BtaINT0072893 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001553 | HNRNPA1
Description
Bos taurus heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001045911]
Coordinates
chr5:25939737-25940756:-
Coord C1 exon
chr5:25940691-25940756
Coord A exon
chr5:25940456-25940690
Coord C2 exon
chr5:25939737-25940455
Length
235 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
TATTCCATATTGTTCAACAGGAA
3' ss Score
8.23
Exon sequences
Seq C1 exon
GTGGCTATGGTGGCTCCAGCAGCAGCAGTAGCTATGGCAGTGGCAGAAGGTTTTAATTACTGCCAG
Seq A exon
GTAAGTGAACACCTTTTTTTGTTGTTATTCTCACTTAATTGTAATTTATAATGAACCCAGTAACCCTAATATAGCTGAGCAGTGCAACATAGTTAACATTATAATTACAGTAAAATTGTGGATATTAAGTTAATATTCAGATCAGCAAAATTTGTGGGAAACAACTTGCTATTGGATTGTAGCCTTGAGTCTTAATATGTTTAGATTAACAACTTTATTCCATATTGTTCAACAG
Seq C2 exon
GAAACAAAGCTTAGCAGGAGAGGAGAGCCAGAGAAGTGACAGGGAAGCTACAGGTTACAACAGATTTGTGAACTCAGCCAAGCACAGTGGTGGCAGGGCCTAGCTGCTACAAAGAAGACATGTTTTAGACAATACTCATGTGTATGGGCAAAAAACTCGAGGACTGTACTTGTGACTAATTGTATAACAGGTTATTTTAGTTTCTGTTCTGTGGAAAGTGTAAAGCATTCCAACAAAGGGTTTTAATGTAGATTTTTTTTTTGCACCCATGCTGTTGATTGCTAAATGTAATAGTCTGATCATGACGCTGAATAAATGTCTTTTTTTTTTTTTTTAATGTGCTGTGTAAAGTTAGTCTACTCTGAAGCCATTTTGGTAAACTACCCCAACAGTGTGAAGTTAGAATTCCTTCAGGGTGATGCCAGGTTCCATTTGAAATTTATTTACAACCTGCTTGGTGGAGAAGCTGTTGTCTTCAGAACCTTGGTGTAGTTGAACTGACAGTTACTGTGTTGTGACCTGGAGTCCACCATTAAAAGGGTCACCCATGCAAAGTCATGGAGTTTTTTTTTATTTTTTTTGGTTATTAATGATTGTTGGCACATCCTATGCAATATATCTAAATTGAATTATGGTACCAGATAAAGTTATAGATGGGAATGAAGCTTGTGTATCATCCATTATCATGTGTAATCAATAAAAGATTTAATACCCTCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001553:ENSBTAT00000002033:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCAGCAGCAGCAGTAGC
R:
ACCCTTTGTTGGAATGCTTTACAC
Band lengths:
294-529
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]