RetrogeneDB ID: retro_cpor_1374

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_76:622146..622670(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C15ORF29
• Ensembl ID: ENSCPOG00000011153
• Aliases: None
• Description: None

Sequence

>retro_cpor_1374
AGAACAGTTGGACAAGCTGTGAAAATCCCAGATATACTACATAAGGAGATGTATTCAGAAAGAAAGTTCATCTTCCCTTT
GCAAGTCCTTGTCACAGAAAAAATCAGTCCCTAGAAGGGGGGCTGTGACATGGCAAATAAAGACGATGGACTGGCTTGCA
TAGGCCACCTGCCTGAAGAATTACTCCCTGATAGTCAGACAAACGTGGTTAACTCCAGTCACTCCAGTTCTTCACGGACA
GTAAGCCCATCATCCAAATACCCTGGATTTTTCTCTGAGGTTTCTCGTGATCATGAAAGCACAGCTCAAGTTTGGTTCAG
CAGGAATTTGGGATTGAACATAGCTTTAACTTTCAGGAGAAAGAGAAGTGTACGTGAACTTGTAGATTGTTTGGTGAGAA
TAGAAGACCTTGGAGCTGTGTTGGATTCCTTCCTGCACTCACCAATAGTTTACAGGAAGAAAAACAGTATATCTCACTTG
GCTGATGTGTGGATGTATTTCCTCTAGTAAAGTCATTACTAGAA

Alignment

ORF - retro_cpor_1374 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.78 %
• Parental protein coverage: 57.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RTVGQAVKSPGILHKVINR-RKKVHHPFPNPCYRKKES-PR-SGGCDMANKENELACAGHLPEKLHHDSR
          RTVGQAVK.P.ILHK.....RKKVH.PF..PC.RK..S.PR..GGCDMANK...LAC.GHLPE.L..DS.
Retrocopy RTVGQAVKIPDILHKEMYS<RKKVHLPFASPCHRKNQS<PR<KGGCDMANKDDGLACIGHLPEELLPDSQ

Parental  TYVVNSSDSSSSQTESPSSKYSGFFSEVSQDHETMAQVLFSRNLRLNVALTFWRKRSISELVAYLVRIED
          T.VVNSS.SSSS.T.SPSSKY.GFFSEVS.DHE..AQV.FSRNL.LN.ALTF.RKRS..ELV..LVRIED
Retrocopy TNVVNSSHSSSSRTVSPSSKYPGFFSEVSRDHESTAQVWFSRNLGLNIALTFRRKRSVRELVDCLVRIED

Parental  LGVVVDC-LPVLTNSLQEEKQYISLGCCVDLLPLVKSLLK
          LG.V.D..LP.LTNSLQEEKQYISLG.CVD..PLVKSLL.
Retrocopy LGAVLDS<LPALTNSLQEEKQYISLG*CVDVFPLVKSLLE

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	4.72 RPM
SRP017611_kidney	0.00 RPM	7.22 RPM
SRP017611_liver	0.00 RPM	2.05 RPM
SRP040447_lung	0.00 RPM	5.93 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.95 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1374 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1374 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 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006413	2 retrocopies	retro_btau_1198, retro_btau_1776,
Callithrix jacchus	ENSCJAG00000021110	3 retrocopies	retro_cjac_1971, retro_cjac_265, retro_cjac_2971,
Cavia porcellus	ENSCPOG00000011153	2 retrocopies	retro_cpor_1374 , retro_cpor_1410,
Dasypus novemcinctus	ENSDNOG00000016279	5 retrocopies	retro_dnov_1586, retro_dnov_2201, retro_dnov_2253, retro_dnov_248, retro_dnov_957,
Dipodomys ordii	ENSDORG00000013172	2 retrocopies	retro_dord_378, retro_dord_730,
Equus caballus	ENSECAG00000023450	1 retrocopy	retro_ecab_841,
Echinops telfairi	ENSETEG00000001640	7 retrocopies	retro_etel_1169, retro_etel_1341, retro_etel_2032, retro_etel_2062, retro_etel_319, retro_etel_518, retro_etel_635,
Homo sapiens	ENSG00000134152	3 retrocopies	retro_hsap_3171, retro_hsap_3677, retro_hsap_425,
Gorilla gorilla	ENSGGOG00000014230	3 retrocopies	retro_ggor_1347, retro_ggor_2486, retro_ggor_415,
Macropus eugenii	ENSMEUG00000015610	4 retrocopies	retro_meug_1035, retro_meug_1899, retro_meug_1900, retro_meug_646,
Myotis lucifugus	ENSMLUG00000001532	2 retrocopies	retro_mluc_214, retro_mluc_633,
Macaca mulatta	ENSMMUG00000000013	1 retrocopy	retro_mmul_2005,
Mustela putorius furo	ENSMPUG00000008019	1 retrocopy	retro_mputfur_1258,
Nomascus leucogenys	ENSNLEG00000010772	2 retrocopies	retro_nleu_1020, retro_nleu_2679,
Oryctolagus cuniculus	ENSOCUG00000017654	5 retrocopies	retro_ocun_1065, retro_ocun_343, retro_ocun_614, retro_ocun_877, retro_ocun_975,
Otolemur garnettii	ENSOGAG00000015633	3 retrocopies	retro_ogar_1643, retro_ogar_2219, retro_ogar_3301,
Ochotona princeps	ENSOPRG00000010379	1 retrocopy	retro_opri_446,
Pongo abelii	ENSPPYG00000006309	2 retrocopies	retro_pabe_2634, retro_pabe_646,
Pan troglodytes	ENSPTRG00000006877	3 retrocopies	retro_ptro_2271, retro_ptro_2491, retro_ptro_323,
Sorex araneus	ENSSARG00000007891	1 retrocopy	retro_sara_345,
Ictidomys tridecemlineatus	ENSSTOG00000003813	1 retrocopy	retro_itri_1292,
Tupaia belangeri	ENSTBEG00000001614	7 retrocopies	retro_tbel_1267, retro_tbel_127, retro_tbel_1362, retro_tbel_2139, retro_tbel_3276, retro_tbel_4552, retro_tbel_984,
Tarsius syrichta	ENSTSYG00000011059	1 retrocopy	retro_tsyr_2135,
Vicugna pacos	ENSVPAG00000007170	1 retrocopy	retro_vpac_632,