BtaINT0088997 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019075 | MAP1D
Description
Bos taurus methionyl aminopeptidase type 1D (mitochondrial) (METAP1D), mRNA. [Source:RefSeq mRNA;Acc:NM_001046342]
Coordinates
chr2:24527589-24529917:-
Coord C1 exon
chr2:24529732-24529917
Coord A exon
chr2:24527739-24529731
Coord C2 exon
chr2:24527589-24527738
Length
1993 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTG
5' ss Score
8.56
3' ss Seq
TTCAATCCTTTTTCCTCAAGCAC
3' ss Score
4.89
Exon sequences
Seq C1 exon
CTTAACATACGTCTATTTCTGCTCCCAGGTTGTCATAGGATTTTCTCGTCACCACTCAATCATATCTACTTACACACACAGTCAACCAGTCAACAAAGAAGAAATTTCTTTTTCCGGAGACAAAGAGAGATTTCCCACAATATAGTTTTGCCGGCTGCAGTTTCTTCAGCTCATCCAGTCCCGAAG
Seq A exon
GTACTGCATTGCCTAGTATCTGTTGCTTTTTCCAGCCAAGATAAAGGTTAACTGCAGAAGCCATGGAGTGTTTTCGCGCCTTTGATTTCTGAGGCATCTGAATTATAATTTTTAAACTTAGTCTGTGATATAAAACTGTGGTTTGGGAAGTGTTAACATCCTGCAGTTCTATAATATTCACTTTTTAAAATAAGGCACTGAGCTTCTAACTGCTTAGTTCTTTAGAATTTAAATTTCTATCATGAAATTTTCCATATTAAATTTCTACCATGAAGATAAGATTCTATGTATATAGTTTCTTTAACTTTAAAAAAAAATTTTTTGACAACAGTTGGAATCATTTAAGAAAGATTCCTTGAAACCAATACACTAGGCGTTTTTTTCCTAAAGCTTGCTGTTACATTTTCTGTGTTACTATTAATGCTGTCTTTCAATTGCCCTTTAGAGTAAATTAAATAAAACATCTTGTCTCAAAGCATTCTTGATTTTTTTCAGAGAGTATAGTTCTGTGAAAGACAATCTATCCATTTTTCCAGATGCAATGTAAAGGAGGTGTGGGGATCAATTAGGAAGAGTGAGAATAGCTGAAAGAAATAAAGATTTGCCACGAAAATCACCTGCTTTCCCTCTTTCTATGACTTTTTTTGCAGGGTAGTAAATCAACATTAAGTATATCATACTCCCTGAAGGTGAGTGGCTCATTTTTGTGACAAGGGCTGACAAGACAGGCCACCAGAGCCCAGAGTATGTTTCTGGTATTTCCTTAGTAGAAAACAAAAAAGAAGTCTCCAGAGAGGTGAATGTATTGTTTTAGAATTTCAGTGACAAGCCAACAGCCCTTCTGCCTGTGGTTGTAACCTGGCCAGATTGCAAAGCCAGGAGGAGGCGGGGCTGTGGAGATGGGAGTGCTTTGTGGGCACTGGTACCGAAGCCAGAGGGAAGATGCTCACTCCACGCTTGGCTGTGGCAGCCCAAGTGGTGATGTTACCTGTGTCAGAAAGGCCCATCTGAACACAGGGATAAGTGAAGGTCCTTAAATCCTGTGTGATGCAGTTCACAAAGCACAGAGCCCTAACCTTAGCCCTTCCAGAGTTGCTGTGATGTTCATTGAATAGTGTTATCTCCCTCAGCTTCCTGTCCCCAAAGTCTGTGTAGCCTTACTGGGTGCTGTTCAACAAAACTTATGTAGCTGTTGCCATAAATAGTTGGTAAAGAGCTGTGCAAAACCTGGGTCTGAAAGGAGCTCTGTGTGTGAGACAGTATTTATTTGCTGAATACCGCCCATGGATTTAAGTTAGTGGGGGAGAAGGTTCTCCAAGGGTGGTCAGAGTTGAACATTTTGAGTTTCAGAGGAGGAAGGAGTTTGTTTTTGACAAATTATGAAAGTGTGCAAAGTATTTTTTATGTACTTGGGGGAAAAGAAAGGAAAAGGCAAAAGAGCTGTTTTGTTTTGTCCTCTAGTTCCTTCTTAGTTTGGGTACAGTTGCAACATGTAGGGGAAGTGTGTATTTGATAGGCATCCATGAACTTGACAGTCTGCCTTTTACATACATTCATTGGGAGAGGGTGTTGTGGGCTACCCTTTGCATAAATTTTATCTTTGTGTCGAGGAGATGAAAGCACTCTTAATTAACCATTTGGCGGTTGGGGAACTGGGTGCTATTTGTCATCAATAACAATTCTAAGAGGGTTGGAGGAGGAAGAAAAGAAAACTCCTGTTTGTTTTGACCAGAAGTCTCCTTCAGTCCAGTGTGACTCAAAGCACCAGTAAGGTTAACAGACCATCCAGAGGCAGCACTAACAGGCCACGTTAAGTTCAAAAGGGCAGGGGAAGGAACCGGGGGCAGCCTGGAGGGTCTGTTGTGCTGGCTTCGGAGGTCGGTGCTCCGGCAGGAAGGGCAGAGCTCCATGAAGCAGGAGGCTGTGTGCGAAAAAATGATCCCATTGTCGTGCGCTGGGTTCTGATCTTCGTTTTCAATCCTTTTTCCTCAAG
Seq C2 exon
CACATAAAGAAGCCAGACTATGTGACGACAGGAATTGTACCCGACTGGGGAGACAGCATAGAAGTTAAGAATGAAGATCAGATTCAAGGGCTTCTCCAGGCTTGTCAGCTGGCCCGACATGTCCTCCTCTTGGCCGGGAAGAGTTTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019075:ENSBTAT00000025394:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0055719=Peptidase_M24=PU(9.2=42.0)
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:
TAACATACGTCTATTTCTGCTCCCA
R:
CTTTAAACTCTTCCCGGCCAAGA
Band lengths:
334-2327
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]