RetrogeneDB ID: retro_cpor_466

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:16609190..16609774(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000013652
• Aliases: None
• Description: None

Sequence

>retro_cpor_466
AAGGATGGCTGTGGTTTGGGAGAAGTGGCTATGGGGAATGAGCAGCAGCTTAACCTGGGTATTTCTAAGGCTGTGTTTGT
GGAAGATGTAGACTCCATGAAACTGCCTAGGAATGAGACTGCAGGTACAGTACTAAAGAAGCTAGACGAACAGTATCAGA
AGTATAAATTATGGAACTCAATCTTGCTCAAAAGAAACAGAGATTAAAAGGCTAAATTTCTGAAATCAAGCAGACTTTGG
AAATTCTAAAATACATGCAGAAGAAAAAAGACTGTATCACTTCACTGGAAACCATATTCTTACTGGCAGATAACCTGTAC
TGCAAAGCTTCGGTTCCTCCTACTGATAAAGTGTGTTTGTGGTTGGGGTCTAATGTAATGCTTGAGTATGATACTGATGA
AGCTCACGCTTTGTAGGAAAAGAATTTACCAGCTTCCATGAAGAATCTTGATTCTCTTGAGTAAGACCTTGACTTTCTTC
GAGATCAATTTACTGCGACAGAAGTCATTCCTACAGATACGGCCAGAGTTTGCAACTGGGATGTCAAAAGAAGAAAGAAA
GATGATCCTACCAAGGAAAAAAGC

Alignment

ORF - retro_cpor_466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.17 %
• Parental protein coverage: 97.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDGCGLAEAATGNGRRLHLGIPEAVFVEDVDSFMKQPGNETADTVLKKLDEQYQKYKF-MELNLAQKKRR
          KDGCGL.E.A.GN...L.LGI..AVFVEDVDS.MK.P.NETA.TVLKKLDEQYQKYK..MELNLAQKK.R
Retrocopy KDGCGLGEVAMGNEQQLNLGISKAVFVEDVDS-MKLPRNETAGTVLKKLDEQYQKYKL<MELNLAQKKQR

Parental  LKSQIPEIKQTLEILKYMQKKKESTTSLETRFLLADNLYCKASVPPTDKVCLWLGANVMLEYDIDEAQAL
          LK..I.EIKQTLEILKYMQKKK...TSLET.FLLADNLYCKASVPPTDKVCLWLG.NVMLEYD.DEA.AL
Retrocopy LKG*ISEIKQTLEILKYMQKKKDCITSLETIFLLADNLYCKASVPPTDKVCLWLGSNVMLEYDTDEAHAL

Parental  LEKNLSTATKNLDSLEEDLDFLRDQFTTTEV---NMARVYNWDVKRRNKDDSTKNKA
          .EKNL....KNLDSLE.DLDFLRDQFT.TEV.....ARV.NWDVKRR.KDD.TK.K.
Retrocopy *EKNLPASMKNLDSLE*DLDFLRDQFTATEVIPTDTARVCNWDVKRRKKDDPTKEKS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	16.39 RPM
SRP017611_kidney	0.00 RPM	27.85 RPM
SRP017611_liver	0.00 RPM	17.58 RPM
SRP040447_lung	0.00 RPM	14.70 RPM
SRP040447_skeletal_muscle	0.00 RPM	10.67 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_466 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_466 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus 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 20 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009058	2 retrocopies	retro_amel_1232, retro_amel_1346,
Canis familiaris	ENSCAFG00000019639	2 retrocopies	retro_cfam_1030, retro_cfam_573,
Cavia porcellus	ENSCPOG00000013652	1 retrocopy	retro_cpor_466 ,
Dasypus novemcinctus	ENSDNOG00000019432	1 retrocopy	retro_dnov_694,
Dipodomys ordii	ENSDORG00000004628	2 retrocopies	retro_dord_213, retro_dord_587,
Echinops telfairi	ENSETEG00000017655	2 retrocopies	retro_etel_2085, retro_etel_552,
Latimeria chalumnae	ENSLACG00000016144	1 retrocopy	retro_lcha_18,
Loxodonta africana	ENSLAFG00000016507	2 retrocopies	retro_lafr_1200, retro_lafr_163,
Myotis lucifugus	ENSMLUG00000015396	3 retrocopies	retro_mluc_1600, retro_mluc_2019, retro_mluc_986,
Macaca mulatta	ENSMMUG00000015095	1 retrocopy	retro_mmul_124,
Mus musculus	ENSMUSG00000031197	1 retrocopy	retro_mmus_2220,
Nomascus leucogenys	ENSNLEG00000014475	1 retrocopy	retro_nleu_537,
Oryctolagus cuniculus	ENSOCUG00000017448	2 retrocopies	retro_ocun_233, retro_ocun_747,
Otolemur garnettii	ENSOGAG00000016566	1 retrocopy	retro_ogar_3121,
Sarcophilus harrisii	ENSSHAG00000002823	1 retrocopy	retro_shar_7,
Sus scrofa	ENSSSCG00000012811	1 retrocopy	retro_sscr_131,
Ictidomys tridecemlineatus	ENSSTOG00000006684	1 retrocopy	retro_itri_1492,
Tupaia belangeri	ENSTBEG00000007833	5 retrocopies	retro_tbel_3084, retro_tbel_3369, retro_tbel_3652, retro_tbel_553, retro_tbel_632,
Tarsius syrichta	ENSTSYG00000002205	1 retrocopy	retro_tsyr_2032,
Tursiops truncatus	ENSTTRG00000016258	1 retrocopy	retro_ttru_988,