RetrogeneDB ID: retro_cpor_623

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_20:786889..787426(-)
• Located in intron of: ENSCPOG00000007411

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX6
• Ensembl ID: ENSCPOG00000011091
• Aliases: None
• Description: None

Sequence

>retro_cpor_623
AACTTTGAGGCTAACACTAAGTTGGTTGCATCCATTCCCATGACTTTCTGGGGGACCCATGGGACACCCTCTTCTCCTGC
CCATGGGAGTTGATACCTGTGTGCACCACAGAGCTTGGCAGGACAGCGAAGCTGGCGCTACAATCTGCCAAGAGGAATGC
TAAGTCAGTTGCCATTTCAACAGACAGGGGTGAGGCCCATCCTTCCTGCTGCAAGGACACAGTGCAAACAGGTGATGAGG
AGTCCACAGAAGACTTACCACCCCATCACCGTGACGAGAATCAGGACCTTGCCATCCTTGTGGGCATGCCGGACCCAGCA
GAAAGGGACAAAAAGGGCATGCTGTGAGAGCTCATGTGGTAATAACTGTTTTTGCTACCAACAAGAAACTGAAGCTATCC
ATCTGCTATCCAGCTATCACTGGCAGAAATTTCAGTGAGATTCTCAGAGTAGTTATCTCTCTCCAGCTCACAGTGGAAAA
AAGGTTGCTGCCCCAGCTGATGAGAAGGATGGGGACAGTGTGATGGTCCTTCCCACC

Alignment

ORF - retro_cpor_623 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.04 %
• Parental protein coverage: 79.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NFEANTT-IGRIRFHDFLGDSWGILFSHPRDFTPVCTTELGRAAKLTPEFAKRNVKLIALSIDSVEDHLA
          NFEANT...G.I..HDFLGD.W..LFS.P....PVCTTELGR.AKL....AKRN.K..A.S.D..E.H..
Retrocopy NFEANTK<VGCIHSHDFLGDPWDTLFSCPWELIPVCTTELGRTAKLALQSAKRNAKSVAISTDRGEAHPS

Parental  WSKDINAYNGDEPTEKLPFPIIDDKNRDLAILLGMLDPAEKDEKGM-PVTARVVF-IFGPDKKLKLSILY
          ..KD.......E.TE.LP.P...D.N.DLAIL.GM.DPAE.D.KGM..V.A.VV...F...KKLKLSI.Y
Retrocopy CCKDTVQTGDEESTEDLP-PHHRDENQDLAILVGMPDPAERDKKGM<AVRAHVVITVFATNKKLKLSICY

Parental  PATTGRNFDEILRVVISLQLTAEKR-VATPVDWKDGDSVMVLPT
          PA.TGRNF.EILRVVISLQLT.EKR.VA.P.D.KDGDSVMVLPT
Retrocopy PAITGRNFSEILRVVISLQLTVEKR<VAAPADEKDGDSVMVLPT

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	40.32 RPM
SRP017611_kidney	0.10 RPM	347.25 RPM
SRP017611_liver	0.00 RPM	241.84 RPM
SRP040447_lung	0.03 RPM	179.45 RPM
SRP040447_skeletal_muscle	0.00 RPM	133.05 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_623 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_623 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 21 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015560	1 retrocopy	retro_amel_493,
Bos taurus	ENSBTAG00000004855	2 retrocopies	retro_btau_1325, retro_btau_1477,
Canis familiaris	ENSCAFG00000014579	1 retrocopy	retro_cfam_492,
Choloepus hoffmanni	ENSCHOG00000011367	6 retrocopies	retro_chof_1143, retro_chof_1361, retro_chof_1364, retro_chof_225, retro_chof_2483, retro_chof_2598,
Callithrix jacchus	ENSCJAG00000009355	6 retrocopies	retro_cjac_1903, retro_cjac_2188, retro_cjac_3008, retro_cjac_3239, retro_cjac_3830, retro_cjac_4000,
Cavia porcellus	ENSCPOG00000011091	1 retrocopy	retro_cpor_623 ,
Equus caballus	ENSECAG00000022468	1 retrocopy	retro_ecab_215,
Erinaceus europaeus	ENSEEUG00000004040	1 retrocopy	retro_eeur_475,
Homo sapiens	ENSG00000117592	2 retrocopies	retro_hsap_1046, retro_hsap_3017,
Gorilla gorilla	ENSGGOG00000026357	1 retrocopy	retro_ggor_2086,
Macaca mulatta	ENSMMUG00000008776	1 retrocopy	retro_mmul_1928,
Monodelphis domestica	ENSMODG00000004032	2 retrocopies	retro_mdom_462, retro_mdom_661,
Mustela putorius furo	ENSMPUG00000004648	1 retrocopy	retro_mputfur_1328,
Mus musculus	ENSMUSG00000026701	2 retrocopies	retro_mmus_181, retro_mmus_2334,
Nomascus leucogenys	ENSNLEG00000015278	2 retrocopies	retro_nleu_2244, retro_nleu_917,
Pan troglodytes	ENSPTRG00000042455	1 retrocopy	retro_ptro_70,
Pteropus vampyrus	ENSPVAG00000002596	2 retrocopies	retro_pvam_1389, retro_pvam_805,
Rattus norvegicus	ENSRNOG00000002896	3 retrocopies	retro_rnor_2084, retro_rnor_754, retro_rnor_806,
Sarcophilus harrisii	ENSSHAG00000003248	1 retrocopy	retro_shar_478,
Tarsius syrichta	ENSTSYG00000010073	2 retrocopies	retro_tsyr_1395, retro_tsyr_193,
Tursiops truncatus	ENSTTRG00000008478	1 retrocopy	retro_ttru_1274,