RetrogeneDB ID: retro_opri_169

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3189:72896..73721(+)
• Located in intron of: ENSOPRG00000009566

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000015790
• Aliases: None
• Description: None

Sequence

>retro_opri_169
GAAAAAGATATTGTGGACAATTGGGATGAGAAGAAACCGGAAGAAGTAGTGGATGAGAAGCATGGTGAGGTGGAAAACAA
AAAACCAGAAACTCAAATAGTGTCCAAACATTTCCCTGAAGCCATTGAAAACAAGTATGGCTGGTTTGGGGTTTGCCCTG
GAGGGGGTGATAATTGCATGGTTGGCATGCACTTGCTCCTGGATTTGTGTCAAAAAAAGACAAAGAGGAGAAAGAAGATG
AAATTGCAGTTAAGGATCTAATTGAAAGAGAATGTCCTGCCCTAGGCCCAAATGTTACCAAATCACTCTAGAATCTTTTC
TTGCATGGCAAAAAAAAGGAAAAGACAAGGAAAGATTGATAAACTCGGACAAGATATGGAAGGAAGAAAAGCCAGTTTCA
AAGCAGGCGAAGCACTAGTGATCAGTGGTTGTGATTTGTTTGAATTTCATCCTGAGTTGGTCACCGATGAGGAGGAAGCA
GATGATACCCGTCACAGCCAGGGAACAGGTGGTGATGAGGCTGATGATTCAATGAATGTAAATGACATAGATTTTAGTTT
GTGCATCCCGAGAGGTGTAGATGAGACAGGTATTCCTGTAGCCAGTCTTGCAAGGTTCAGCACATATACTTCAGATAAAG
AAAACAAGTTAAGTGAAGTTTCTGGTGGCAGGGCTGAAAATGGTGGAAGAAGTGATCTGGAAGATGACATTGAAGGGAAA
GCTCAGGAAAATGGAGCTATTGATGCCATCCCTGTTGATGAATGTTTTATTACTGGGGAAGATTTAGATGAACTAGAAGA
AGAATTAAACACACCTGATTTAGAA

Alignment

ORF - retro_opri_169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.18 %
• Parental protein coverage: 76.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKDTMDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCKHFLEAIENNKYGWFWVCPGGGDNCMYR-HALPPG
          EKD..DNWDEKK.EEVV..KHGE.E.KKP.TQIV.KHF.EAIEN.KYGWF.VCPGGGDNCM...HAL.PG
Retrocopy EKDIVDNWDEKKPEEVVDEKHGEVENKKPETQIVSKHFPEAIEN-KYGWFGVCPGGGDNCMVG<HALAPG

Parental  FVLKKDKKKEEKEDEISLEDLIERERSALGPNVTKITLESFL-AWKKRKRQEKIDKLEQDMERRKADFKA
          FV.KKDK..EEKEDEI...DLIERE..ALGPNVTK.....FL......KRQ.KIDKL.QDME.RKA.FKA
Retrocopy FVSKKDK--EEKEDEIAVKDLIERECPALGPNVTKSL*NLFL>MXXXXKRQGKIDKLGQDMEGRKASFKA

Parental  GKALVISGREVFEFRPELVNDDDEEADDTRYTQGTGGDEVDDSVNVNDIDLSLYVPRDVDETGITVASLE
          G.ALVISG...FEF.PELV.D..EEADDTR..QGTGGDE.DDS.NVNDID.SL..PR.VDETGI.VASL.
Retrocopy GEALVISGCDLFEFHPELVTDE-EEADDTRHSQGTGGDEADDSMNVNDIDFSLCIPRGVDETGIPVASLA

Parental  RFSTYALDKDENKLSEASGGRAENGERSDLEEDNEGEAQENGAIDAVPVDENLFTGEDLDELEEELNTLD
          RFSTY..DK.ENKLSE.SGGRAENG.RSDLE.D.EG.AQENGAIDA.PVDE...TGEDLDELEEELNT.D
Retrocopy RFSTYTSDK-ENKLSEVSGGRAENGGRSDLEDDIEGKAQENGAIDAIPVDECFITGEDLDELEEELNTPD

Parental  LE
          LE
Retrocopy LE

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_169 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 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021762	1 retrocopy	retro_btau_1223,
Choloepus hoffmanni	ENSCHOG00000011958	1 retrocopy	retro_chof_2120,
Callithrix jacchus	ENSCJAG00000005931	2 retrocopies	retro_cjac_2883, retro_cjac_3986,
Cavia porcellus	ENSCPOG00000012965	2 retrocopies	retro_cpor_1294, retro_cpor_919,
Dipodomys ordii	ENSDORG00000011664	1 retrocopy	retro_dord_666,
Loxodonta africana	ENSLAFG00000001563	1 retrocopy	retro_lafr_941,
Myotis lucifugus	ENSMLUG00000007741	2 retrocopies	retro_mluc_1494, retro_mluc_2467,
Monodelphis domestica	ENSMODG00000027565	5 retrocopies	retro_mdom_1230, retro_mdom_1321, retro_mdom_1744, retro_mdom_1942, retro_mdom_871,
Oryctolagus cuniculus	ENSOCUG00000011903	1 retrocopy	retro_ocun_886,
Otolemur garnettii	ENSOGAG00000002182	2 retrocopies	retro_ogar_1093, retro_ogar_611,
Ochotona princeps	ENSOPRG00000015790	2 retrocopies	retro_opri_169 , retro_opri_609,
Pan troglodytes	ENSPTRG00000012717	1 retrocopy	retro_ptro_348,
Rattus norvegicus	ENSRNOG00000005256	4 retrocopies	retro_rnor_2628, retro_rnor_284, retro_rnor_662, retro_rnor_925,
Sorex araneus	ENSSARG00000012071	1 retrocopy	retro_sara_363,