RetrogeneDB ID: retro_cpor_1039

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:40274255..40274892(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000024964
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FYTTD1
• Ensembl ID: ENSCPOG00000011463
• Aliases: None
• Description: None

Sequence

>retro_cpor_1039
AACCGGTTTGGTACCGGATTGGTAGAGGCCACGGGGACCCTGTTGCCAGCCCTGAAAGCACATAGCAATGAAAACCTCGA
CAAAATCGATACGTCTCTAGATGATATTATCAAATTGAATCGGAAGGAAGGAAAGAAGCACAAGTTTCCAAGACTAAACA
GAAGACTCCAGCAAAGTAGTGCTGGGCAGGTCAGGGTAAGAGTACGGTGGGGAACCCAGCAGAATTGTGGTTTGGGTAAA
ACTAGCCTGAGCAAAAGAGGAAAAGCAATGCCTGGGAAGAGACGTCCTTACCAAGTGATCACTGGCCTTGTAGCTAGAAA
AGCAACTGGAATTCAAAAACAAGTAGTCCTATGCATCGTCCTCCTGTAAGCGACAAGAACATAGAACGATATTTTCCATT
GTTAAAAAGGAAAGCAAACCTTCTGAGACAAAATGATGTGCAAAGAAAACCAGCTGCAGTTCTCAAGAGACTGAACAAGT
TTAACAGAAAAATAACATTCCAGCTAATTTTACCAGGAGTGGAAATAAATTAAGGCATCAGAAAGATACTCGTCAGGCAA
CTTTTCTTTTCCAGAGAGGTCTGAAGGTTCAGGCCCAGTTGAACACAGAACTGCTAGAGGATGTAGCAGCAAAGAGA

Alignment

ORF - retro_cpor_1039 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.48 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NRFSARLVGATATPSPPPKARSNENLDKIDMSLDDIIKLNRKEGKKHNFPRLNRRLQQSSARQFRMRVRW
          NRF...LV.AT.T..P..KA.SNENLDKID.SLDDIIKLNRKEGKKH.FPRLNRRLQQSSA.Q.R.RVRW
Retrocopy NRFGTGLVEATGTLLPALKAHSNENLDKIDTSLDDIIKLNRKEGKKHKFPRLNRRLQQSSAGQVRVRVRW

Parental  GIQQNSGFGKTSLSRRGKVMPGKRRPYGVITGLAARKATGIRKGV-SPMNRPPLSDKNIERYFPVLKRKA
          G.QQN.G.GKTSLS.RGK.MPGKRRPY.VITGL.ARKATGI.K.V.SPM.RPP.SDKNIERYFP.LKRKA
Retrocopy GTQQNCGLGKTSLSKRGKAMPGKRRPYQVITGLVARKATGIQKQV<SPMHRPPVSDKNIERYFPLLKRKA

Parental  NLLRQNDVQRKPATVLKRPNQLNR-KSNIPANFTRSANKLSHQKDTRQATFLFRRGLKVQAQLNTEQLLD
          NLLRQNDVQRKPA.VLKR.N..NR.K.NIPANFTRS.NKL.HQKDTRQATFLF.RGLKVQAQLNTE.LL.
Retrocopy NLLRQNDVQRKPAAVLKRLNKFNR<KNNIPANFTRSGNKLRHQKDTRQATFLFQRGLKVQAQLNTE-LLE

Parental  DVVAKR
          DV.AKR
Retrocopy DVAAKR

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	14.67 RPM
SRP017611_kidney	0.10 RPM	14.03 RPM
SRP017611_liver	0.09 RPM	8.84 RPM
SRP040447_lung	0.00 RPM	12.36 RPM
SRP040447_skeletal_muscle	0.00 RPM	17.99 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1039 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1039 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 17 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014874	1 retrocopy	retro_btau_1572,
Canis familiaris	ENSCAFG00000029695	1 retrocopy	retro_cfam_70,
Choloepus hoffmanni	ENSCHOG00000002881	2 retrocopies	retro_chof_1068, retro_chof_114,
Callithrix jacchus	ENSCJAG00000016488	2 retrocopies	retro_cjac_1639, retro_cjac_623,
Cavia porcellus	ENSCPOG00000011463	2 retrocopies	retro_cpor_1039 , retro_cpor_586,
Dasypus novemcinctus	ENSDNOG00000007807	6 retrocopies	retro_dnov_1010, retro_dnov_1224, retro_dnov_1311, retro_dnov_2013, retro_dnov_442, retro_dnov_570,
Erinaceus europaeus	ENSEEUG00000001433	1 retrocopy	retro_eeur_13,
Echinops telfairi	ENSETEG00000000700	1 retrocopy	retro_etel_765,
Homo sapiens	ENSG00000122068	2 retrocopies	retro_hsap_4291, retro_hsap_476,
Gorilla gorilla	ENSGGOG00000011665	1 retrocopy	retro_ggor_450,
Macaca mulatta	ENSMMUG00000006626	1 retrocopy	retro_mmul_577,
Nomascus leucogenys	ENSNLEG00000015547	2 retrocopies	retro_nleu_1047, retro_nleu_889,
Pongo abelii	ENSPPYG00000014456	2 retrocopies	retro_pabe_258, retro_pabe_3497,
Pan troglodytes	ENSPTRG00000015796	1 retrocopy	retro_ptro_357,
Sorex araneus	ENSSARG00000009996	1 retrocopy	retro_sara_148,
Sarcophilus harrisii	ENSSHAG00000005704	1 retrocopy	retro_shar_242,
Tupaia belangeri	ENSTBEG00000005595	4 retrocopies	retro_tbel_2469, retro_tbel_2943, retro_tbel_4257, retro_tbel_791,