RetrogeneDB ID: retro_cpor_417

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_149:296292..296635(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMPK1
• Ensembl ID: ENSCPOG00000014747
• Aliases: None
• Description: None

Sequence

>retro_cpor_417
ACAATGGCTGCCAATGCCCAGAAGAATAAACCCTTGATGGATGGGTTTCCAAAAATCAAGATGACCTGCAAGGTTGGAAC
AAGACCATGGATGGAAAGCAGATATATCTTTTGTTGTTTTTTGACTGTAATAATGAGATCTGTATTGAACTGTATCAAGA
GGGGGAAAGTAGTGGTGGAGGTGAAGACAACAGGGGAAGCTTGCAAAAGAGGATTCAGACTTAGCTTCAGGCAAAGAAGC
CAGTTATGGACTCATCTGAAGAAATGGGGAAAGTCAAGTAACAGATGCATCCAGTTCTGCTAAAGTGTTTGACGAAGTTA
TGAAGATTTTTGATAAAGAAGGC

Alignment

ORF - retro_cpor_417 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.0 %
• Parental protein coverage: 56.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TMAANAQKNKFLIDGFPR-NQDNLQGWNKTMDGKADVSFVLFFDCNNEICIERCLERGKSSGRSDDNRES
          TMAANAQKNK.L.DGFP..NQD.LQGWNKTMDGK......LFFDCNNEICIE.....G.SSG...DNR.S
Retrocopy TMAANAQKNKPLMDGFPK<NQDDLQGWNKTMDGK-QIYLLLFFDCNNEICIE-LYQEGESSGGGEDNRGS

Parental  LEKRIQTYLQSTKPIIDLYEEMGKVK-KIDASRSVDEVFDEVMKIFDKEG
          L.KRIQT.LQ..KP..D..EEMGKVK...DAS.S...VFDEVMKIFDKEG
Retrocopy LQKRIQT*LQAKKPVMDSSEEMGKVK<VTDASSSA-KVFDEVMKIFDKEG

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	52.69 RPM
SRP017611_kidney	0.10 RPM	59.04 RPM
SRP017611_liver	0.00 RPM	65.46 RPM
SRP040447_lung	0.00 RPM	35.46 RPM
SRP040447_skeletal_muscle	0.00 RPM	12.10 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_417 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_417 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 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004030	1 retrocopy	retro_cfam_1729,
Choloepus hoffmanni	ENSCHOG00000004014	2 retrocopies	retro_chof_609, retro_chof_840,
Cavia porcellus	ENSCPOG00000014747	4 retrocopies	retro_cpor_1070, retro_cpor_1295, retro_cpor_417 , retro_cpor_799,
Macaca mulatta	ENSMMUG00000017375	2 retrocopies	retro_mmul_1572, retro_mmul_66,
Mustela putorius furo	ENSMPUG00000012394	1 retrocopy	retro_mputfur_1061,
Mus musculus	ENSMUSG00000028719	1 retrocopy	retro_mmus_2576,
Rattus norvegicus	ENSRNOG00000007775	1 retrocopy	retro_rnor_1940,
Sus scrofa	ENSSSCG00000003885	1 retrocopy	retro_sscr_454,