RetrogeneDB ID: retro_opri_337

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_5366:151236..152433(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT19
• Ensembl ID: ENSOPRG00000007908
• Aliases: None
• Description: keratin 19 [Source:HGNC Symbol;Acc:6436]

Sequence

>retro_opri_337
ATGACTTCCTACAGTTACCTCCAGTCATCCTCCGCCTCAACCTTCGGGGGCCTGGGTGGCGGCCCCGCGCGCTTTGGGGG
TGGGAGCAGCTTTCGCGCCCCCAGCATCCACGGGGGCTCCGGCGGCCGTGGGGTGTCTGTGTCCTCTGCCCGTTTTGTGT
CCTCGTCCTCTGGGGGCTACGGTGGTGGCTATGGGGTCTCACTGGCCGGGTCCGACGGGCTCCTCTCTGGCAACGAGAAG
ATCACCATGCAGAACCTCAACGACCGCTTGGCATCTTACCTGGAAAAGGTGCGCGCCCTGGAGCAGGCCAATGGCGAGCT
GGAGGTGAAGATCCGCGACTGGTACCAGAAGCAGGGACCCGGACCCTCCCGCGACTACAGCCACTATTTTAAGACCATCG
AGGATCTACGTGATAAGATTCACGGGGCCACCATTGACAACTCCAAGATCGTCCTGCAGATCGACAATGCCCGTCTGGCT
GCAGATGACTTCCGCACCAAATTCGAGACAGAGCAGGCCCTGCGCCTGAGTGTGGAGGCCGACATCAACGGGCTGCGCAG
GGTGCTGGACGAGCTGACCCTGGCCAGGACCAACCTGGAGATGCAGATCGAAGGCCTGAAGGAGGAGCTGGCTTACCTGA
AGAAGAACCACGAGGAGGAAATCAGTGTCCTGAAGGGCCAGGTGGGTGGCCAAGTGAGTGTGGAGGTGGATTCGGCTCCA
GGTGTTGACCTTGCCAAGATCCTGAGTGAGATGAGAAGCCAGTATGAGGTCATGGCTGAGAAGAACCGGAAGGATGCCGA
GGCCTGGTTCGTCAGCCGGACTGAGGAGCTGAACCAGGAGGTGGCTATTAATACAGAACAGCTGAAGACGAGCAGATCAG
AGGTCACTGACCTGCGGCGGACCCTGCAGGGTCTTGAGACCGAGCTGCAGTCGCAGCTCAGCATGAAAGCGGCCCTGGAA
GGCACGCTGGCAGAGACGGAGGCCTGTTTCGGTGCGCAGCTGGCACAGATCCAGGCGTTAATCAGCAGCATCGAGGCGCA
GCTGAGCGACGTGCGGGCTGACACCGAGTGGCAGAACCAGGAGTACCAGCAGCTCATGGGCATCAAGTCACGGCTGGAGC
AGGAGATTGCCACCTACCGCAGCCTGCTTGAGGGCCAGGACATCCACTAAAACAACCTGCCCACCCCCAAGGTTGTC

Alignment

ORF - retro_opri_337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTSYSYRQSSSASTFGGLGGGPARFGGGSSFRAPSIHGGSGGRGVSVSSARFVSSSSGGYGGGYGVSLAG
          MTSYSY.QSSSASTFGGLGGGPARFGGGSSFRAPSIHGGSGGRGVSVSSARFVSSSSGGYGGGYGVSLAG
Retrocopy MTSYSYLQSSSASTFGGLGGGPARFGGGSSFRAPSIHGGSGGRGVSVSSARFVSSSSGGYGGGYGVSLAG

Parental  SDGLLSGNEKITMQNLNDRLASYLEKVRALEQANGELEVKIRDWYQKQGPGPSRDYSHYFKTIEDLRDKI
          SDGLLSGNEKITMQNLNDRLASYLEKVRALEQANGELEVKIRDWYQKQGPGPSRDYSHYFKTIEDLRDKI
Retrocopy SDGLLSGNEKITMQNLNDRLASYLEKVRALEQANGELEVKIRDWYQKQGPGPSRDYSHYFKTIEDLRDKI

Parental  HGATIDNSKIVLQIDNARLAADDFRTKFETEQALRLSVEADINGLRRVLDELTLARTDLEMQIEGLKEEL
          HGATIDNSKIVLQIDNARLAADDFRTKFETEQALRLSVEADINGLRRVLDELTLART.LEMQIEGLKEEL
Retrocopy HGATIDNSKIVLQIDNARLAADDFRTKFETEQALRLSVEADINGLRRVLDELTLARTNLEMQIEGLKEEL

Parental  AYLKKNHEEEISVLKGQVGGQVSVEVDSAPGVDLAKILSEMRSQYEVMAEKNRKDAEAWFVSRTEELNQE
          AYLKKNHEEEISVLKGQVGGQVSVEVDSAPGVDLAKILSEMRSQYEVMAEKNRKDAEAWFVSRTEELNQE
Retrocopy AYLKKNHEEEISVLKGQVGGQVSVEVDSAPGVDLAKILSEMRSQYEVMAEKNRKDAEAWFVSRTEELNQE

Parental  VAINTEQLKTSRSEVTDLRRTLQGLEIELQSQLSMKAALEGTLAETEARFGAQLAQIQALISSIEAQLSD
          VAINTEQLKTSRSEVTDLRRTLQGLE.ELQSQLSMKAALEGTLAETEA.FGAQLAQIQALISSIEAQLSD
Retrocopy VAINTEQLKTSRSEVTDLRRTLQGLETELQSQLSMKAALEGTLAETEACFGAQLAQIQALISSIEAQLSD

Parental  VRADTERQNQEYQQLMGIKSRLEQEIATYRSLLEGQDIH-NNLPTPKVV
          VRADTE.QNQEYQQLMGIKSRLEQEIATYRSLLEGQDIH.NNLPTPKVV
Retrocopy VRADTEWQNQEYQQLMGIKSRLEQEIATYRSLLEGQDIH*NNLPTPKVV

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_337 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 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000029756	9 retrocopies	retro_cjac_1151, retro_cjac_1812, retro_cjac_2347, retro_cjac_2646, retro_cjac_3108, retro_cjac_3198, retro_cjac_3237, retro_cjac_3358, retro_cjac_633,
Equus caballus	ENSECAG00000014086	2 retrocopies	retro_ecab_76, retro_ecab_931,
Echinops telfairi	ENSETEG00000007881	6 retrocopies	retro_etel_1217, retro_etel_1319, retro_etel_191, retro_etel_480, retro_etel_685, retro_etel_95,
Homo sapiens	ENSG00000171345	3 retrocopies	retro_hsap_3486, retro_hsap_585, retro_hsap_959,
Gorilla gorilla	ENSGGOG00000016901	3 retrocopies	retro_ggor_2352, retro_ggor_518, retro_ggor_773,
Macropus eugenii	ENSMEUG00000016158	3 retrocopies	retro_meug_1860, retro_meug_403, retro_meug_826,
Macaca mulatta	ENSMMUG00000018653	4 retrocopies	retro_mmul_1770, retro_mmul_717, retro_mmul_774, retro_mmul_790,
Nomascus leucogenys	ENSNLEG00000010787	3 retrocopies	retro_nleu_1609, retro_nleu_2204, retro_nleu_800,
Oryctolagus cuniculus	ENSOCUG00000016132	1 retrocopy	retro_ocun_1884,
Otolemur garnettii	ENSOGAG00000024306	1 retrocopy	retro_ogar_1301,
Ochotona princeps	ENSOPRG00000007908	2 retrocopies	retro_opri_337 , retro_opri_673,
Pongo abelii	ENSPPYG00000008416	3 retrocopies	retro_pabe_2880, retro_pabe_603, retro_pabe_820,
Pan troglodytes	ENSPTRG00000009168	3 retrocopies	retro_ptro_2074, retro_ptro_2359, retro_ptro_430,
Ictidomys tridecemlineatus	ENSSTOG00000014403	2 retrocopies	retro_itri_1514, retro_itri_697,