RetrogeneDB ID: retro_opri_308

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_5019:264735..265175(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAGOHB
• Ensembl ID: ENSOPRG00000000548
• Aliases: None
• Description: mago-nashi homolog B (Drosophila) [Source:HGNC Symbol;Acc:25504]

Sequence

>retro_opri_308
GCCATGGAGAGTGACTTTTACCTGCGCTACTACGTGGGCCACAAGGGCAAGTTCAGCCATGAATTATTGGAGTTTGAGTT
CCAACCCAATGGGAAATTAAGATATGCCAACAACAGTAATTACAAAAATGATGTCATGACCAGAAAAGGGGCTTATGACA
TAAAAGTGTGATGAAGGAACTGAAGAGAATAATTGATGACAGTGAAATTACCAAAGAGGACGAAGCTTTGTGGCTTTCTC
CTGATCGAGTGGGCCTGCAGGAACTTGAAATCGTCATTGGAGATGAACACATTTCTTTCACAACGTCAAAAGTTGGTTCC
CTTATTGATGTCAATAGGGCCAAGGATCCAGAAGGCTTGCGATTATTTTATTATCTTGTCCAGGATCTGAAGTGCTTGGT
CTTCAGTCTCATTGGTTTACACTTCAAGATTAAACCAATC

Alignment

ORF - retro_opri_308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.16 %
• Parental protein coverage: 99.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SMASDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYV-HKSVMEELKRIIDDSE
          .M.SDFYLRYYVGHKGKF.HE.LEFEF.P.GKLRYANNSNYKNDVM.RK.AY..HKSVM.ELKRIIDDSE
Retrocopy AMESDFYLRYYVGHKGKFSHELLEFEFQPNGKLRYANNSNYKNDVMTRKGAYD<HKSVMKELKRIIDDSE

Parental  ITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIG
          ITKED.ALW..PDRVG.QELEIVIGDEHISFTTSK.GSLIDVN..KDPEGLR.FYYLVQDLKCLVFSLIG
Retrocopy ITKEDEALWLSPDRVGLQELEIVIGDEHISFTTSKVGSLIDVNRAKDPEGLRLFYYLVQDLKCLVFSLIG

Parental  LHFKIKPI
          LHFKIKPI
Retrocopy LHFKIKPI

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_308 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 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019235	1 retrocopy	retro_btau_399,
Choloepus hoffmanni	ENSCHOG00000004382	1 retrocopy	retro_chof_1730,
Callithrix jacchus	ENSCJAG00000021662	7 retrocopies	retro_cjac_1336, retro_cjac_1840, retro_cjac_1858, retro_cjac_2354, retro_cjac_3234, retro_cjac_3250, retro_cjac_546,
Dasypus novemcinctus	ENSDNOG00000005997	4 retrocopies	retro_dnov_140, retro_dnov_347, retro_dnov_423, retro_dnov_891,
Echinops telfairi	ENSETEG00000016591	3 retrocopies	retro_etel_1022, retro_etel_1566, retro_etel_2147,
Homo sapiens	ENSG00000111196	1 retrocopy	retro_hsap_1360,
Macropus eugenii	ENSMEUG00000001782	1 retrocopy	retro_meug_324,
Myotis lucifugus	ENSMLUG00000003527	2 retrocopies	retro_mluc_1039, retro_mluc_2484,
Macaca mulatta	ENSMMUG00000005082	1 retrocopy	retro_mmul_1246,
Monodelphis domestica	ENSMODG00000000462	1 retrocopy	retro_mdom_424,
Nomascus leucogenys	ENSNLEG00000003355	1 retrocopy	retro_nleu_1395,
Ochotona princeps	ENSOPRG00000000548	2 retrocopies	retro_opri_1171, retro_opri_308 ,
Ochotona princeps	ENSOPRG00000009020	1 retrocopy	retro_opri_521,
Pan troglodytes	ENSPTRG00000004679	2 retrocopies	retro_ptro_1179, retro_ptro_932,
Sus scrofa	ENSSSCG00000000635	1 retrocopy	retro_sscr_971,
Ictidomys tridecemlineatus	ENSSTOG00000000835	1 retrocopy	retro_itri_212,
Tupaia belangeri	ENSTBEG00000014820	7 retrocopies	retro_tbel_1250, retro_tbel_1393, retro_tbel_210, retro_tbel_2259, retro_tbel_2723, retro_tbel_2878, retro_tbel_451,
Tarsius syrichta	ENSTSYG00000010452	7 retrocopies	retro_tsyr_1730, retro_tsyr_1748, retro_tsyr_383, retro_tsyr_658, retro_tsyr_81, retro_tsyr_908, retro_tsyr_966,
Tursiops truncatus	ENSTTRG00000001272	2 retrocopies	retro_ttru_515, retro_ttru_647,