RetrogeneDB ID: retro_cpor_1339

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_7:46773089..46773669(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000004634
• Aliases: None
• Description: None

Sequence

>retro_cpor_1339
GTACCTCTGGGCTTTGGGGACCGCTGCACAAAGCACCTCAGTGGGGAGTTCAGGAAACCGTATTTTATACAGCATGGGAC
TTGTTGCAGAATAAAACATCACACTATTTATCCACCCCACCCCCAGGCTCCCTCCAGACCCCACTGTGTGACATCAAGAT
GTGACAGTGGTCATCCTAGGACAGACAGTTCCTCATCTCGGACCCATCAGGCTCACAGGCTCCACTTTAGCAGAGTCCTG
CCCTGGCCCAGACCTTTGGAAAAAGTCTGTGAAGAGCCGACCACAGACACAGATGGCTTTGTTCATCCTGGCCAAGGAGA
TGCATCTAGGTGGACCGAGCAAGGCGTCTGCCTGCTCAGCACCACCCTTACTATCTGGGCCATCAGGCAATCCACGTACA
CAGAGAGGCTGGGAGCAGTTTGCCCTTGAGGTCCTGACCCACTCGGTCAGAATCTAACCAGTCTTGTCTTCCTGCTCGGA
GCTCTGATGTTTGGAAAAGGGGCAGAGCCAGGGACAGAAAGTGGCACAAGCCCCACAGTCCGCTCAGCCCTCGCCACTGT
CTACCTGGTGAGGAAGCTTT

Alignment

ORF - retro_cpor_1339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.48 %
• Parental protein coverage: 65.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  VPVGFGDSWKKHLSGEFGKPYFIK-LMGFVAEERKRYTVYPPPHQVFTWTQMCDI-QDVKVVILGQD-PY
          VP.GFGD...KHLSGEF.KPYFI.............Y...PPP......T..CDI.QDV.VVILGQ..P.
Retrocopy VPLGFGDRCTKHLSGEFRKPYFIQ<AWDLLQNKTSHYLSTPPPGSL--QTPLCDI<QDVTVVILGQTVPH

Parental  HGP-SQAHGLCFSVQRPVPPPPSLENIYKELSTDIDGFLHPGHGDLSGWAKQGVLLLNAVLTVRA-HQA-
          .GP..QAH.L.FS..R..P.P..LE....E..TD.DGF.HPG.GD.S.W..QGV.LL...LT..A.HQA.
Retrocopy LGP<HQAHRLHFS--RVLPWPRPLEKVCEEPTTDTDGFVHPGQGDASRWTEQGVCLLSTTLTIWA<HQA<

Parental  NSHKEQGWEQFTDAVVAW-LNQNLNGLVFLLW-GSYAQKKGSVIDRKRH-HVLQTAHPSPLSVYRGFF
          N.....GWEQF...V....L.QNL..LVFLL...S...K.G...DRK.H....Q.A.PSPLS...G.F
Retrocopy NPRTQRGWEQFALEVLTH<LGQNLTSLVFLLG<SSDVWKRGRARDRKWH<QAPQSAQPSPLSTW*GSF

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	0.12 RPM	4.20 RPM
SRP017611_kidney	0.00 RPM	3.56 RPM
SRP017611_liver	0.00 RPM	5.75 RPM
SRP040447_lung	0.00 RPM	5.62 RPM
SRP040447_skeletal_muscle	0.00 RPM	6.94 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1339 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1339 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 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016525	1 retrocopy	retro_amel_153,
Canis familiaris	ENSCAFG00000011144	1 retrocopy	retro_cfam_1567,
Callithrix jacchus	ENSCJAG00000010134	2 retrocopies	retro_cjac_1467, retro_cjac_520,
Cavia porcellus	ENSCPOG00000004634	3 retrocopies	retro_cpor_1339 , retro_cpor_6, retro_cpor_863,
Dasypus novemcinctus	ENSDNOG00000005335	2 retrocopies	retro_dnov_1001, retro_dnov_627,
Equus caballus	ENSECAG00000008080	1 retrocopy	retro_ecab_747,
Felis catus	ENSFCAG00000008349	1 retrocopy	retro_fcat_445,
Macropus eugenii	ENSMEUG00000015792	3 retrocopies	retro_meug_1594, retro_meug_1877, retro_meug_2077,
Myotis lucifugus	ENSMLUG00000010755	3 retrocopies	retro_mluc_1305, retro_mluc_2060, retro_mluc_989,
Macaca mulatta	ENSMMUG00000006957	2 retrocopies	retro_mmul_1564, retro_mmul_2115,
Mustela putorius furo	ENSMPUG00000003463	1 retrocopy	retro_mputfur_1592,
Nomascus leucogenys	ENSNLEG00000001442	3 retrocopies	retro_nleu_1325, retro_nleu_1950, retro_nleu_2802,
Oryctolagus cuniculus	ENSOCUG00000003145	1 retrocopy	retro_ocun_1767,
Otolemur garnettii	ENSOGAG00000007441	2 retrocopies	retro_ogar_1593, retro_ogar_2716,
Pongo abelii	ENSPPYG00000004929	3 retrocopies	retro_pabe_1354, retro_pabe_1355, retro_pabe_2792,
Pan troglodytes	ENSPTRG00000005419	1 retrocopy	retro_ptro_1108,
Sus scrofa	ENSSSCG00000009938	1 retrocopy	retro_sscr_1202,
Ictidomys tridecemlineatus	ENSSTOG00000006894	1 retrocopy	retro_itri_661,