RetrogeneDB ID: retro_opri_372

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_10227:39703..40233(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000018592
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000016593
• Aliases: None
• Description: None

Sequence

>retro_opri_372
GTATCACATGGAAAAGACTGTTACAGTGGCCCACCTTGAAGGGAATCCCTGTCCTCTAGCAGAGGTGTTTATTTGTCACC
AAGAGTTGATGGAGACTCTGCTAAAGACAGCTATTCAAGCAGAGATTGCCCAAGTTCCCATGATACCTGAGATTACGCAC
CCCAACAAGAGACTATACTTACAGTGATTATGGTCATTCCAGTTCATGGTGATGACTGTCTATCCAGAGGCTCTAGTGAT
AGAGACGGCTGTGGTCGTGATCAGGACTATTGACATCATCCAAGTGGAGGTGCCTATTGAGATTCCTGTGAGAGCTGTGG
TAACTCACGTAGTGCTACACCTACACGAGGGCCCCCCGCCATCTTATGGTGGATGCAGTTGCTATGATGATTACAGGGAT
GGATATGGTGGAAAGTCGAGACAGTTAACTCAGGCAGCCAAAGTGATTCTTTGCTCAAGTGGTCCTAGATTGTGTTGGCA
GACAAGAAGGAGGCTTTCCTCCTTCTGTGGAAAGGGGATTCCTCCCTCCC

Alignment

ORF - retro_opri_372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.85 %
• Parental protein coverage: 84.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VSRGRDSYGGPPRREPLPSRRDVYLSPRDDGYSTKDSYSSRDYPSSRDTRDYAP-PPRDYTYRDYGHSSS
          VS.G.D.Y.GPP.RE.L.S.R.VYLSPR.DG.S.KDSYSSRD.PSS.DT.DYAP.P.RDYTY.DYGHSSS
Retrocopy VSHGKDCYSGPP*RESLSSSRGVYLSPRVDGDSAKDSYSSRDCPSSHDT*DYAP<PTRDYTYSDYGHSSS

Parental  -RDDYPSRGYSDRDGYGRDRDYSDHPSGGSYRDSYESYGNSRSAPPTR-GPPPSYGGSSRYDDYSSSRDG
          ..DD..SRG.SDRDG.GRD.DY..HPSGG.Y.DS.ES.GNSRSA.PTR.GPPPSYGG.S.YDDY...RDG
Retrocopy >GDDCLSRGSSDRDGCGRDQDY*HHPSGGAY*DSCESCGNSRSATPTR>GPPPSYGGCSCYDDY---RDG

Parental  YGG-SRDSYSSSRSDLYSSG-RDRVGRQERGLPPSMERGYPPP
          YGG.SR.........L.SSG..D.VGRQE.G.PPS.ERG..PP
Retrocopy YGGKSRQLTQAAKVILCSSG>LDCVGRQEGGFPPSVERGFLPP

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_372 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 17 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni	ENSCHOG00000012369	3 retrocopies	retro_chof_1240, retro_chof_2596, retro_chof_880,
Dipodomys ordii	ENSDORG00000015481	1 retrocopy	retro_dord_793,
Echinops telfairi	ENSETEG00000013178	1 retrocopy	retro_etel_1952,
Homo sapiens	ENSG00000147274	7 retrocopies	retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Gorilla gorilla	ENSGGOG00000006944	1 retrocopy	retro_ggor_657,
Loxodonta africana	ENSLAFG00000005568	3 retrocopies	retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Myotis lucifugus	ENSMLUG00000013209	5 retrocopies	retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Mustela putorius furo	ENSMPUG00000001855	2 retrocopies	retro_mputfur_1539, retro_mputfur_956,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus	ENSOCUG00000007220	1 retrocopy	retro_ocun_3,
Ochotona princeps	ENSOPRG00000007990	2 retrocopies	retro_opri_24, retro_opri_930,
Ochotona princeps	ENSOPRG00000016593	1 retrocopy	retro_opri_372 ,
Pongo abelii	ENSPPYG00000020771	3 retrocopies	retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus	ENSRNOG00000000866	1 retrocopy	retro_rnor_268,
Sorex araneus	ENSSARG00000000397	1 retrocopy	retro_sara_169,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,