RetrogeneDB ID: retro_cpor_343

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_13:45355680..45356475(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCED1A
• Ensembl ID: ENSCPOG00000025475
• Aliases: None
• Description: None

Sequence

>retro_cpor_343
AGACCCAGGCCCTTCGGTATGACCCACCTGCGGACCTGCCAAGTCCGCCAACTGCTCCACAACAAGTTCGTGGTGATCAT
GGGCGACTCGATCCAGCGCGCCGTGTACAAGGACCTGGTGCTGCTGCTGCAGAGGGACAGCCTGCTGTCCTCCCGCCAGC
TCAACACCAAGGGCGAGCTGAGCTTCGAGCAAGATGTGCTGCTCGAGGGCGGCAGGTGGGGCCGCATGCACAATGACATC
TACTACCGCGAGGTGCGCCAGTTCTGCACCGGCCACCACCTGGTGCGCTTCTACTTCCTCACGCGCGCCTATTCGGCCTA
CCTGGAGGAGGTGCTGTGGGCGCTGCGCTGGGACCAGTACGCGCCGGACCTGGTCGTCCTCAACTCGTGCCTCTGGGACC
TGGCGAGGCACGGCCGCCACTTCCACAGCCGGTACCGCGAGGACCTAGCGTGCCTGTTCCGCCGCATGGACCGCATGCTG
CCCGAGTCCTGCCTGCTGGTGTGGAACACCGCCCTGCCGGTGGCCGACGTCGTGTCGGGCGGCTTCCTCCCGCAGCGGGC
CCTGGCCGTCCCGGGCCGCCTGCGCGACGACGTCATCGAGGCCAACTTCTACAGCGCCGTGGAGGCGGCCCGCCGCGGCT
TCGACCTGCTCGACCTGCACTTCCACTTCCGCCACGCGGGCCGGCACCAGCTGCGCGACGGCGTGCACTGGGACGAGCGC
GCGCACCGGCGGCTGTCGCAGCTGCTGCTGGCGCACGTGGCGGATGCCTGGGGCGTGAACCTTCCGGGCCAGGAG

Alignment

ORF - retro_cpor_343 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.3 %
• Parental protein coverage: 63.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RPLRSAMVHIQASEVQQLLHNKFVVILGDSIQRAVYKDLVLLLQKDSLLTVAQLKAKGELSFEQDQLVAG
          RP....M.H.....V.QLLHNKFVVI.GDSIQRAVYKDLVLLLQ.DSLL...QL..KGELSFEQD.L..G
Retrocopy RPRPFGMTHLRTCQVRQLLHNKFVVIMGDSIQRAVYKDLVLLLQRDSLLSSRQLNTKGELSFEQDVLLEG

Parental  GQLGELHNGTQYREVRQFCSGSGHHLVRFYFLTRVYSEYLEDVLEELTYGP-APDLVIINSCLWDLSRYG
          G..G..HN...YREVRQFC.G..HHLVRFYFLTR.YS.YLE.VL..L.....APDLV..NSCLWDL.R.G
Retrocopy GRWGRMHNDIYYREVRQFCTG--HHLVRFYFLTRAYSAYLEEVLWALRWDQYAPDLVVLNSCLWDLARHG

Parental  RCSMESYRENLERVFVRMDQVLPDSCLLVWNMAMPLGERVTGGFLLPELQPLAATLRRDVVEGNFYSATL
          R.....YRE.L...F.RMD..LP.SCLLVWN.A.P....V.GGFL..........LR.DV.E.NFYSA..
Retrocopy RHFHSRYREDLACLFRRMDRMLPESCLLVWNTALPVADVVSGGFLPQRALAVPGRLRDDVIEANFYSAVE

Parental  AGDHYFDVLDLHFHFRHAVQHRHRDGVHWDQHAHRHLSHLLLTHVADAWGVELPKRD
          A....FD.LDLHFHFRHA..H..RDGVHWD..AHR.LS.LLL.HVADAWGV.LP...
Retrocopy AARRGFDLLDLHFHFRHAGRHQLRDGVHWDERAHRRLSQLLLAHVADAWGVNLPGQE

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	22.20 RPM
SRP017611_kidney	0.00 RPM	12.98 RPM
SRP017611_liver	0.00 RPM	4.09 RPM
SRP040447_lung	0.00 RPM	14.20 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.02 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_343 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_343 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 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003863	1 retrocopy	retro_btau_182,
Cavia porcellus	ENSCPOG00000025475	2 retrocopies	retro_cpor_343 , retro_cpor_79,
Equus caballus	ENSECAG00000016497	1 retrocopy	retro_ecab_87,
Felis catus	ENSFCAG00000002886	1 retrocopy	retro_fcat_18,
Homo sapiens	ENSG00000132635	2 retrocopies	retro_hsap_2207, retro_hsap_82,
Microcebus murinus	ENSMICG00000016578	2 retrocopies	retro_mmur_163, retro_mmur_278,
Myotis lucifugus	ENSMLUG00000028662	2 retrocopies	retro_mluc_222, retro_mluc_647,
Macaca mulatta	ENSMMUG00000005200	2 retrocopies	retro_mmul_333, retro_mmul_341,
Mus musculus	ENSMUSG00000037773	2 retrocopies	retro_mmus_1001, retro_mmus_332,
Otolemur garnettii	ENSOGAG00000004701	1 retrocopy	retro_ogar_81,
Pongo abelii	ENSPPYG00000010833	2 retrocopies	retro_pabe_192, retro_pabe_2080,
Pan troglodytes	ENSPTRG00000013185	1 retrocopy	retro_ptro_105,
Pteropus vampyrus	ENSPVAG00000006834	1 retrocopy	retro_pvam_9,
Sus scrofa	ENSSSCG00000007168	1 retrocopy	retro_sscr_23,
Ictidomys tridecemlineatus	ENSSTOG00000016356	2 retrocopies	retro_itri_1190, retro_itri_783,
Tursiops truncatus	ENSTTRG00000003464	1 retrocopy	retro_ttru_16,