RetrogeneDB ID: retro_opri_820

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_3452:75281..75673(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED6
• Ensembl ID: ENSOPRG00000008957
• Aliases: None
• Description: mediator complex subunit 6 [Source:HGNC Symbol;Acc:19970]

Sequence

>retro_opri_820
ATGGTGATGGAGGATACCTGAGATAATCTGCTGGAAATCTCTTGGGCTGACAGCTGTTGGATCCCATTTTGAACCGTGGT
AGTGCCCTGGATTACTTTTCAGAAAGAAGTAACCCTTTCCATGACAGGGCAAGTAATAACGAAGTGGTCAAAATGTAGAG
ACTAACATTAGAACACTTGAATCAGATGGTTGGAGTTGAATTGTTCTTTTACATGCTTAACAGCCCATTGTTTTCATCGT
TAGGAAGCAACAGTGGCAGTGCCCCCATCAAGTGTTCCCACAGCTGATCATTACATCTTTGCTGGAGTGATCTATCAGGC
ACCAGGCTGGGATCAGTTATAAACTCCGGAGTGCTTACTGCAGTGCATGGCATCCAGTCAGTATTTGATGAG

Alignment

ORF - retro_opri_820 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.26 %
• Parental protein coverage: 53.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAVDIRDNLLGISWVDSSWIP-ILNSGSVLDYFSERSNPFYDRTCNNEVVKMQRLTLEHLNQMVGIE-Y
          M...D..DNLL.ISW.DS.WIP.ILN.GS.LDYFSERSNPF.DR..NNEVVKM.RLTLEHLNQMVG.E..
Retrocopy MVMEDT*DNLLEISWADSCWIP<ILNRGSALDYFSERSNPFHDRASNNEVVKM*RLTLEHLNQMVGVE<I

Parental  ILLHAQEPILFIVRKQQRQSPSQVF-PLADYYIIAGVIYQAPD-LGSVINSRVLTAVNRIQSAFDE
          .LLHA..PI.FIVRKQQ.Q.P.QVF.P.AD.YI.AGVIYQAP..LGSVINS.VLTAV..IQS.FDE
Retrocopy VLLHA*QPIVFIVRKQQWQCPHQVF<PTADHYIFAGVIYQAPG<LGSVINSGVLTAVHGIQSVFDE

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_820 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000013091	1 retrocopy	retro_fcat_1612,
Myotis lucifugus	ENSMLUG00000017357	1 retrocopy	retro_mluc_265,
Monodelphis domestica	ENSMODG00000007174	3 retrocopies	retro_mdom_1190, retro_mdom_524, retro_mdom_625,
Otolemur garnettii	ENSOGAG00000001311	1 retrocopy	retro_ogar_2597,
Ochotona princeps	ENSOPRG00000008957	1 retrocopy	retro_opri_820 ,
Sorex araneus	ENSSARG00000002553	1 retrocopy	retro_sara_495,
Tupaia belangeri	ENSTBEG00000002302	1 retrocopy	retro_tbel_2272,