RetrogeneDB ID: retro_cpor_425

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_15:30759507..30760022(+)
• Located in intron of: ENSCPOG00000024916

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAF4
• Ensembl ID: ENSCPOG00000007618
• Aliases: None
• Description: None

Sequence

>retro_cpor_425
GGGGCTTTGGTGACCTAGGCAGTGAGGTGTTTCAATTTAGAGAACCCAGTAGAGCAGGAAATCAGCAAGATGAAGCATCC
ACAGCCCCGAGGCACCCGTCCATGCAGTGTCCTGCAGAGCAGGCGAGTGACTATCCAGAAATGAAGAGAGAAATTGCTAG
GAAAAAAGAAAAGCTGCTGTCTTTACTAAAAGATATATATGTTGATTTCCAAGATCCTGTTTCATCCCAGATGGTAAATG
ATGCTGTAACCCAGCAAGAGACAAAGGAATTCAGATTGCCCAAAGGCCATCACTTTGGTATGGACATTAAGAACATTCCC
AAGGGCAAAATTTCCATTGTTGAGGCCACGACACTACTCAATAATCATGAACTTTATCCAGAAACATAGACTGCTGAGAA
AATAGCACAAGAATGCCATTTAAAACTGGAAGGCATAAATTCTCTTTGCAAGTATTTTGTTACTTTTGAAGTCAAGATCT
TTTCTCCTGAACACAAGAAAACAGTAGTATCAAAA

Alignment

ORF - retro_cpor_425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.29 %
• Parental protein coverage: 99.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GARVSRAVRNFNLENRAEREISKVK-PSMAPRHPSTQSVLREQKSDHAEIEREIARKNEKLLSLLKDVYV
          GA.V..AVR.FNLEN..E.EISK.K..S.APRHPS.Q....EQ.SD..E..REIARK.EKLLSLLKD.YV
Retrocopy GALVT*AVRCFNLENPVEQEISKMK<ASTAPRHPSMQCPA-EQASDYPEMKREIARKKEKLLSLLKDIYV

Parental  DSKDPVSSQVVKDAATQQEPKEFRLPKGHHFGMDIKNIPMGKISIVEAVTLLNNHKLYPETWTAEKIAQE
          D..DPVSSQ.V.DA.TQQE.KEFRLPKGHHFGMDIKNIP.GKISIVEA.TLLNNH.LYPET.TAEKIAQE
Retrocopy DFQDPVSSQMVNDAVTQQETKEFRLPKGHHFGMDIKNIPKGKISIVEATTLLNNHELYPET*TAEKIAQE

Parental  YHLKLEDVNSLLKYFVTFEVKNFSPENKNIIESK
          .HLKLE..NSL.KYFVTFEVK.FSPE.K....SK
Retrocopy CHLKLEGINSLCKYFVTFEVKIFSPEHKKTVVSK

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	0.06 RPM	10.07 RPM
SRP017611_kidney	0.00 RPM	11.41 RPM
SRP017611_liver	0.00 RPM	3.70 RPM
SRP040447_lung	0.00 RPM	3.51 RPM
SRP040447_skeletal_muscle	0.29 RPM	9.16 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_425 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_425 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 15 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003174	1 retrocopy	retro_btau_1763,
Choloepus hoffmanni	ENSCHOG00000005145	2 retrocopies	retro_chof_2271, retro_chof_891,
Callithrix jacchus	ENSCJAG00000001235	2 retrocopies	retro_cjac_1613, retro_cjac_1700,
Cavia porcellus	ENSCPOG00000007618	1 retrocopy	retro_cpor_425 ,
Homo sapiens	ENSG00000123545	4 retrocopies	retro_hsap_1494, retro_hsap_2774, retro_hsap_3761, retro_hsap_477,
Gorilla gorilla	ENSGGOG00000012070	4 retrocopies	retro_ggor_1147, retro_ggor_1931, retro_ggor_2529, retro_ggor_451,
Microcebus murinus	ENSMICG00000015734	1 retrocopy	retro_mmur_1624,
Macaca mulatta	ENSMMUG00000018843	4 retrocopies	retro_mmul_1717, retro_mmul_2138, retro_mmul_578, retro_mmul_734,
Mus musculus	ENSMUSG00000028261	3 retrocopies	retro_mmus_1153, retro_mmus_1290, retro_mmus_3668,
Nomascus leucogenys	ENSNLEG00000013568	4 retrocopies	retro_nleu_171, retro_nleu_1716, retro_nleu_678, retro_nleu_890,
Oryctolagus cuniculus	ENSOCUG00000002152	1 retrocopy	retro_ocun_1162,
Pongo abelii	ENSPPYG00000016857	4 retrocopies	retro_pabe_1244, retro_pabe_2241, retro_pabe_257, retro_pabe_3160,
Pan troglodytes	ENSPTRG00000018435	4 retrocopies	retro_ptro_1013, retro_ptro_1877, retro_ptro_2552, retro_ptro_358,
Rattus norvegicus	ENSRNOG00000007506	3 retrocopies	retro_rnor_1617, retro_rnor_2973, retro_rnor_675,
Tursiops truncatus	ENSTTRG00000010911	1 retrocopy	retro_ttru_628,