RetrogeneDB ID: retro_cpor_1299

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_67:4337193..4337784(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000022330
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HPRT1
• Ensembl ID: ENSCPOG00000002512
• Aliases: None
• Description: None

Sequence

>retro_cpor_1299
ATTAGTGATGATGAACCAGGCTATGACCTAGATTTATTTTGTATTCCTAATCATCACACTAAGGTTTGGAAAAGCTGCTT
ATCCATCATGCACTAATTATGAACAGGACAAAAGGCTTGCTGGAGGTATGATGGAGATGGGATGTCATCCCATTGTAGCT
CTCTGTTCTCAAGGGGGGCTGTAAATTCTTTAATGACCTGCTAGATTACCAAAAACACTGAACAGAAATTTTGATGAATC
CATCCCTATGACTGTAGAGTTTATCAGACTGGAGAGCTACTGTAATGAATAGTAACAGGGGACATCAAAGTAATTGGTGG
AGATGATCTCTCAACTTTAACTGGAAACAATGTCTTGATCATTGAGGATGTGACTGACGCTGGTAGAACAACACAAACAT
GGCTTTCCTTGGTCAAGCGGTATCACCCAAAGACAGTCAAGGTCGCGACCTTGCTGGTGAAGGAGACCCCGCGAGTGTTA
GATATACACCAGACTCTTGGATTTACAATTCCAGACAAATTTGTTGTTGTGCATGCCCTTGACTGTAATAAATACTTCTG
GGATTTGAATCAGGTTTGCATCGTTAGTGAA

Alignment

ORF - retro_cpor_1299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.48 %
• Parental protein coverage: 92.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ISDDEPGYDLDLFCIPHHYIE-DLEKVFIPHGLIMDRTE-RLARDVMKEMGGHHIVA-LCVLKGGYKFFA
          ISDDEPGYDLDLFCIP.H.....LEK..I.H.LIM.RT..RLA...M.EM.G.H....L.VLKGG.KFF.
Retrocopy ISDDEPGYDLDLFCIPNHHTK<GLEKLLIHHALIMNRTK<RLAGGMM-EM-GCHPIV>LSVLKGGCKFFN

Parental  DLLDYIK-TLNRNCDKSIPMTVDFIRLKSYCND-QSTGDIKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQ
          DLLDY.K.TLNRN.D.SIPMTV.FIRL.SYCN....TGDIKVIGGDDLSTLTG.NVLI.ED..D.G.T.Q
Retrocopy DLLDYQK<TLNRNFDESIPMTVEFIRLESYCNE<IVTGDIKVIGGDDLSTLTGNNVLIIEDVTDAGRTTQ

Parental  TLLSLVKQYNPKMVKVASLLVKRTPRSVGYRPDFVGFEIPDKFVVGYALDYNEYFRDLNHVCVISE
          T.LSLVK.Y.PK.VKVA.LLVK.TPR.........GF.IPDKFVV..ALD.N.YF.DLN.VC..SE
Retrocopy TWLSLVKRYHPKTVKVATLLVKETPRVLDIHQT-LGFTIPDKFVVVHALDCNKYFWDLNQVCIVSE

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	27.21 RPM
SRP017611_kidney	0.00 RPM	23.14 RPM
SRP017611_liver	0.00 RPM	33.39 RPM
SRP040447_lung	0.00 RPM	17.05 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1299 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1299 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 24 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001339	1 retrocopy	retro_amel_129,
Bos taurus	ENSBTAG00000014685	3 retrocopies	retro_btau_162, retro_btau_179, retro_btau_721,
Canis familiaris	ENSCAFG00000018870	1 retrocopy	retro_cfam_2014,
Cavia porcellus	ENSCPOG00000002512	1 retrocopy	retro_cpor_1299 ,
Dasypus novemcinctus	ENSDNOG00000008495	5 retrocopies	retro_dnov_1480, retro_dnov_1908, retro_dnov_2057, retro_dnov_255, retro_dnov_763,
Equus caballus	ENSECAG00000017534	1 retrocopy	retro_ecab_734,
Felis catus	ENSFCAG00000004575	2 retrocopies	retro_fcat_104, retro_fcat_1608,
Homo sapiens	ENSG00000165704	1 retrocopy	retro_hsap_917,
Gorilla gorilla	ENSGGOG00000008050	1 retrocopy	retro_ggor_740,
Loxodonta africana	ENSLAFG00000009892	2 retrocopies	retro_lafr_1042, retro_lafr_475,
Microcebus murinus	ENSMICG00000006547	1 retrocopy	retro_mmur_1186,
Myotis lucifugus	ENSMLUG00000003591	1 retrocopy	retro_mluc_2107,
Macaca mulatta	ENSMMUG00000008303	1 retrocopy	retro_mmul_1118,
Mustela putorius furo	ENSMPUG00000012699	3 retrocopies	retro_mputfur_1317, retro_mputfur_1638, retro_mputfur_836,
Oryctolagus cuniculus	ENSOCUG00000003186	1 retrocopy	retro_ocun_1082,
Otolemur garnettii	ENSOGAG00000003881	3 retrocopies	retro_ogar_1886, retro_ogar_3298, retro_ogar_3463,
Pongo abelii	ENSPPYG00000020733	2 retrocopies	retro_pabe_3601, retro_pabe_791,
Pan troglodytes	ENSPTRG00000022287	2 retrocopies	retro_ptro_2042, retro_ptro_636,
Rattus norvegicus	ENSRNOG00000031367	2 retrocopies	retro_rnor_1208, retro_rnor_2491,
Sarcophilus harrisii	ENSSHAG00000007965	3 retrocopies	retro_shar_470, retro_shar_513, retro_shar_661,
Tupaia belangeri	ENSTBEG00000000859	5 retrocopies	retro_tbel_1607, retro_tbel_2234, retro_tbel_3627, retro_tbel_4320, retro_tbel_729,
Tarsius syrichta	ENSTSYG00000009579	1 retrocopy	retro_tsyr_2050,
Tursiops truncatus	ENSTTRG00000009954	9 retrocopies	retro_ttru_1007, retro_ttru_1272, retro_ttru_1523, retro_ttru_1598, retro_ttru_1620, retro_ttru_276, retro_ttru_641, retro_ttru_732, retro_ttru_829,
Vicugna pacos	ENSVPAG00000009133	1 retrocopy	retro_vpac_122,