RetrogeneDB ID: retro_cpor_1401

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:36136614..36137440(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DRG1
• Ensembl ID: ENSCPOG00000010791
• Aliases: None
• Description: None

Sequence

>retro_cpor_1401
ATGAGCAGCACTTTAATAAAGATTGTGGAGATCAAAGCTGAGATGGCTTGGACTCAGAGGAACAAGGCCACAGCACATCA
CTTAGAGCCGCTTAAGGCTCACCCTGCTAAGCTTCATAGAGAACTCATTACACCAAAAGGTAGCGGTGGGCCAGAAGAAG
GTTTTGGTATGTCCAGGGCAGGTGATGCTTGAATTGGTTTTGTGGGCTTTCCGTCTGTGGGGAAGTCAACGCTGCTGAGT
AACCTGGCAGGAGTATGTTCTGAGACAGCAGCCTGTGATTTCACTACTCTGATGATTATGCCTGCTGTCATCAGGTGCAG
AGGTGCCAAGATCCAGCTCCGAGGTCTCCCAGGTATCACTGAAGTTGCCAAGGATTGGAAAAGTAGAGGTCGTCAAGTCA
TTGCAGTGACCCATACTTGTAATCTGATCCTAACCATTCTGAATGTCTTGAAACCCTTGGGACCCAAGAAGATAATTGAA
AACAAGCTGAAAGACTTCGGCATTTTCTTGAATAGCAAACCTCTTAACATTGGCTTTAGGAAGAAAGACAGGGAGGCATT
AATCTCACAGCTACTTGCCCTCTGAGTAAGCTGCATGCTGAAACTGTCAAGAGTATTCTGGTTGAGTACAAAATTCAAAA
TGCTGAAATAACTTTGCATACTGATGCCTCAGCTGATGACCTCATTGACGTAGTGGAAGGAAACAGTGTATATCCCTGTA
CTGTGTATTAAACACGATTGACTAGATTTCCAATGAGAAATTGGACATCATTGATAAGGTGCCACACTGTGTACCTATCT
CTGCCCATCACTACTGGAATTTTGAC

Alignment

ORF - retro_cpor_1401 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.73 %
• Parental protein coverage: 76.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSTLAKIAEIEAEMARTQKNKATAHHLGLLKARLAKLRRELITPKGGGGGGPGEGFDVAKTGDARIGFV
          MSSTL.KI.EI.AEMA.TQ.NKATAHHL..LKA..AKL.RELITPKG.GG..P.EGF.....GDA.IGFV
Retrocopy MSSTLIKIVEIKAEMAWTQRNKATAHHLEPLKAHPAKLHRELITPKGSGG--PEEGFGMSRAGDA*IGFV

Parental  GFPSVGKSTLLSNLAGVYSEVAAYEFTTLTTVPGVIRYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVAR
          GFPSVGKSTLLSNLAGV.SE.AA..FTTL...P.VIR..GAKIQL..LPGI.E.AKD.K.RGRQVIAV..
Retrocopy GFPSVGKSTLLSNLAGVCSETAACDFTTLMIMPAVIRCRGAKIQLRGLPGITEVAKDWKSRGRQVIAVTH

Parental  TCNLILIVLDVLKPLGHKKIIENELEGFGIRLNSKPPNIGFKKKDK-GGINLTATCPQSELDAETVKSIL
          TCNLIL..L.VLKPLG.KKIIEN.L..FGI.LNSKP.NIGF.KKD..GGINLTATCP.S.L.AETVKSIL
Retrocopy TCNLILTILNVLKPLGPKKIIENKLKDFGIFLNSKPLNIGFRKKDR<GGINLTATCPLSKLHAETVKSIL

Parental  AEYKIHNADVTLRSDATADDLIDVVEGNRVYIPCIY-VLNKIDQISIEELDIIYKVPHCVPISAHHRWNF
          .EYKI.NA..TL..DA.ADDLIDVVEGN.VY.PC...VLN.ID.IS.E.LDII.KVPHCVPISAHH.WNF
Retrocopy VEYKIQNAEITLHTDASADDLIDVVEGNSVY-PCTV<VLNTID*ISNEKLDIIDKVPHCVPISAHHYWNF

Parental  D
          D
Retrocopy D

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	24.44 RPM
SRP017611_kidney	0.00 RPM	30.15 RPM
SRP017611_liver	0.00 RPM	26.55 RPM
SRP040447_lung	0.00 RPM	24.19 RPM
SRP040447_skeletal_muscle	0.00 RPM	23.44 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1401 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1401 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 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007040	1 retrocopy	retro_amel_1448,
Canis familiaris	ENSCAFG00000032601	6 retrocopies	retro_cfam_1535, retro_cfam_1807, retro_cfam_382, retro_cfam_415, retro_cfam_453, retro_cfam_607,
Ciona intestinalis	ENSCING00000003305	1 retrocopy	retro_cint_1,
Callithrix jacchus	ENSCJAG00000011009	4 retrocopies	retro_cjac_1104, retro_cjac_2246, retro_cjac_2606, retro_cjac_855,
Cavia porcellus	ENSCPOG00000010791	1 retrocopy	retro_cpor_1401 ,
Ciona savignyi	ENSCSAVG00000006503	1 retrocopy	retro_csav_10,
Dasypus novemcinctus	ENSDNOG00000001312	1 retrocopy	retro_dnov_531,
Homo sapiens	ENSG00000185721	1 retrocopy	retro_hsap_2231,
Gorilla gorilla	ENSGGOG00000011185	1 retrocopy	retro_ggor_1665,
Myotis lucifugus	ENSMLUG00000007033	1 retrocopy	retro_mluc_1447,
Macaca mulatta	ENSMMUG00000019099	1 retrocopy	retro_mmul_999,
Mustela putorius furo	ENSMPUG00000012810	1 retrocopy	retro_mputfur_339,
Mus musculus	ENSMUSG00000020457	1 retrocopy	retro_mmus_2366,
Nomascus leucogenys	ENSNLEG00000027001	1 retrocopy	retro_nleu_2627,
Pan troglodytes	ENSPTRG00000014272	1 retrocopy	retro_ptro_1578,
Ictidomys tridecemlineatus	ENSSTOG00000014187	1 retrocopy	retro_itri_460,
Tarsius syrichta	ENSTSYG00000010160	3 retrocopies	retro_tsyr_1374, retro_tsyr_1918, retro_tsyr_405,