RetrogeneDB ID: retro_opri_426

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_11545:9..345(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf43
• Ensembl ID: ENSOPRG00000007244
• Aliases: None
• Description: chromosome 1 open reading frame 43 [Source:HGNC Symbol;Acc:29876]

Sequence

>retro_opri_426
ACACCAGCACTCCTTTCAAGTGTGCATAAAGCCCTGATCGATACCCTGCTGGACGGCTACGAGACGGCACACTATGGAAC
CGGGGTCTTTGGCCAGTATGAGTACCTGCGCTATCAGGAGGCACTGAGTGAGCTGGCCACCGTGGTGAAGGCACGAATGG
GACGCTCTCAGAGGTAACACCAATCAGCAGCCAAGGACCTCACCCAGTCTCCCGAAGTCGCCCCAACAACCATCCAGGTT
AGGTAGCTCCCCTCAAGTCAGAAGAGCAAACGTGCCAAGCACTTCCTCGAATTGAAGAGATTTAAGGACAACTATAACAC
CCTGGAAAGCACTCTG

Alignment

ORF - retro_opri_426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.61 %
• Parental protein coverage: 56.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSTPFKGVRKALIDTLLDGYETARYGTGVFGQNEYLRYQEALSELATVVKARMGSSQRQHQSAAKDLTQS
          T......V.KALIDTLLDGYETA.YGTGVFGQ.EYLRYQEALSELATVVKARMG.SQR.HQSAAKDLTQS
Retrocopy TPALLSSVHKALIDTLLDGYETAHYGTGVFGQYEYLRYQEALSELATVVKARMGRSQR*HQSAAKDLTQS

Parental  PEVSPTTIQVTYLPSSQKSKRAKHFLELKSFKDNYNTLESTL
          PEV.PTTIQV..LPSSQKSKRAKHFLELK.FKDNYNTLESTL
Retrocopy PEVAPTTIQVR*LPSSQKSKRAKHFLELKRFKDNYNTLESTL

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_426 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 14 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009722	1 retrocopy	retro_cjac_175,
Dipodomys ordii	ENSDORG00000005454	1 retrocopy	retro_dord_190,
Echinops telfairi	ENSETEG00000001056	15 retrocopies	retro_etel_1138, retro_etel_1318, retro_etel_1388, retro_etel_1633, retro_etel_2182, retro_etel_2205, retro_etel_2206, retro_etel_394, retro_etel_651, retro_etel_719, retro_etel_720, retro_etel_773, retro_etel_842, retro_etel_957, retro_etel_981,
Macropus eugenii	ENSMEUG00000002600	6 retrocopies	retro_meug_1149, retro_meug_1298, retro_meug_1439, retro_meug_1637, retro_meug_213, retro_meug_69,
Myotis lucifugus	ENSMLUG00000013338	1 retrocopy	retro_mluc_537,
Monodelphis domestica	ENSMODG00000017237	3 retrocopies	retro_mdom_1283, retro_mdom_2003, retro_mdom_323,
Mus musculus	ENSMUSG00000027942	6 retrocopies	retro_mmus_1014, retro_mmus_1018, retro_mmus_1020, retro_mmus_1107, retro_mmus_1792, retro_mmus_490,
Otolemur garnettii	ENSOGAG00000012008	2 retrocopies	retro_ogar_2563, retro_ogar_38,
Ochotona princeps	ENSOPRG00000007244	2 retrocopies	retro_opri_426 , retro_opri_586,
Pongo abelii	ENSPPYG00000000785	2 retrocopies	retro_pabe_3590, retro_pabe_969,
Rattus norvegicus	ENSRNOG00000017758	1 retrocopy	retro_rnor_139,
Sarcophilus harrisii	ENSSHAG00000012915	1 retrocopy	retro_shar_740,
Tupaia belangeri	ENSTBEG00000013866	1 retrocopy	retro_tbel_177,
Tarsius syrichta	ENSTSYG00000012777	1 retrocopy	retro_tsyr_91,