RetrogeneDB ID: retro_cpor_487

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_169:915610..916148(-)
• Located in intron of: ENSCPOG00000010405

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLEKHA3
• Ensembl ID: ENSCPOG00000003906
• Aliases: None
• Description: None

Sequence

>retro_cpor_487
GAGGTGGCCATCTGTGAGACTGAAGTTCACCCAGCAGACCACACAAGAACGGAATTAATCATTCCAGGAGAGCAGCACTT
CTACATGAAGGCAGTAATATGGCTGAAAGACAGCAGGGCTGTTTGCCCTGGGCAGCACCAAAGCGTGTTTGACTGATCCT
AGGATTAAAAAAGGAGAAGAAATAAGTGAAACCAGTGAATCTCTGAAAGCCAAATGGCTGTACTTCGCCCGTACAGTGAC
CTGCTAATGCAGCAGGTTCATAGAACCCAAAAATTTGCCCACCGTGGTGAGAAACATTCATTGCCCAGGATAGAGGACAT
GAACAGAGCCCCTCCCTACTTAATGCCACGCGTGATACATTCAAGGCGACACTCAAGAGTTGTGCAAAGACAGCCCGTGC
TGAGTTTAAGCCTCAGATGTTTCAGTGGCCCCATCTGGTTTCTTCTGTGTCACCTCCTCCTGTTCAAGGACGACGCATTC
TGTCAGTCACCCTGGGTCTTGAGGTTCTGCGAGGAGCAGCTGCTCTATAAAAAAACCC

Alignment

ORF - retro_cpor_487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.96 %
• Parental protein coverage: 61.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KMAVCEIKVHSADNTRMELIIPGEQHFYMKAV-NAAERQR-WLVALGSSKACLTDTRTKKEKEINETSES
          ..A.CE..VH.AD.TR.ELIIPGEQHFYMKAV.N.AERQ...L.ALGS.KACLTD.R.KK..EI.ETSES
Retrocopy EVAICETEVHPADHTRTELIIPGEQHFYMKAV<NMAERQQ<GLFALGSTKACLTDPRIKKGEEISETSES

Parental  LKTK-MSELRLYCDLLMQQVHTIQEFVHHDENHSSPSVENMNEA-SSLLSATCNTFITTLEECVKIANAK
          LK.K.M..LR.Y.DLLMQQVH..Q.F.H..E.HS.P..E.MN.A..SLL.AT..TF..TL..C.K.A.A.
Retrocopy LKAK<MAVLRPYSDLLMQQVHRTQKFAHRGEKHSLPRIEDMNRA<PSLLNATRDTFKATLKSCAKTARAE

Parental  FKPEMFQLPHPDPLVSPVSPSPVQMMK-RSVSHPGSCSSERNSYSVKEP
          FKP.MFQ.PH...LVS.VSP.PVQ.....SVSHPGS..S.R.S.S.K.P
Retrocopy FKPQMFQWPH---LVSSVSPPPVQGRR<HSVSHPGS*GSARSSCSIKKP

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	0.17 RPM	17.83 RPM
SRP017611_kidney	0.00 RPM	24.92 RPM
SRP017611_liver	0.30 RPM	21.55 RPM
SRP040447_lung	1.21 RPM	21.44 RPM
SRP040447_skeletal_muscle	0.08 RPM	4.72 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_487 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_487 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 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013997	5 retrocopies	retro_chof_1366, retro_chof_1559, retro_chof_300, retro_chof_736, retro_chof_985,
Cavia porcellus	ENSCPOG00000003906	1 retrocopy	retro_cpor_487 ,
Dasypus novemcinctus	ENSDNOG00000002717	1 retrocopy	retro_dnov_107,
Erinaceus europaeus	ENSEEUG00000004169	1 retrocopy	retro_eeur_416,
Homo sapiens	ENSG00000116095	1 retrocopy	retro_hsap_2060,
Macropus eugenii	ENSMEUG00000015317	2 retrocopies	retro_meug_1530, retro_meug_341,
Microcebus murinus	ENSMICG00000009898	1 retrocopy	retro_mmur_617,
Myotis lucifugus	ENSMLUG00000005823	2 retrocopies	retro_mluc_1031, retro_mluc_689,
Oryctolagus cuniculus	ENSOCUG00000005495	1 retrocopy	retro_ocun_1273,
Otolemur garnettii	ENSOGAG00000002724	1 retrocopy	retro_ogar_1845,
Tupaia belangeri	ENSTBEG00000007550	3 retrocopies	retro_tbel_4186, retro_tbel_4555, retro_tbel_4723,
Tarsius syrichta	ENSTSYG00000005341	1 retrocopy	retro_tsyr_869,
Tursiops truncatus	ENSTTRG00000009729	2 retrocopies	retro_ttru_1296, retro_ttru_1497,
Vicugna pacos	ENSVPAG00000003490	3 retrocopies	retro_vpac_487, retro_vpac_578, retro_vpac_619,