RetrogeneDB ID: retro_opri_145

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2816:258414..258800(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OAZ2
• Ensembl ID: ENSOPRG00000009548
• Aliases: None
• Description: ornithine decarboxylase antizyme 2 [Source:HGNC Symbol;Acc:8096]

Sequence

>retro_opri_145
GATGCTGCTTACCCACTGTCAAAGATCCCCAATGGGCGAAGGGGTTGCTGGGAGCCTCTGTCTCAGCTCTAACACGTAAG
GACCAGAAGCTCATTGTGACCCCAAGACCTCTGTGTGAATATGGGAAAACTCAGGCCATTCACTGCCAGTATGAGGTCAC
TGAAACAAAAGTCTCTTGCTGGCCTGCAGTCCTGTCCAATTAGAGCCTGTTTGTGGAAATCACAGAAGGTTCATTAGTTA
ATGACAGCCAACCAGGATTGTTAGCTCTGCTTAAGTTTGCTGAAGAGATGATGGAAGTGAAATAGATCTTCATCTGCTTT
GAGAAGGACTGGCAAGCCTCAGAGCCACTCCTGAAAATCTTCAGCATCTTGGGCTGCGAGATTATG

Alignment

ORF - retro_opri_145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.85 %
• Parental protein coverage: 68.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DAPHPLSKIPGGRGGGRDP-SLSALIYKDEKLTVT-QDLPVNDGK-PHIVHFRYEVTEVKVSSWDAVLSS
          DA..PLSKIP.GR.G...P.S.SAL..KD.KL.VT.QDL.VN.GK.....H..YEVTE.KVS.W.AVLS.
Retrocopy DAAYPLSKIPNGRRGCWEP<SVSALTRKDQKLIVT>QDLCVNMGK<TQAIHCQYEVTETKVSCWPAVLSN

Parental  QSLFVEIPDGLLADGSKEGLLALLEFAEEKMKVNYVFICFRKGREDRAPLLKTFSFLGFEIV
          .SLFVEI..G.L...S..GLLALL.FAEE.M.V...FICF.K......PLLK.FS.LG.EI.
Retrocopy *SLFVEITEGSLVNDSQPGLLALLKFAEEMMEVK*IFICFEKDWQASEPLLKIFSILGCEIM

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_145 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000007344	1 retrocopy	retro_mmur_1013,
Myotis lucifugus	ENSMLUG00000022795	2 retrocopies	retro_mluc_1003, retro_mluc_2416,
Mus musculus	ENSMUSG00000040652	2 retrocopies	retro_mmus_1343, retro_mmus_2305,
Oryctolagus cuniculus	ENSOCUG00000017341	1 retrocopy	retro_ocun_1612,
Ochotona princeps	ENSOPRG00000009548	2 retrocopies	retro_opri_1184, retro_opri_145 ,
Tupaia belangeri	ENSTBEG00000008091	1 retrocopy	retro_tbel_2493,
Tursiops truncatus	ENSTTRG00000011834	1 retrocopy	retro_ttru_502,