RetrogeneDB ID: retro_cpor_1042

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:46705041..46705376(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF13
• Ensembl ID: ENSCPOG00000001081
• Aliases: None
• Description: None

Sequence

>retro_cpor_1042
GAGGAAGAGGATCCTAACTTTGAGGAGGAAAATCAGGAAATTGGAGGAGGTGCTAAAGGTAGACATGAGTAGAACAAAGA
GACTTTCTTCTGAAGAATTATAAAGAATGCTGTATGGGTTTGAAAATGACCAGAATCCTTGTGCTGAGTCAGTGGATATT
CTCAATGACCTGGTCATAGAGATCATCATTGAAACGACTCCTAAGGTAATGTCCATTGGAATTCAAGGTGGAGTACAAGT
TGAAGATACTGTCTTCTTGATCAAAAGGACCCAAGAAAGTTAAGGTTAAAGACTTGCTTACTATGAATGAAGAATTGTAA
CGAGCTAGAAAAGCA

Alignment

ORF - retro_cpor_1042 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.83 %
• Parental protein coverage: 91.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEEDPTFEEESEEIGGGAEG-GQGKRKRLFSKELRCMMYGFGDDQNPYTESVDILEDLVIEFITEMTHKA
          EEEDP.FEEE..EIGGGA.G......KRL.S.EL..M.YGF..DQNP..ESVDIL.DLVIE.I.E.T.K.
Retrocopy EEEDPNFEEENQEIGGGAKG>DMSRTKRLSSEEL*RMLYGFENDQNPCAESVDILNDLVIEIIIETTPKV

Parental  MSIGRQGRVQVEDIVFLIR-KDPRKFARVK-DLLTMNEELKRARKA
          MSIG.QG.VQVED.VFLI..KDPRK..R.K.DLLTMNEEL.RARKA
Retrocopy MSIGIQGGVQVEDTVFLIK<KDPRKL-RLK<DLLTMNEEL*RARKA

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	5.52 RPM
SRP017611_kidney	0.00 RPM	2.93 RPM
SRP017611_liver	0.00 RPM	4.35 RPM
SRP040447_lung	0.00 RPM	4.51 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.09 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1042 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1042 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 16 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004542	1 retrocopy	retro_amel_1015,
Canis familiaris	ENSCAFG00000019855	1 retrocopy	retro_cfam_1084,
Choloepus hoffmanni	ENSCHOG00000003347	2 retrocopies	retro_chof_1739, retro_chof_296,
Callithrix jacchus	ENSCJAG00000002701	3 retrocopies	retro_cjac_1241, retro_cjac_1268, retro_cjac_969,
Cavia porcellus	ENSCPOG00000001081	1 retrocopy	retro_cpor_1042 ,
Dasypus novemcinctus	ENSDNOG00000018227	16 retrocopies	retro_dnov_1126, retro_dnov_1140, retro_dnov_1237, retro_dnov_1308, retro_dnov_1539, retro_dnov_1899, retro_dnov_214, retro_dnov_222, retro_dnov_234, retro_dnov_314, retro_dnov_577, retro_dnov_599, retro_dnov_630, retro_dnov_703, retro_dnov_893, retro_dnov_925,
Loxodonta africana	ENSLAFG00000011432	2 retrocopies	retro_lafr_781, retro_lafr_799,
Microcebus murinus	ENSMICG00000008725	5 retrocopies	retro_mmur_1061, retro_mmur_128, retro_mmur_1376, retro_mmur_53, retro_mmur_576,
Mus musculus	ENSMUSG00000048100	2 retrocopies	retro_mmus_1272, retro_mmus_710,
Nomascus leucogenys	ENSNLEG00000002350	1 retrocopy	retro_nleu_27,
Otolemur garnettii	ENSOGAG00000013494	6 retrocopies	retro_ogar_192, retro_ogar_2232, retro_ogar_23, retro_ogar_2399, retro_ogar_2659, retro_ogar_2931,
Procavia capensis	ENSPCAG00000005773	1 retrocopy	retro_pcap_80,
Sorex araneus	ENSSARG00000008033	1 retrocopy	retro_sara_531,
Sus scrofa	ENSSSCG00000006839	1 retrocopy	retro_sscr_87,
Ictidomys tridecemlineatus	ENSSTOG00000011144	8 retrocopies	retro_itri_1094, retro_itri_1650, retro_itri_1717, retro_itri_1728, retro_itri_214, retro_itri_70, retro_itri_812, retro_itri_969,
Tursiops truncatus	ENSTTRG00000003167	1 retrocopy	retro_ttru_730,