RetrogeneDB ID: retro_opri_834

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_35530:39407..39613(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED10
• Ensembl ID: ENSOPRG00000015506
• Aliases: None
• Description: mediator complex subunit 10 [Source:HGNC Symbol;Acc:28760]

Sequence

>retro_opri_834
ATTAGTAACTTTCAGTAGAACAGACAGGCCGGCCTCAGCCAGGAGCTCGATCGGACTGCTCTGGCTTACAGGGTGCTGGT
ATGTGCAGACACTGGCTTCAAGACATTACTGGGCCTATAGAAGGCTTCTGATGCATAGATCAAGGTAGAAATCTCCAACT
CCACAACCAAGACTGCCTGAAGAAGGCTCTAGCTAAAAATAAGCAA

Alignment

ORF - retro_opri_834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.86 %
• Parental protein coverage: 66.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSDFQPSSQAGLNQKLNFIV-TGLQDIDKCRQQLHDITVPLEVFEYIDQGRNPQLYTKECLERALAKNEQ
          .S.FQ...QAGL.Q.L......GLQ....CR..L.DIT.P.E.F..IDQGRN.QL....CL..ALAKN.Q
Retrocopy ISNFQ*NRQAGLSQELDRTA<SGLQGAGMCRHWLQDITGPIEGF*CIDQGRNLQLHNQDCLKKALAKNKQ

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_834 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006767	1 retrocopy	retro_amel_1034,
Canis familiaris	ENSCAFG00000010346	1 retrocopy	retro_cfam_721,
Dasypus novemcinctus	ENSDNOG00000004579	1 retrocopy	retro_dnov_1286,
Equus caballus	ENSECAG00000023738	1 retrocopy	retro_ecab_796,
Echinops telfairi	ENSETEG00000000027	1 retrocopy	retro_etel_1758,
Monodelphis domestica	ENSMODG00000002025	1 retrocopy	retro_mdom_399,
Otolemur garnettii	ENSOGAG00000005988	1 retrocopy	retro_ogar_1830,
Ochotona princeps	ENSOPRG00000015506	1 retrocopy	retro_opri_834 ,
Tupaia belangeri	ENSTBEG00000014579	2 retrocopies	retro_tbel_1647, retro_tbel_4561,
Tarsius syrichta	ENSTSYG00000002763	1 retrocopy	retro_tsyr_792,