RetrogeneDB ID: retro_opri_329

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_5261:259488..259842(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2E2
• Ensembl ID: ENSOPRG00000010615
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 2 [Source:HGNC Symbol;Acc:12478]

Sequence

>retro_opri_329
ACTGCTGCTAAATTATCCGCTGGTGCTAAAAGAATTCAGAAGGAGCTAGCTGAAATAACCTGCGATCCTGTTCCAAACTG
TAGCGCTGGGCCTGAAGGAGATAACATTTATGAGTGGAGATCGACTATACTTGGCCCACTAGGTTCTGTATATAAAGGTG
ATGTGTTTTTTTTCTGGATATCACATTTTCCTCAGATTATCCATTTAAAATTGCCAAAGGTTACGTTCCGAACCAGTATC
TATAACTGTAACATCAACAGTCAGGGAGTCATCTGTTTGGACATCCTTAAGGACAACTGAACTATCTCAAAGGTTTTGCT
GTCGATTTGTTCCCTTTTGAAAGATTGCAATCCC

Alignment

ORF - retro_opri_329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.1 %
• Parental protein coverage: 70. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TAAKLSTSAKRIQKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPD-YPFK
          TAAKLS..AKRIQKELAEIT.DP.PNCSAGP.GDNIYEWRSTILGP.GSVY.G.V....I...P.....K
Retrocopy TAAKLSAGAKRIQKELAEITCDPVPNCSAGPEGDNIYEWRSTILGPLGSVYKGDVXXXWISHFPQIIHLK

Parental  PPKXXXRTRIYHC---ISGVIC-DIRHSDLTISKVSL-ICSLLTDCNP
          .PK...RT.IY.C.....GVIC.DI.....TISKV.L.ICSLL.DCNP
Retrocopy LPKVTFRTSIYNCNINSQGVICLDILKDN*TISKVLLSICSLLKDCNP

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_329 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 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010341	2 retrocopies	retro_chof_1304, retro_chof_674,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Dasypus novemcinctus	ENSDNOG00000005448	7 retrocopies	retro_dnov_1217, retro_dnov_1281, retro_dnov_1360, retro_dnov_156, retro_dnov_2026, retro_dnov_2508, retro_dnov_424,
Felis catus	ENSFCAG00000007748	2 retrocopies	retro_fcat_1582, retro_fcat_913,
Microcebus murinus	ENSMICG00000016799	3 retrocopies	retro_mmur_1075, retro_mmur_15, retro_mmur_419,
Myotis lucifugus	ENSMLUG00000025144	1 retrocopy	retro_mluc_712,
Ochotona princeps	ENSOPRG00000010615	2 retrocopies	retro_opri_329 , retro_opri_788,
Ochotona princeps	ENSOPRG00000011695	9 retrocopies	retro_opri_1042, retro_opri_1189, retro_opri_206, retro_opri_310, retro_opri_447, retro_opri_457, retro_opri_627, retro_opri_77, retro_opri_838,
Tursiops truncatus	ENSTTRG00000005156	1 retrocopy	retro_ttru_1075,
Vicugna pacos	ENSVPAG00000007007	3 retrocopies	retro_vpac_108, retro_vpac_315, retro_vpac_425,