RetrogeneDB ID: retro_cpor_728

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_25:5770730..5771171(-)
• Located in intron of: ENSCPOG00000004486

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAB1
• Ensembl ID: ENSCPOG00000012038
• Aliases: None
• Description: None

Sequence

>retro_cpor_728
GTCCACTGCATGCCCTGGGCCTTGGTGCTGCCACCCGGCTCCCCACACTGGCCCTGGCTCGGACACTCAGTACTGCTTTA
TGTCCCTCAGGAACCCAGATGAGGCCTGGGGTGACGCAGCCAGCCTCAGTACTCGCACAGGCTCCAGGGAGGATTCCACA
GTTTTGCCGTCAGTGTAGCGATGCACCTCCTTTGACATTAGAAGAAATTAAGGATCAGGTACTGTATGTCTCAGAACTCT
ATGAAAAGATTGACCCAAAAAAGCTTTTGGTAAATTCCCATTTTATGAAATACCTGGGTTTAGAAAGTTTGGACCCAGTG
GAGAGTATCATGCCCACGGAGGATGAATTTGGGTTTGAAATTCCTGATTATAGAAGCAGAAAAGTTAATGTGTCCACAAG
AAATTGTCGATTACACTAGTGATAAGAAGAATATATATGAA

Alignment

ORF - retro_cpor_728 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.83 %
• Parental protein coverage: 94.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VRRLPSALVPP-SRLPTLALARTLSTALCAARTQTRLGAAQLALAFAQVPGRIPQFCRQYSDAPPLTLEG
          V...P.ALV.P..RLPTLALARTLSTALC...TQ.R.G..Q.A...AQ.PGRIPQFCRQ.SDAPPLTLE.
Retrocopy VHCMPWALVLP<TRLPTLALARTLSTALCPSGTQMRPGVTQPASVLAQAPGRIPQFCRQCSDAPPLTLEE

Parental  IKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPD-IDAEKLMCPQEIVDY
          IKD.VLYV..LY.KIDP.KL.VNSHFMK.LGL.SLD.VE.IM..EDEFGFEIPD.I.AEKLMCPQEIVDY
Retrocopy IKDQVLYVSELYEKIDPKKLLVNSHFMKYLGLESLDPVESIMPTEDEFGFEIPD>IEAEKLMCPQEIVDY

Parental  IADKKDVYE
          ..DKK..YE
Retrocopy TSDKKNIYE

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	31.46 RPM
SRP017611_kidney	0.00 RPM	83.96 RPM
SRP017611_liver	0.00 RPM	55.93 RPM
SRP040447_lung	0.00 RPM	19.70 RPM
SRP040447_skeletal_muscle	0.00 RPM	115.06 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_728 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_728 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 24 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014304	1 retrocopy	retro_amel_1692,
Canis familiaris	ENSCAFG00000017667	3 retrocopies	retro_cfam_1738, retro_cfam_1821, retro_cfam_450,
Choloepus hoffmanni	ENSCHOG00000003558	2 retrocopies	retro_chof_1517, retro_chof_2498,
Callithrix jacchus	ENSCJAG00000020616	2 retrocopies	retro_cjac_2635, retro_cjac_3099,
Cavia porcellus	ENSCPOG00000012038	2 retrocopies	retro_cpor_728 , retro_cpor_767,
Dasypus novemcinctus	ENSDNOG00000017122	5 retrocopies	retro_dnov_1450, retro_dnov_1733, retro_dnov_2024, retro_dnov_89, retro_dnov_911,
Felis catus	ENSFCAG00000013241	3 retrocopies	retro_fcat_1104, retro_fcat_1181, retro_fcat_2012,
Homo sapiens	ENSG00000004779	1 retrocopy	retro_hsap_3484,
Gorilla gorilla	ENSGGOG00000006320	1 retrocopy	retro_ggor_2349,
Loxodonta africana	ENSLAFG00000001032	1 retrocopy	retro_lafr_330,
Macropus eugenii	ENSMEUG00000012681	3 retrocopies	retro_meug_1780, retro_meug_303, retro_meug_830,
Microcebus murinus	ENSMICG00000007778	2 retrocopies	retro_mmur_1193, retro_mmur_120,
Macaca mulatta	ENSMMUG00000020522	1 retrocopy	retro_mmul_101,
Monodelphis domestica	ENSMODG00000016352	1 retrocopy	retro_mdom_389,
Mustela putorius furo	ENSMPUG00000012142	2 retrocopies	retro_mputfur_1135, retro_mputfur_466,
Mus musculus	ENSMUSG00000030869	6 retrocopies	retro_mmus_1724, retro_mmus_2073, retro_mmus_2188, retro_mmus_2947, retro_mmus_3094, retro_mmus_3332,
Oryctolagus cuniculus	ENSOCUG00000008457	1 retrocopy	retro_ocun_1712,
Otolemur garnettii	ENSOGAG00000005562	2 retrocopies	retro_ogar_2916, retro_ogar_325,
Pongo abelii	ENSPPYG00000007192	1 retrocopy	retro_pabe_2879,
Pan troglodytes	ENSPTRG00000007889	1 retrocopy	retro_ptro_2358,
Rattus norvegicus	ENSRNOG00000018129	2 retrocopies	retro_rnor_1353, retro_rnor_2058,
Sus scrofa	ENSSSCG00000010795	1 retrocopy	retro_sscr_1017,
Ictidomys tridecemlineatus	ENSSTOG00000024657	2 retrocopies	retro_itri_281, retro_itri_916,
Tursiops truncatus	ENSTTRG00000005258	2 retrocopies	retro_ttru_1229, retro_ttru_989,