RetrogeneDB ID: retro_opri_1078

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_6691:21255..21511(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000008349
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DSTN
• Ensembl ID: ENSOPRG00000000976
• Aliases: None
• Description: destrin (actin depolymerizing factor) [Source:HGNC Symbol;Acc:15750]

Sequence

>retro_opri_1078
TGTGGCTATGCTTTGTATGACGCCAGATTTGAAACCAAGGAATCCAGAAAAGAAGAACTGATATTCCTTTTGGTGGGCAT
CAGAACCAGCACCTCTGAAAAGTGAAATGAGCTCTGCAGATTCCAAGGATGCAATCAGAAGAAATTGCAAGGGATAAAAC
CTGCATGTCAGGCCCATGCGCCAGAAGACCTCAGTCGGGCACAGTGCAGAGAAGCTGGGTGGGTCCTTAACTGCAGCTTT
TGAAGGATGCCCCGTG

Alignment

ORF - retro_opri_1078 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.29 %
• Parental protein coverage: 52.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CRYALYDASFETKESRKEELMF-FLWAPELAPLKSKMIYASSKDAIK-KKFQGIKHECQANGPEDLNRAC
          C.YALYDA.FETKESRKEEL.F.F.WA.E.APLKS.M..A.SKDAI..KK.QGIK..CQA..PEDL.RA.
Retrocopy CGYALYDARFETKESRKEELIF>FWWASEPAPLKSEMSSADSKDAIR<KKLQGIKPACQAHAPEDLSRAQ

Parental  IAEKLGGSLIVAF-EGCPV
          ..E..G..L...F.EGCPV
Retrocopy CRE-AGWVLNCSF>EGCPV

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_1078 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 20 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015434	1 retrocopy	retro_btau_880,
Choloepus hoffmanni	ENSCHOG00000003110	5 retrocopies	retro_chof_1308, retro_chof_1656, retro_chof_1758, retro_chof_2297, retro_chof_72,
Cavia porcellus	ENSCPOG00000005573	2 retrocopies	retro_cpor_700, retro_cpor_812,
Dasypus novemcinctus	ENSDNOG00000000934	1 retrocopy	retro_dnov_24,
Erinaceus europaeus	ENSEEUG00000011893	1 retrocopy	retro_eeur_529,
Homo sapiens	ENSG00000125868	1 retrocopy	retro_hsap_952,
Gorilla gorilla	ENSGGOG00000009007	1 retrocopy	retro_ggor_768,
Microcebus murinus	ENSMICG00000013687	1 retrocopy	retro_mmur_765,
Macaca mulatta	ENSMMUG00000013786	1 retrocopy	retro_mmul_782,
Mus musculus	ENSMUSG00000015932	1 retrocopy	retro_mmus_3314,
Nomascus leucogenys	ENSNLEG00000009679	1 retrocopy	retro_nleu_2458,
Oryctolagus cuniculus	ENSOCUG00000027456	1 retrocopy	retro_ocun_1891,
Ochotona princeps	ENSOPRG00000000976	2 retrocopies	retro_opri_1078 , retro_opri_696,
Pongo abelii	ENSPPYG00000010727	1 retrocopy	retro_pabe_812,
Pan troglodytes	ENSPTRG00000013275	1 retrocopy	retro_ptro_659,
Pteropus vampyrus	ENSPVAG00000000420	1 retrocopy	retro_pvam_1275,
Rattus norvegicus	ENSRNOG00000005924	1 retrocopy	retro_rnor_1710,
Sus scrofa	ENSSSCG00000007085	1 retrocopy	retro_sscr_954,
Tupaia belangeri	ENSTBEG00000017634	8 retrocopies	retro_tbel_1206, retro_tbel_1977, retro_tbel_2425, retro_tbel_2880, retro_tbel_2881, retro_tbel_4020, retro_tbel_679, retro_tbel_851,
Tursiops truncatus	ENSTTRG00000007291	1 retrocopy	retro_ttru_1503,