAGCCAGCCCCGCTTCTCAGAGCTACAGTTACCACTCTTCGGGAGAATACAGCTCCGATTTCTTAACTCCAGAGTTTGTCAAGTTTAGCATGGACCTCACCAACACTGAAATCACTGCCACCACTTCTCTCCCCAGCTTCAGTACCTTTATGGACAACTACAGCACAGGCTACGACGTCAAGCCACCTTGCTTGTACCAAATGCCCCTGTCCGGACAGCAGTCCTCCATTAAGGTAGAAGACATTCAGATGCACAACTACCAGCAACACAGCCACCTGCCCCCACAGTCCGAGGAGATGATGCCGCACTCCGGGTCCGTTTACTACAAGCCCTCCTCGCCCCCGACGCCCACCACCCCGGGCTTCCAGGTGCAGCACAGCCCCATGTGGGACGACCCAGGCTCCCTCCACAACTTCCACCAGAACTACGTGGCCACTACCCACATGATCGAACAGAGGAAAACGCCGGTCTCCCGCCTTTCCCTCTTCTCCTTTAAGCAGTCGCCCCCCGGAACCCCCGTGTCTAGCTGCCAGATGCGCTTCGATGGGCCCCTGCACGTCCCCATGAACCCGGAGCCAGCGGGCAGCCACCACGTGGTGGACGGGCAGACCTTCGCCGTGCCCAACCCCATCCGAAAGCCCGCGTCCATGGGCTTCCCTGGCCTGCAGATCGGCCACGCGTCGCAGCTGCTCGATACGCAGGTGCCCTCCCCGCCGTCGCGGGGCTCCCCCTCCAATGAAGGGCTGTGCGCTGTGTGCGGTGACAACGCGGCCTGCCAGCACTACGGCGTGCGCACCTGTGAGGGCTGCAAAGGGTTCTTTAAG
Seq A exon
GTGAGCCAGGTCGGGGGCGGAGGAGGCAGCTAGGGGCCCCCTACTGTCCAGAGCCTCAGAGTGCTTGCTCCGCTGGGGCGCAGGCTTCGGACTCTAACTGGTCTCCAGCGACTCCCCGGGTCCCTGGAAGCTGCCTTGCCGCCGCCCCTAGGCTGTGGCGGGGGTTTCTGGGTGCCTGAGAAAGGCAAGTAGGAAGGCGGGGAGACCCGGGGTCGCATCTCCTCACGAGGCCGACGCTGGCCACCCCCCGCCTGAAGTTGCTGGAGCTGAGGTGGAAGAGGGTCATTTGCATGTGCTAGGAGCTGTCTTCTTGGTTCAGATTGAAATTGGTTAGGACAGAGAACCGTGTCTGAGCTAACCAAGTGGAACAGAATTCCCTGTGGTCAAATTAAGTGATCTCTTTATTTCGCCATCCTGATTGAATAATCTTATCATTTTAAATAGAGAAGGTCTCTAAGGAATGTAAATAATATGAATGCCCACGAATTTGTATTTACTGAGCGTCTCCTTCTCCTTCTCTTGGCATATAAAACACAGCAAGGAGCGGAAGGTTAGCTCAAATGTTAACGCTATCAATTTTCTTCTGTTAAATGCCCTGGGGGAGGGGAAAGAAAAGAGAGAGAAAGGAAAAAGGAAAAAATAAAAAGGAGTTGTGTATGTGTTTGTTTATGGTGAGGGAGTGTGGACCCTGTCCTCTCAGAAATTGTCCCTGGATTCCCTGAATTGTTGGATTTTCAAGAGAAAAAAAAAATTTTTTCCCGGCCTATATTGTCTCCTTTTGCAG
Seq C2 exon
CGCACGGTGCAAAAAAACGCGAAATACGTGTGTTTAGCAAATAAAAACTGCCCAGTGGACAAGCGGCGCAGGAATCGCTGTCAGTACTGCCGGTTTCAGAAGTGCCTGGCTGTTGGGATGGTCAAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003650:ENSBTAT00000004758:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.507 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PU(38.6=9.4)
A:
NA
C2:
PF0010513=zf-C4=PD(58.6=93.2)
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:
GTGTCTAGCTGCCAGATGCG
R:
TGCTAAACACACGTATTTCGCG
Band lengths:
345-1129
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]