RetrogeneDB ID: retro_opri_1168

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_8411:75791..76333(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAR1
• Ensembl ID: ENSOPRG00000012089
• Aliases: None
• Description: GAR1 ribonucleoprotein homolog (yeast) [Source:HGNC Symbol;Acc:14264]

Sequence

>retro_opri_1168
GCAGAAGAGATCATGTCTTTCGAGGCGGAGGTCGTGGAGGCTTTAATAGGGGTGGTGGGGGTGGCGGTTTCAACCGTGGC
GGCGGCAACAGCCATTTCCGAGGCGGAGGAGGCGGCTTCCGAGGCGGCGGCGGCAGAGGAGGATTCGGACGAGGGGGTGG
CCGTGGGGGCTTTAACAAGGGCCAGGACCAAGGACCTCCGGAACACGTAGTCATATTAGGAGAGTTCATGCACCCTTGTG
AAGATGACATAGTTTGTAAATGCACCACAGATGAAAATAAAGTGCCTTATTTCAATGCTCCTGTGTATTTAGAAAACAAA
GAACAAATTGGAAAAGTGGATGAAATATTTGGACAACTTAGAGATTTTTATTTTTCAGTTAAGTTGTCAGAGAACATGAA
GGCGTCTTCCTTTAAAAAACTACAGAAGTTTTACATAGATCCCTATAAGCTGCTGCCGCTGCAGAGGTTCCCGCCCCGGC
CCCCCGGGGAGAAAGGCCCTCCCAGAGGCGGAGGCCGGGGCGGCGCTGGAGGAGGCGGCAGA

Alignment

ORF - retro_opri_1168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.99 %
• Parental protein coverage: 73.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEEIMS-FRGGGRGGFNRGGGGGGFNRGGGNSHFRGGGGGFRGGGGRGGFGRGGGRGGFNKGQDQGPPEH
          AEEIMS.FRGGGRGGFNRGGGGGGFNRGGGNSHFRGGGGGFRGGGGRGGFGRGGGRGGFNKGQDQGPPEH
Retrocopy AEEIMS<FRGGGRGGFNRGGGGGGFNRGGGNSHFRGGGGGFRGGGGRGGFGRGGGRGGFNKGQDQGPPEH

Parental  VVILGEFMHPCEDDIVCKCTTDENKVPYFNAPVYLENKEQIGKVDEIFGQLRDFYFSVKLSENMKASSFK
          VVILGEFMHPCEDDIVCKCTTDENKVPYFNAPVYLENKEQIGKVDEIFGQLRDFYFSVKLSENMKASSFK
Retrocopy VVILGEFMHPCEDDIVCKCTTDENKVPYFNAPVYLENKEQIGKVDEIFGQLRDFYFSVKLSENMKASSFK

Parental  KLQKYYIDPYK-PPLQEGPWPRPPGRKGPPRGGGGAGAGGAGR
          KLQK.YIDPYK..PLQ..P.PRPPG.KGPPRGGG..GAGG.GR
Retrocopy KLQKFYIDPYKLLPLQRFP-PRPPGEKGPPRGGGRGGAGGGGR

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_1168 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 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004605	2 retrocopies	retro_amel_1932, retro_amel_682,
Homo sapiens	ENSG00000109534	1 retrocopy	retro_hsap_3130,
Gorilla gorilla	ENSGGOG00000008681	1 retrocopy	retro_ggor_2144,
Myotis lucifugus	ENSMLUG00000003776	1 retrocopy	retro_mluc_1866,
Macaca mulatta	ENSMMUG00000021225	1 retrocopy	retro_mmul_1992,
Mustela putorius furo	ENSMPUG00000008615	2 retrocopies	retro_mputfur_1491, retro_mputfur_689,
Mus musculus	ENSMUSG00000028010	1 retrocopy	retro_mmus_2012,
Nomascus leucogenys	ENSNLEG00000016578	1 retrocopy	retro_nleu_2251,
Oryctolagus cuniculus	ENSOCUG00000003901	1 retrocopy	retro_ocun_414,
Otolemur garnettii	ENSOGAG00000004693	1 retrocopy	retro_ogar_1017,
Ochotona princeps	ENSOPRG00000012089	1 retrocopy	retro_opri_1168 ,
Pongo abelii	ENSPPYG00000014996	1 retrocopy	retro_pabe_2586,
Pan troglodytes	ENSPTRG00000016364	1 retrocopy	retro_ptro_2119,
Tarsius syrichta	ENSTSYG00000013668	2 retrocopies	retro_tsyr_355, retro_tsyr_613,
Tursiops truncatus	ENSTTRG00000016318	1 retrocopy	retro_ttru_1539,