RetrogeneDB ID: retro_opri_1092

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_7023:103616..103845(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSBP1
• Ensembl ID: ENSOPRG00000005658
• Aliases: None
• Description: heat shock factor binding protein 1 [Source:HGNC Symbol;Acc:5203]

Sequence

>retro_opri_1092
GAAACTGACCCCCCCACCCCATAGATGGTACAGGGTCTTATCTCGGCAGTAAAGACACTTCTGCAACAGGTGCAAGACGT
GTCAGTTACATCTTGTCAGTTCAATCATGGGGAGAAATAATGGTATGAGCAAACACATCAAAGAAATGAAGCAAAACATA
ACAGACCTCACAACACAGGCTGGGGTGGAAGAGCTGGAAAGTGCAAATAAGATCCCCGTCGCACAGAAG

Alignment

ORF - retro_opri_1092 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.85 %
• Parental protein coverage: 96.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ETDPKT---VQDLTSVVQTLLQQMQDKFQT-MSDQIIGRTLDDMSSRIDDLERNIADLMTQAGVEELEGE
          ETDP.T...VQ.L.S.V.TLLQQ.QD...T.....I.GR....MS..I.....NI.DL.TQAGVEELE..
Retrocopy ETDPPTP*MVQGLISAVKTLLQQVQDVSVT>LVSSIMGRN-NGMSKHIKEMKQNITDLTTQAGVEELESA

Parental  NKIPATHK
          NKIP...K
Retrocopy NKIPVAQK

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_1092 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 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006485	3 retrocopies	retro_amel_20, retro_amel_261, retro_amel_646,
Canis familiaris	ENSCAFG00000019973	4 retrocopies	retro_cfam_1712, retro_cfam_395, retro_cfam_772, retro_cfam_874,
Callithrix jacchus	ENSCJAG00000000641	5 retrocopies	retro_cjac_1824, retro_cjac_2156, retro_cjac_3997, retro_cjac_708, retro_cjac_762,
Dasypus novemcinctus	ENSDNOG00000015303	3 retrocopies	retro_dnov_2535, retro_dnov_607, retro_dnov_7,
Equus caballus	ENSECAG00000026920	1 retrocopy	retro_ecab_580,
Homo sapiens	ENSG00000230989	2 retrocopies	retro_hsap_3076, retro_hsap_3367,
Latimeria chalumnae	ENSLACG00000022519	1 retrocopy	retro_lcha_96,
Loxodonta africana	ENSLAFG00000014112	2 retrocopies	retro_lafr_108, retro_lafr_15,
Macropus eugenii	ENSMEUG00000011483	2 retrocopies	retro_meug_1525, retro_meug_47,
Myotis lucifugus	ENSMLUG00000007636	1 retrocopy	retro_mluc_653,
Macaca mulatta	ENSMMUG00000020115	4 retrocopies	retro_mmul_169, retro_mmul_2120, retro_mmul_2184, retro_mmul_291,
Nomascus leucogenys	ENSNLEG00000026776	3 retrocopies	retro_nleu_1827, retro_nleu_2018, retro_nleu_963,
Otolemur garnettii	ENSOGAG00000015437	7 retrocopies	retro_ogar_1493, retro_ogar_2454, retro_ogar_2898, retro_ogar_488, retro_ogar_558, retro_ogar_796, retro_ogar_826,
Ochotona princeps	ENSOPRG00000005658	1 retrocopy	retro_opri_1092 ,
Procavia capensis	ENSPCAG00000004899	2 retrocopies	retro_pcap_322, retro_pcap_445,
Pan troglodytes	ENSPTRG00000008401	3 retrocopies	retro_ptro_2075, retro_ptro_2288, retro_ptro_920,
Pteropus vampyrus	ENSPVAG00000006994	1 retrocopy	retro_pvam_1024,
Tupaia belangeri	ENSTBEG00000006478	1 retrocopy	retro_tbel_25,
Tarsius syrichta	ENSTSYG00000006648	7 retrocopies	retro_tsyr_1351, retro_tsyr_1428, retro_tsyr_1655, retro_tsyr_424, retro_tsyr_646, retro_tsyr_756, retro_tsyr_824,
Tursiops truncatus	ENSTTRG00000008666	3 retrocopies	retro_ttru_1618, retro_ttru_849, retro_ttru_866,