RetrogeneDB ID: retro_opri_995

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_53732:5078..5568(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC42
• Ensembl ID: ENSOPRG00000005331
• Aliases: None
• Description: cell division cycle 42 [Source:HGNC Symbol;Acc:1736]

Sequence

>retro_opri_995
AACACATTCCCATCTGAACATGCACCTACTGTTTCTGACAGCTGTGCAGTCACAGTTATGATTGGTGGAGAGCCACATAC
TCCTGGACTTTTTCATACTGCAGGACAAGAGGTTTATGATGGATTACGGCCACTGAGTTATCCACAAACAGATGCATTTT
TAATCTGTTTTTCAGTGGTTTCTCTATCCTCATTTGAAAATGTGAAAGAAAAGTGAGTGCCTGGGATAATTCACTGTCCA
GAGACTCCTTTCTTGGCTGGTCGGGACCCAAACTGATGTCAGAGAAGACCCCTATACTATTGAGAAACTTGCCAAGAACA
AACAGAAGCCCATCACTCCAGTGACTGCTGCAAAGCTGGCCTGTGATCTGAAAGCTTCCCAGGATGCGGAGTGTTCTGCG
CTCACACAGAAAGGCCTAAAGAATGTATTTGATGAAGCAGTATTGTCAGACCTGGAGCCTCCGGCCCTGAAGAAGAGCCA
CAGGTGTGTG

Alignment

ORF - retro_opri_995 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.58 %
• Parental protein coverage: 85.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKE
          N.FPSE..PTV.D..AVTVMIGGEP.T.GLF.TAGQE.YD.LRPLSYPQTD.FL.CFSVVS.SSFENVKE
Retrocopy NTFPSEHAPTVSDSCAVTVMIGGEPHTPGLFHTAGQEVYDGLRPLSYPQTDAFLICFSVVSLSSFENVKE

Parental  KWVPEITHHCPKTPFL-LVGTQIDLRDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQKG
          K.VP.I..HCP.TPFL.LVGTQ.D.R.DP.TIEKLAKNKQKPITP.TA.KLA.DLKA....ECSALTQKG
Retrocopy K*VPGII-HCPETPFL>LVGTQTDVREDPYTIEKLAKNKQKPITPVTAAKLACDLKASQDAECSALTQKG

Parental  LKNVFDEAILAALEPPEPKKSRRCV
          LKNVFDEA.L..LEPP..KKS.RCV
Retrocopy LKNVFDEAVLSDLEPPALKKSHRCV

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_995 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 13 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014707	5 retrocopies	retro_cfam_1587, retro_cfam_1970, retro_cfam_2189, retro_cfam_88, retro_cfam_89,
Choloepus hoffmanni	ENSCHOG00000005306	10 retrocopies	retro_chof_103, retro_chof_1044, retro_chof_1195, retro_chof_1853, retro_chof_2055, retro_chof_2105, retro_chof_2331, retro_chof_2407, retro_chof_50, retro_chof_800,
Callithrix jacchus	ENSCJAG00000005912	6 retrocopies	retro_cjac_1275, retro_cjac_1808, retro_cjac_1826, retro_cjac_2251, retro_cjac_751, retro_cjac_911,
Cavia porcellus	ENSCPOG00000006543	4 retrocopies	retro_cpor_1168, retro_cpor_286, retro_cpor_33, retro_cpor_887,
Equus caballus	ENSECAG00000019180	1 retrocopy	retro_ecab_11,
Echinops telfairi	ENSETEG00000004443	1 retrocopy	retro_etel_2010,
Felis catus	ENSFCAG00000004853	4 retrocopies	retro_fcat_129, retro_fcat_1421, retro_fcat_1579, retro_fcat_896,
Monodelphis domestica	ENSMODG00000016078	3 retrocopies	retro_mdom_18, retro_mdom_181, retro_mdom_537,
Mustela putorius furo	ENSMPUG00000015999	2 retrocopies	retro_mputfur_308, retro_mputfur_957,
Oryctolagus cuniculus	ENSOCUG00000009986	1 retrocopy	retro_ocun_60,
Otolemur garnettii	ENSOGAG00000014261	1 retrocopy	retro_ogar_131,
Ochotona princeps	ENSOPRG00000005331	2 retrocopies	retro_opri_868, retro_opri_995 ,
Sorex araneus	ENSSARG00000005184	3 retrocopies	retro_sara_10, retro_sara_220, retro_sara_3,