RetrogeneDB ID: retro_opri_233

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3991:41421..41740(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2D
• Ensembl ID: ENSOPRG00000005327
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide D [Source:HGNC Symbol;Acc:9191]

Sequence

>retro_opri_233
CTGCTGCTGGAGCATCAAAAGCAGCAGAACAAGAGTGCAGATGGTGAACAGGAGCTGTTGGAGACCTTCATGTAGACTTT
GACTGACACGGCTTGTATTAGTCATTTTGAAAATAGAGGGACCATGACTAGGATCCATAGCTTGCTGCTCCAAAAAATGT
TTTTGGAACTTGGAGTTGGCATGTTTTGGCCAACCTTGATCCAGAGTTTGCCAAAGGAGTCTGAGGAAGTCCCTGATCCC
AGGCCTGAAGGGGAGATTGGAAGATGAGGAGCTGCAGAAAATTCTTGATGATGCCTAGACAAAGCACAACTTTCGGTAT

Alignment

ORF - retro_opri_233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.14 %
• Parental protein coverage: 88.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLLEHRKQQNESAEDEQELSEVFMKTLTYTARFSRFKNRETIASVRSLLLQKKLHKF-ELACLANLCPET
          .LLEH.KQQN.SA..EQEL.E.FM.TLT.TA..S.F.NR.T.....SLLLQK......ELAC........
Retrocopy LLLEHQKQQNKSADGEQELLETFM*TLTDTACISHFENRGTMTRIHSLLLQKMFLEL>ELACFGQP*SRV

Parental  AEES--KALIPSLEGRFEDEELQQILDDIQTKRSFQY
          ...S..K.LIP.L.GR.EDEELQ.ILDD..TK..F.Y
Retrocopy CQRSLRKSLIPGLKGRLEDEELQKILDDA*TKHNFRY

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_233 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 17 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011746	1 retrocopy	retro_amel_1020,
Canis familiaris	ENSCAFG00000004311	2 retrocopies	retro_cfam_1403, retro_cfam_2188,
Choloepus hoffmanni	ENSCHOG00000013850	3 retrocopies	retro_chof_1003, retro_chof_1568, retro_chof_1920,
Dasypus novemcinctus	ENSDNOG00000008527	1 retrocopy	retro_dnov_734,
Felis catus	ENSFCAG00000027816	1 retrocopy	retro_fcat_1148,
Gorilla gorilla	ENSGGOG00000004723	1 retrocopy	retro_ggor_1658,
Macaca mulatta	ENSMMUG00000001989	1 retrocopy	retro_mmul_1011,
Monodelphis domestica	ENSMODG00000018653	4 retrocopies	retro_mdom_1320, retro_mdom_457, retro_mdom_689, retro_mdom_851,
Mustela putorius furo	ENSMPUG00000016685	1 retrocopy	retro_mputfur_611,
Mus musculus	ENSMUSG00000024258	1 retrocopy	retro_mmus_1331,
Oryctolagus cuniculus	ENSOCUG00000021449	1 retrocopy	retro_ocun_35,
Ochotona princeps	ENSOPRG00000005327	2 retrocopies	retro_opri_233 , retro_opri_725,
Pongo abelii	ENSPPYG00000012759	1 retrocopy	retro_pabe_1933,
Pan troglodytes	ENSPTRG00000012436	1 retrocopy	retro_ptro_1571,
Sorex araneus	ENSSARG00000009037	1 retrocopy	retro_sara_420,
Sarcophilus harrisii	ENSSHAG00000014817	1 retrocopy	retro_shar_728,
Ictidomys tridecemlineatus	ENSSTOG00000023329	3 retrocopies	retro_itri_1323, retro_itri_145, retro_itri_600,