BtaINT0072891 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001553 | HNRNPA1
Description
Bos taurus heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001045911]
Coordinates
chr5:25940997-25942129:-
Coord C1 exon
chr5:25942055-25942129
Coord A exon
chr5:25941153-25942054
Coord C2 exon
chr5:25940997-25941152
Length
902 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGT
5' ss Score
11.81
3' ss Seq
GTCCTCTTTTCCATTCTTAGGAA
3' ss Score
10.59
Exon sequences
Seq C1 exon
GTGGCTTTGGTGGCAGCCGTGGTGGTGGCGGATATGGTGGCAGTGGGGATGGATATAATGGATTTGGTAATGACG
Seq A exon
GTAAGTTTTTTTAAAGAACCACAGGTAAAAAATTTTGGCAACCTTTAGAATAGGTTAGTAGAGACTAAAACCCTAGTGCATGATAAGCTCAACAATGATCTAATAGCATGTTGTGAGCAGGCCTTTAGCCATGCTTGCACAGAATTTGACTGCTGAATACTTTTGTCTTATTGAGAAGACTTGTATTCTTGTAGGTGGTTATGGAGGAGGCGGCCCTGGTTACTCTGGAGGAAGCAGAGGCTATGGAAGTGGTGGACAGGGTTATGGAAACCAGGGCAGTGGCTATGGCGGGAGTGGCAGCTATGACAGCTATAACAACGGTGGAGGCGGAGGCGGCTTTGGCGGTGGTAGTGGTAGGTATCCAGTGATCCAAGTACTTGGTGCAATAGCTAGATTAGCCTTTTAGAGTTTATCCTTAGGAGGATTTGATGGTTTTAAAGCATTGTGTGTTGTGCTGCATGGTACTTTTTTTTAATGGGCTTGCAATGCTACCTCCTCCTAGCTTTAAGCTGGGGCCGCCTCACTCCCAAATAGATAGATGGTTAAGTGGATAGTGGTGTCTTCAATTGGAATTAGATTAGCGTCTAGCAGGATTTAGTGTTAACTCTTGGGATCTTAGGCGCTTAGTTGATGTATCCAGCATGTGTTTGCTGTGCCCCTGGCTGGGTGAAGGCCTTAAAGGCGAGAGAATGTGTACCTTTTGTTATGCCATGGTGAGTTGGGTGAAGTTTTAGTTAATTGGATTATTCAATTGAGTGCCTTGCACATGAAATACAAAGATGATTGAAATTGGAGCCACAGAAGTTTGGGAGCAAGGCAGATCAAGCAACTTTTTTACCCTGAACACTAGGATTTCTCATTTTCCCTGAATAACATATAAAGGTCCTCTTTTCCATTCTTAG
Seq C2 exon
GAAGCAATTTTGGAGGTGGCGGAAGCTACAATGATTTTGGCAATTACAACAATCAATCTTCAAATTTTGGACCCATGAAAGGAGGAAACTTTGGAGGCAGAAGTTCTGGCCCCTATGGTGGTGGAGGCCAATACTTTGCCAAACCACGAAACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001553:ENSBTAT00000002033:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.692 A=NA C2=0.830
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF116273=HnRNPA1=WD(100=67.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTTGGTGGCAGCCGTGG
R:
TGGTTTCGTGGTTTGGCAAAG
Band lengths:
225-1127
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]