RetrogeneDB ID: retro_opri_749

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_28025:6499..6784(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNIH4
• Ensembl ID: ENSOPRG00000001589
• Aliases: None
• Description: cornichon homolog 4 (Drosophila) [Source:HGNC Symbol;Acc:25013]

Sequence

>retro_opri_749
ATTACTGCTCGATCCTGCAGCTGGAAATCGAACAAGTGGGTAATTTGAGACTTGATTGGCCATACCCTTGTCTTGTATTG
ATGCTTTATTTTATTGCCCTGCTCCATCTTCCTTCTCAACTGACCTGTTGCCTCTTGGAATCTAAATGGTTTCATTATGC
TGCCGAGTGGCAATGCGGGAATGTTTGATCCCACAGGAATGTGCAATAGAGACCAGCAGAAGTCACCCATGAAAGAAACC
ATAATCGCGTTTGGTTCCCACTTGCTCTGTCTTTACTTAGCTCTG

Alignment

ORF - retro_opri_749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.89 %
• Parental protein coverage: 81.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  INARSCCSKLNKWVIPELIGHTIVAVLMLISLHWFIFLLNLPVATWNIYRFIMVPSGNMRVFDPTEIHNR
          I.ARSC..K.NKWVI..LIGHT.V.....I.L...IFLLN.PVA.WN...FIM.PSGN...FDPT...NR
Retrocopy ITARSCSWKSNKWVI*DLIGHTLVLY*CFILLPCSIFLLN*PVASWNLNGFIMLPSGNAGMFDPTGMCNR

Parental  GQLKSHMKEAMIKLGFHLLCFFMYL
          .Q.KS.MKE..I..G.HLLC....L
Retrocopy DQQKSPMKETIIAFGSHLLCLYLAL

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_749 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 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006544	1 retrocopy	retro_chof_327,
Callithrix jacchus	ENSCJAG00000008013	1 retrocopy	retro_cjac_2474,
Cavia porcellus	ENSCPOG00000007310	1 retrocopy	retro_cpor_777,
Dasypus novemcinctus	ENSDNOG00000007093	1 retrocopy	retro_dnov_1669,
Homo sapiens	ENSG00000143771	1 retrocopy	retro_hsap_3656,
Gorilla gorilla	ENSGGOG00000005708	1 retrocopy	retro_ggor_2470,
Myotis lucifugus	ENSMLUG00000003134	1 retrocopy	retro_mluc_1314,
Macaca mulatta	ENSMMUG00000009936	1 retrocopy	retro_mmul_1796,
Nomascus leucogenys	ENSNLEG00000013549	1 retrocopy	retro_nleu_514,
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,
Pongo abelii	ENSPPYG00000000183	1 retrocopy	retro_pabe_3003,
Pan troglodytes	ENSPTRG00000002025	1 retrocopy	retro_ptro_2481,
Pteropus vampyrus	ENSPVAG00000014034	1 retrocopy	retro_pvam_692,
Ictidomys tridecemlineatus	ENSSTOG00000027396	2 retrocopies	retro_itri_1502, retro_itri_1552,
Vicugna pacos	ENSVPAG00000012521	2 retrocopies	retro_vpac_180, retro_vpac_215,