RetrogeneDB ID: retro_opri_198

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3486:32890..33244(-)
• Located in intron of: ENSOPRG00000010972

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNIH
• Ensembl ID: ENSOPRG00000005287
• Aliases: None
• Description: cornichon homolog (Drosophila) [Source:HGNC Symbol;Acc:19431]

Sequence

>retro_opri_198
ATTGTAGCATTTGATACGCTGAAGATCGATTACAAGAATCCTATAGACCAGTGCAATGCCCTGAATCCTCTTGTACTGCC
AGAGTACCTCATCCATGCTTTCTTCTGTGTCATGCTTCTTGGTGCAGCAGAATGGCTTACGCTGGGTCTCAATATACCCC
TGTTGGCATACCATATTTAGAGGTGTATGAATAGACCAGTGATGAGCAGACCAGGACTCTATAACTCCACAACCATCATG
AATGCAGATATTCTAGCATATTGTCAGAAAGAAGAACGGTACAAGTTAGCTTTTTATCTTCTAGCAGGTTTTTTTTTTTA
CTACTTATGTGGCATGATCTATGTGTTGATGAGC

Alignment

ORF - retro_opri_198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.12 %
• Parental protein coverage: 80.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IIAFDELKTDYKNPIDQCNTLNPLVLPEYLIHAFFCVMFLCAADH-TLGLNMPLLAYHIWRYMSRPVMSG
          I.AFD.LK.DYKNPIDQCN.LNPLVLPEYLIHAFFCVM.L.AA...TLGLN.PLLAYHI.R.M.RPVMS.
Retrocopy IVAFDTLKIDYKNPIDQCNALNPLVLPEYLIHAFFCVMLLGAAEWLTLGLNIPLLAYHI*RCMNRPVMSR

Parental  PGLYDPTTIMNADILAYCQKEGWCKLAFYLLS--FFYYLYGMIYVLVS
          PGLY..TTIMNADILAYCQKE...KLAFYLL......YL.GMIYVL.S
Retrocopy PGLYNSTTIMNADILAYCQKEERYKLAFYLLAXXXXXYLCGMIYVLMS

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_198 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031178	2 retrocopies	retro_cfam_658, retro_cfam_697,
Callithrix jacchus	ENSCJAG00000007306	1 retrocopy	retro_cjac_103,
Equus caballus	ENSECAG00000026814	1 retrocopy	retro_ecab_685,
Loxodonta africana	ENSLAFG00000014841	1 retrocopy	retro_lafr_963,
Nomascus leucogenys	ENSNLEG00000012704	1 retrocopy	retro_nleu_1896,
Otolemur garnettii	ENSOGAG00000024582	1 retrocopy	retro_ogar_2271,
Ochotona princeps	ENSOPRG00000001589	1 retrocopy	retro_opri_749,
Ochotona princeps	ENSOPRG00000005287	4 retrocopies	retro_opri_198 , retro_opri_269, retro_opri_366, retro_opri_894,
Tupaia belangeri	ENSTBEG00000010265	3 retrocopies	retro_tbel_2080, retro_tbel_3728, retro_tbel_572,
Tarsius syrichta	ENSTSYG00000011295	1 retrocopy	retro_tsyr_1540,
Tursiops truncatus	ENSTTRG00000008259	1 retrocopy	retro_ttru_261,