RetrogeneDB ID: retro_opri_890

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_41397:8798..9056(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPY30
• Ensembl ID: ENSOPRG00000011833
• Aliases: None
• Description: dpy-30 homolog (C. elegans) [Source:HGNC Symbol;Acc:24590]

Sequence

>retro_opri_890
ATGGAGCCTGAGCAGATGCTGGAGGGAGAGACATAGGTTGCAGAGAATCCTCATTCTGAGTATGGCTTCACAGACAACAT
GGAAAGAATAGGAGAAAATGAGAAGGTTAATAATGAAGAGTCACAGAGGGTGGATCTGCAGTTTTTGCCAACTCATGCCT
ACATGTATCAGACAATTGTGCCTATCTTGTTACAGGGAATTGCTGTGCTTGCAAAGGAAAGACCACCAAAGCCTATTGAG
TTTCTAGTATCTTATCTT

Alignment

ORF - retro_opri_890 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 89.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEPEQMLEGQTQVAENPHSEYGLTDNVERIVENEKINAEKSSKQKVDLQSLPTRAYLDQTVVPILLQGLA
          MEPEQMLEG.T.VAENPHSEYG.TDN.ERI.ENEK.N.E.S..Q.VDLQ.LPT.AY..QT.VPILLQG.A
Retrocopy MEPEQMLEGET*VAENPHSEYGFTDNMERIGENEKVNNEES--QRVDLQFLPTHAYMYQTIVPILLQGIA

Parental  VLAKEXXXXXIEFLASLL
          VLAKE.....IEFL.S.L
Retrocopy VLAKERPPKPIEFLVSYL

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_890 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 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007768	1 retrocopy	retro_amel_89,
Canis familiaris	ENSCAFG00000005708	1 retrocopy	retro_cfam_1794,
Equus caballus	ENSECAG00000019630	1 retrocopy	retro_ecab_676,
Erinaceus europaeus	ENSEEUG00000012471	1 retrocopy	retro_eeur_239,
Echinops telfairi	ENSETEG00000006389	4 retrocopies	retro_etel_1156, retro_etel_1592, retro_etel_1796, retro_etel_682,
Felis catus	ENSFCAG00000026246	1 retrocopy	retro_fcat_1883,
Macropus eugenii	ENSMEUG00000006193	1 retrocopy	retro_meug_335,
Myotis lucifugus	ENSMLUG00000015346	2 retrocopies	retro_mluc_2327, retro_mluc_2367,
Monodelphis domestica	ENSMODG00000015481	1 retrocopy	retro_mdom_1962,
Mustela putorius furo	ENSMPUG00000005211	1 retrocopy	retro_mputfur_1063,
Mus musculus	ENSMUSG00000024067	1 retrocopy	retro_mmus_1867,
Oryctolagus cuniculus	ENSOCUG00000017877	1 retrocopy	retro_ocun_1751,
Otolemur garnettii	ENSOGAG00000034197	2 retrocopies	retro_ogar_3326, retro_ogar_3420,
Ochotona princeps	ENSOPRG00000011833	1 retrocopy	retro_opri_890 ,
Pteropus vampyrus	ENSPVAG00000005599	1 retrocopy	retro_pvam_1128,
Rattus norvegicus	ENSRNOG00000027126	1 retrocopy	retro_rnor_2141,
Ictidomys tridecemlineatus	ENSSTOG00000013372	2 retrocopies	retro_itri_361, retro_itri_75,
Tupaia belangeri	ENSTBEG00000017486	5 retrocopies	retro_tbel_1154, retro_tbel_1311, retro_tbel_1312, retro_tbel_3073, retro_tbel_4675,
Tarsius syrichta	ENSTSYG00000000146	1 retrocopy	retro_tsyr_1052,