RetrogeneDB ID: retro_opri_659

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_22445:13278..13620(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RBM8A
• Ensembl ID: ENSOPRG00000013316
• Aliases: None
• Description: RNA binding motif protein 8A [Source:HGNC Symbol;Acc:9905]

Sequence

>retro_opri_659
ATGGCGGACGTCCTGGATCTTCACGAGGCTGGGGGCGAAGATTTCACCATGGATGAGGATGGGGACGAGAGCATCCACAA
ACTGAAAGAAAAAGCCAAGAAGCGGAAGGGCCGCGGCTTTGGCTCAGAAGAGGGGTCACGGGCACGGATGCGAGAGGATT
ATGACAGTGTGGAGCAGGATGGGGATGAACCCGGACCGCAACGCTCTGTTGAAGGTTGGATTCTCTTTGTTACTGGAGTC
CATGAGGAGGCCACTGAGGAAGACATTCATGACAAATTCGCAGAATATGGAGAAATAAAAAATATCCAACTCAACCTGGA
CAGACGTACAGGATACTTGAAG

Alignment

ORF - retro_opri_659 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.25 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADVLDLHEAGGEDFAMDEDGDESIHKLKEKAKKRKGRGFGSEEGSRARMREDYDSVEQDGDEPGPQRSV
          MADVLDLHEAGGEDF.MDEDGDESIHKLKEKAKKRKGRGFGSEEGSRARMREDYDSVEQDGDEPGPQRSV
Retrocopy MADVLDLHEAGGEDFTMDEDGDESIHKLKEKAKKRKGRGFGSEEGSRARMREDYDSVEQDGDEPGPQRSV

Parental  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK
          EGWILFVTGVHEEATEEDIHDKFAEYGEIKNI.LNLDRRTGYLK
Retrocopy EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIQLNLDRRTGYLK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_659 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016021	1 retrocopy	retro_dnov_47,
Echinops telfairi	ENSETEG00000008411	1 retrocopy	retro_etel_1200,
Felis catus	ENSFCAG00000026379	1 retrocopy	retro_fcat_955,
Homo sapiens	ENSG00000131795	1 retrocopy	retro_hsap_1349,
Macropus eugenii	ENSMEUG00000016058	2 retrocopies	retro_meug_873, retro_meug_952,
Myotis lucifugus	ENSMLUG00000017436	2 retrocopies	retro_mluc_179, retro_mluc_1932,
Mus musculus	ENSMUSG00000038374	2 retrocopies	retro_mmus_137, retro_mmus_776,
Otolemur garnettii	ENSOGAG00000000202	2 retrocopies	retro_ogar_2694, retro_ogar_771,
Ochotona princeps	ENSOPRG00000013316	2 retrocopies	retro_opri_1146, retro_opri_659 ,
Rattus norvegicus	ENSRNOG00000021215	2 retrocopies	retro_rnor_1434, retro_rnor_1828,
Sorex araneus	ENSSARG00000013289	2 retrocopies	retro_sara_116, retro_sara_217,
Tupaia belangeri	ENSTBEG00000014947	2 retrocopies	retro_tbel_3548, retro_tbel_804,