RetrogeneDB ID: retro_opri_732

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_26751:8051..8534(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMCE1
• Ensembl ID: ENSOPRG00000011452
• Aliases: None
• Description: non-SMC element 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29897]

Sequence

>retro_opri_732
ATGCAGGAGAGTGCGAGAAAGCCGGGAGTCATGACCGACGTCCACCGGGGGTTCCTGCAGCTGCTGATGACTCCCGGCGT
GCTGGAGGAGTGGGAAGTGGAGCGTATACAGAGACACTGCTACAAGGTCCACGGCCGCAACGCTCCTGTGGAGAAGCTGG
AGGACTTCATCTACACCGTCAACAGTGCCTTGCAGTCTCTCTACATGGAGATCAAGAAAGGAGTCACGGAAGACGACGGC
CGACCCATTTATGCACTGGTGAACCTCACCACCACGCCCATTTCCAAAATGGCCACGGATTTTGCTAAGAACGAACTGGA
CCTATTCAGAAAGGCGCTGGAGCTGATCACCGACTCTGAAACGGGCTTTGCGTCCTCCACCAACATCCTGAACCTGGTCG
ATCAGCTGAAAGGCAAGAAGATGAAGAAGAAGGAGGCCGAGCAGGTGCTGCAGAAGTTCGTGCAGAGCAAATGGCTGATC
GAG

Alignment

ORF - retro_opri_732 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.17 %
• Parental protein coverage: 60.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQGSARKPGVMTDVHRRFLQLMMTHGVLEEWEVERLQRHCYKVHDRNAPVDKLEDFIYTINSALQSLYME
          MQ.SARKPGVMTDVHR.FLQL.MT.GVLEEWEVER.QRHCYKVH.RNAPV.KLEDFIYT.NSALQSLYME
Retrocopy MQESARKPGVMTDVHRGFLQLLMTPGVLEEWEVERIQRHCYKVHGRNAPVEKLEDFIYTVNSALQSLYME

Parental  IKKGVTEDDGRPIYALVNLTTTPISKMATDFAKNELDLLR-GLELITDSETGFASSTNILNLVDQLKGKK
          IKKGVTEDDGRPIYALVNLTTTPISKMATDFAKNELDL.R..LELITDSETGFASSTNILNLVDQLKGKK
Retrocopy IKKGVTEDDGRPIYALVNLTTTPISKMATDFAKNELDLFRKALELITDSETGFASSTNILNLVDQLKGKK

Parental  MKKKEAEQVLQKFVQSKWLIE
          MKKKEAEQVLQKFVQSKWLIE
Retrocopy MKKKEAEQVLQKFVQSKWLIE

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_732 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011003	2 retrocopies	retro_chof_1394, retro_chof_339,
Callithrix jacchus	ENSCJAG00000020515	1 retrocopy	retro_cjac_2191,
Dasypus novemcinctus	ENSDNOG00000013271	1 retrocopy	retro_dnov_641,
Mus musculus	ENSMUSG00000030750	2 retrocopies	retro_mmus_1564, retro_mmus_2488,
Ochotona princeps	ENSOPRG00000011452	1 retrocopy	retro_opri_732 ,