RetrogeneDB ID: retro_opri_814

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_336:489987..490579(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1G
• Ensembl ID: ENSOPRG00000014563
• Aliases: None
• Description: eukaryotic translation elongation factor 1 gamma [Source:HGNC Symbol;Acc:3213]

Sequence

>retro_opri_814
AAGAGAACAAAGTCCCAGGCTGAATGGAAAGAGGAGAAAAAGACAGCTGCCCCAACTCCTGAGGAAGAAATAGATGTGTG
TGAGCAGGCCTCGGCCACTGAGCCTAAGGCCAAGGAACCTTTACTCATCGTTCTAAGGCTACCTTTGTCTTGGGTGAGTT
TAAGTACAAGTACTCCACCAAGGACACCTGTCTGTGGCACTGCTATATTTCTGGGAATGTTTTGACAAGGATAGCTGGTT
CCTGTGATACACCAAATACCATTTCCTGAGGAGCTCAAAGCAGATTTTAATGAGCTGCAACCTCAGCACTGGAATGTTCT
AGCAGTTGGATAAGCTGAGGAAGAATGTCTTTGCCAGTGTCATCCTCTTTGGAACCAACAATAGCAGCTCTATTTCTGGA
ATCTGGGTCTTCCGAGGCAAAGAGCTTGCCTTTCCGCTGAGTCCAGATTGGCAGATGAAGTATGAGTCGTATACATGGGA
GAAGCTGGATCCAAGCAGCAAGGAAATCCAGATGCTGGTTCAGGGGTACTTTTCCTAGGAAGGAGCTTTCCAGCATGTGG
GCAAAGCCTTCAATCAGCTCAAGATCTTCAGG

Alignment

ORF - retro_opri_814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.0 %
• Parental protein coverage: 75.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKQKPQAERKEEKKAAAPAPEEEMDECEQALGAEPKAKDP-FAXXXXXTFVLDEFKRKYSNEDT-LSVAL
          ...K.QAE.KEEKK.AAP.PEEE.D.CEQA...EPKAK.P.F......TFVL.EFK.KYS..DT.LSVAL
Retrocopy KRTKSQAEWKEEKKTAAPTPEEEIDVCEQASATEPKAKEP<FTHRSKATFVLGEFKYKYSTKDT<LSVAL

Parental  PYFWEHFDKDGWSLWYAEYRFPEELTQTFMSCNLITGMFQRLDKLRKNAFASVILFGTNNSSSISGIWVF
          .YFWE.FDKD.W.L.Y..Y.F.....Q..MSCNL.TGMF..LDKLRKN.FASVILFGTNNSSSISGIWVF
Retrocopy LYFWECFDKDSWFL*YTKYHFLRSSKQILMSCNLSTGMF*QLDKLRKNVFASVILFGTNNSSSISGIWVF

Parental  RGQELAFPLSPDWQVDYESYTWRKLDPSSEETQTLVREYFAWEGAFQHVGKAFNQGKVFK
          RG.ELAFPLSPDWQ..YESYTW.KLDPSS.E.Q.LV..YF..EGAFQHVGKAFNQ.K.F.
Retrocopy RGKELAFPLSPDWQMKYESYTWEKLDPSSKEIQMLVQGYFS*EGAFQHVGKAFNQLKIFR

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_814 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.

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011843	1 retrocopy	retro_btau_1600,
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Callithrix jacchus	ENSCJAG00000018949	6 retrocopies	retro_cjac_1464, retro_cjac_1770, retro_cjac_1942, retro_cjac_3147, retro_cjac_841, retro_cjac_874,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Myotis lucifugus	ENSMLUG00000000342	1 retrocopy	retro_mluc_1110,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Nomascus leucogenys	ENSNLEG00000003528	2 retrocopies	retro_nleu_1510, retro_nleu_681,
Otolemur garnettii	ENSOGAG00000000827	1 retrocopy	retro_ogar_1344,
Ochotona princeps	ENSOPRG00000014563	1 retrocopy	retro_opri_814 ,
Pan troglodytes	ENSPTRG00000003768	3 retrocopies	retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Pteropus vampyrus	ENSPVAG00000003440	1 retrocopy	retro_pvam_1239,
Rattus norvegicus	ENSRNOG00000020075	8 retrocopies	retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,
Sus scrofa	ENSSSCG00000013064	1 retrocopy	retro_sscr_164,
Tursiops truncatus	ENSTTRG00000002459	3 retrocopies	retro_ttru_1082, retro_ttru_1544, retro_ttru_1603,