RetrogeneDB ID: retro_opri_271

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4429:19333..20059(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000011058
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEPHS1
• Ensembl ID: ENSOPRG00000006587
• Aliases: None
• Description: selenophosphate synthetase 1 [Source:HGNC Symbol;Acc:19685]

Sequence

>retro_opri_271
GAGCGAGAGAAGGTGACGCCCCTCATGATCAAGGGCTTTCGAGATGCCGCGGAGGAAGGAGGGACCGCAGTGACCGGTGG
ACAGACCGTGGTCAACCCCTGGATTATCATCGGCGGCGTGGCCACGGTGGTGTGTCAGCCAAACGAGTTCATAATGCCCG
ACAGCGCGGTCGTTGGAGATGTGCTTGTGCTCACCAAACCCCTGGGGACCCAAGTGGCTGTTAATGCCCACCTGTGGCTG
GATAACCCGGAGAGATGGAACAAGATCAAGATGGTGGTCTCCAGGGAGGAGGTGGAGCTGGCCTATCAGGAGGCGATGTT
CAACATGGCTACGCTCAACAGAACTGCTGCCGGCTTAATGCACACCTTTAATGCCCATGCAGCCACAGACATCACGGGCT
TCGGCATCCTGGGACACTCTCAGAACCTGGCGAAACAACAGCGCAATGAGGTGTCCTTCGTCATTCACAATTTGCCCATC
ATCGCCAAGATGGCCGCCGTCAGCAAGGCCAGCGGGCGCTACGGCCTGCTGCAGGGCACCTCGGCCGAAACCTCGGGAGG
CTTGCTGATTTGTCTGCCCAGGGAACAGGCCGCTCGCTTCTGCTCTGAGATCAAATCCTCCAAGTACGGCGAGGGTCACC
AAGCTTGGATCGTGGGCATTGTGGAGAAGGGCAACCGGACAGCCCGCATCATTGACAAACCTCGAGTCATTGAGGTCCCA
CCTCGT

Alignment

ORF - retro_opri_271 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.13 %
• Parental protein coverage: 74.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERDKVIPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGT
          ER.KV.PL.I.GF.DAAEE.GT.VTGGQTV.NPWI..GGVAT.VCQPNEFIMPD.AV.GDVLVLTKPLGT
Retrocopy EREKVTPLMIKGFRDAAEEGGTAVTGGQTVVNPWIIIGGVATVVCQPNEFIMPDSAVVGDVLVLTKPLGT

Parental  QVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHA
          QVAV..H.WLD.PE.WNKIK.VV..E.VELAYQEAM.NMA.LNRTAAGLMHTFNAHAATDITGFGILGH.
Retrocopy QVAVNAHLWLDNPERWNKIKMVVSREEVELAYQEAMFNMATLNRTAAGLMHTFNAHAATDITGFGILGHS

Parental  QNLAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKY
          QNLAKQQRNEVSFVIHNLP..AKMAAVSKA.G...GL..GT..ETSGGLLICLPREQAARFC.EIKS.KY
Retrocopy QNLAKQQRNEVSFVIHNLPIIAKMAAVSKASGR-YGLLQGTSAETSGGLLICLPREQAARFCSEIKSSKY

Parental  GEGHQAWIIGIVEKGNRTARIIDKPRIIEVAPQ
          GEGHQAWI.GIVEKGNRTARIIDKPR.IEV.P.
Retrocopy GEGHQAWIVGIVEKGNRTARIIDKPRVIEVPPR

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_271 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Equus caballus	ENSECAG00000014281	1 retrocopy	retro_ecab_77,
Nomascus leucogenys	ENSNLEG00000012205	7 retrocopies	retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Ochotona princeps	ENSOPRG00000006587	3 retrocopies	retro_opri_271 , retro_opri_655, retro_opri_670,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,