RetrogeneDB ID: retro_cpor_1365

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_72:3530353..3530707(+)
• Located in intron of: ENSCPOG00000013524

Retrocopy information

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

Parental gene information

• Parental gene symbol: NACA2
• Ensembl ID: ENSCPOG00000012654
• Aliases: None
• Description: None

Sequence

>retro_cpor_1365
GAAGAACAGTCAGTAAAGCAGAACAGTCCAAGCAACAAGCAGGCACAGAAGGTTGGTTCCAAGCTAGATCACTGGAAAGT
TACAGCGATTACTAGAATCACTATCCAGAAGCCTAAGGCTGTCCCAAAACCAGATGTCTACAAGAGTCCAGCTTCAGATG
CCTACATAATTTTAAAGGAAGCCAAGACTGAGGGTTTGTCTCAGCAAGCACAGTTAGCAGCTACTGCAAAATCCAGAGTT
CAAGGTGAAGCTGTCTCAGACTTCAAGAAAATACAGATTCCAACTGTACAAGAATGAAAAAGAAGTTGATAAAATAGGTG
TGAGGTTAAGGACATAGAATTGTTTACAAGCAAA

Alignment

ORF - retro_cpor_1365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.34 %
• Parental protein coverage: 59.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EPVSKAKQSRSEKKARKAMSKLGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDL
          E..S....S.S.K.A.K..SKL....VT..TR.TI.K.K.......KPDVYKSPASD.YI...EAK.E.L
Retrocopy EEQSVKQNSPSNKQAQKVGSKLDHWKVTAITRITIQKPK----AVPKPDVYKSPASDAYIILKEAKTEGL

Parental  SQQAQLAAAEKFKVQGEAVSNIQENTQTPTVQE-ESEEEEVDETGVEVK-DIELVMSQ
          SQQAQLAA..K..VQGEAVS......Q.PTVQE.E.E.......GV....DIEL..S.
Retrocopy SQQAQLAATAKSRVQGEAVSDFKK-IQIPTVQE>EKEVDKI---GVRLR<DIELFTSK

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	0.29 RPM	117.97 RPM
SRP017611_kidney	0.10 RPM	233.35 RPM
SRP017611_liver	0.04 RPM	158.35 RPM
SRP040447_lung	0.03 RPM	179.93 RPM
SRP040447_skeletal_muscle	0.04 RPM	97.27 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1365 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1365 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 8 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004175	3 retrocopies	retro_amel_1725, retro_amel_1821, retro_amel_643,
Canis familiaris	ENSCAFG00000000141	8 retrocopies	retro_cfam_1502, retro_cfam_1561, retro_cfam_1884, retro_cfam_1913, retro_cfam_2096, retro_cfam_2169, retro_cfam_710, retro_cfam_974,
Callithrix jacchus	ENSCJAG00000010701	8 retrocopies	retro_cjac_1063, retro_cjac_1452, retro_cjac_1875, retro_cjac_2202, retro_cjac_2453, retro_cjac_2696, retro_cjac_2975, retro_cjac_3232,
Cavia porcellus	ENSCPOG00000012654	3 retrocopies	retro_cpor_1025, retro_cpor_1365 , retro_cpor_617,
Loxodonta africana	ENSLAFG00000004598	6 retrocopies	retro_lafr_1107, retro_lafr_113, retro_lafr_1251, retro_lafr_166, retro_lafr_491, retro_lafr_958,
Myotis lucifugus	ENSMLUG00000001169	16 retrocopies	retro_mluc_1147, retro_mluc_1653, retro_mluc_1668, retro_mluc_1756, retro_mluc_1767, retro_mluc_1851, retro_mluc_1881, retro_mluc_1941, retro_mluc_2587, retro_mluc_2600, retro_mluc_414, retro_mluc_492, retro_mluc_526, retro_mluc_641, retro_mluc_725, retro_mluc_861,
Pteropus vampyrus	ENSPVAG00000008015	8 retrocopies	retro_pvam_1007, retro_pvam_1097, retro_pvam_1154, retro_pvam_1173, retro_pvam_1382, retro_pvam_1384, retro_pvam_290, retro_pvam_580,
Vicugna pacos	ENSVPAG00000004028	2 retrocopies	retro_vpac_485, retro_vpac_611,