RetrogeneDB ID: retro_opri_171

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3191:165079..165414(-)
• Located in intron of: ENSOPRG00000014531

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCMT1
• Ensembl ID: ENSOPRG00000002833
• Aliases: None
• Description: protein-L-isoaspartate (D-aspartate) O-methyltransferase [Source:HGNC Symbol;Acc:8728]

Sequence

>retro_opri_171
GGATGTCATGGGAAAGCAAAAGAATTCATCACATTAAAGAGTTAGTAGACAATTCCCTAAGTAATGTCAGAAAACACAAT
TCAATGCCTCAGTCTTGGATGAGTGTAAATGGCTATGGGGGGAATGGAAGAATGGATACATTAAAGAAACTCCTTATGAA
GCTATTCATGTAAGAGCTGCAGCTCCTACTGTGCCCCAAGCACGTACAGACCACTCAAAGCCTAGGAGAAAACTGAAGTT
GCCAGTGTGTCCTGCAAGTGGGAGCCAACTATTCAAGCATGTGACAAATACAAAACAACAGCATCAAAATGAAATCTCTG
ATGAGCATCATATAT

Alignment

ORF - retro_opri_171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.99 %
• Parental protein coverage: 58.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GCSGKVIG-IDHIKELVDDSINNVRKDDPTLLSSGRVQLVVGDGRM-GYAEEAPYDAIHVGAAAPVVPQA
          GC.GK....I.HIKELVD.S..NVRK......S...V....G.GRM.GY..E.PY.AIHV.AAAP.VPQA
Retrocopy GCHGKAKE<IHHIKELVDNSLSNVRKHNSMPQSWMSVNGYGGNGRM<GYIKETPYEAIHVRAAAPTVPQA

Parental  LIDQLKPGGRLILPVGPAGGNQM-LEQYDK-LQDGSVKMKPLMGVIY
          ..D..KP...L.LPV.PA.G.Q......DK..Q..S.KMK.LM..IY
Retrocopy RTDHSKPRRKLKLPVCPASGSQL<IQACDK<IQNNSIKMKSLMSIIY

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_171 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
Callithrix jacchus	ENSCJAG00000009230	1 retrocopy	retro_cjac_75,
Macaca mulatta	ENSMMUG00000029462	1 retrocopy	retro_mmul_134,
Oryctolagus cuniculus	ENSOCUG00000000499	2 retrocopies	retro_ocun_871, retro_ocun_955,
Ochotona princeps	ENSOPRG00000002833	2 retrocopies	retro_opri_171 , retro_opri_434,
Tupaia belangeri	ENSTBEG00000000451	1 retrocopy	retro_tbel_883,