RetrogeneDB ID: retro_opri_1026

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_592:41451..41931(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNC
• Ensembl ID: ENSOPRG00000012972
• Aliases: None
• Description: cyclin C [Source:HGNC Symbol;Acc:1581]

Sequence

>retro_opri_1026
CTGTTGCTTTCTTATCAGGGCAAGCTGTGCTCTGTGGCAGTGAACTTTTGGTGGAGCCTTGGCTATTTGCAGTGGGTCTT
GGATAAACAAGATGTGCTGGAGGAGCACCAAAAGGACTTTCTGTTAGAAGAGGATTGGAAATCACAGTTATTTTTAAAAG
TATTATTCAAATGTTGGATGAACTGAGACAATAAGAAATTGCCACAGCTACAATCTGTTTGAAGAAATTCCATGCCAGGT
TTCTCTGAAGAGCATACATCCTGCAGTAATGGCTTCTACATGCATGTTTTTGGCATGCACAGCAGAGGAATTTGGAGTAG
TTTCAAATATAAGATTGATGGCTACTGCTGTATCTGTTTTAAAAACTGGATTTTCATATGCCTTTCCAAAGGAATTTTTT
TGCAGGATGAGTCATATATTGGAATGTGAATTATATCTTTCAGAGCTAATGGATATTGCTTAATAGTGTATTGTCCTTAT

Alignment

ORF - retro_opri_1026 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.06 %
• Parental protein coverage: 55.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LVLSYQDKLYSMAGNFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIF-FTNVIQALGEHLKLR
          L.LSYQ.KL.S.A.NFW.S..YLQW.LDKQD.L.E.QKD..FL.EE..WK.Q.F.F...IQ.L.E...LR
Retrocopy LLLSYQGKLCSVAVNFWWSLGYLQWVLDKQDVLEEHQKD--FLLEED-WKSQLF<FKSIIQMLDE---LR

Parental  QQVIATATVYFKRFYARY-SLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVXXXXXXXXXXXX
          Q..IATAT...K.F.AR..SLKSI.P..MA.TC.FLA...EEFGVVSN.RL.A.A.SV............
Retrocopy Q*EIATATICLKKFHARF<SLKSIHPAVMASTCMFLACTAEEFGVVSNIRLMATAVSVLKTGFSYAFPKE

Parental  XXXXXXXILECEFYLLELMDC-CLIVYHPY
          .......ILECE.YL.ELMD..CLIVY.PY
Retrocopy FFCRMSHILECELYLSELMDI<CLIVYCPY

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_1026 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008954	1 retrocopy	retro_amel_1828,
Canis familiaris	ENSCAFG00000003525	1 retrocopy	retro_cfam_1774,
Dasypus novemcinctus	ENSDNOG00000011999	3 retrocopies	retro_dnov_1153, retro_dnov_216, retro_dnov_2243,
Dipodomys ordii	ENSDORG00000008393	2 retrocopies	retro_dord_230, retro_dord_75,
Myotis lucifugus	ENSMLUG00000012815	1 retrocopy	retro_mluc_1582,
Oryctolagus cuniculus	ENSOCUG00000003309	2 retrocopies	retro_ocun_1753, retro_ocun_888,
Ochotona princeps	ENSOPRG00000012972	2 retrocopies	retro_opri_1026 , retro_opri_151,
Sus scrofa	ENSSSCG00000004353	1 retrocopy	retro_sscr_760,
Tupaia belangeri	ENSTBEG00000017525	1 retrocopy	retro_tbel_677,