RetrogeneDB ID: retro_cpor_464

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:5803486..5804187(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000006626
• Aliases: None
• Description: None

Sequence

>retro_cpor_464
AAGAGTTCTTCTCCAGCACCTGCAGACATAGCTCAGACAGTGCGAGAAGATTTTGAGGACGTTTTGTTGGGTATCTATGA
CCACTAAGAACCTCCATCCTAGCAGAGCTGTTTCTGTTACTGTGACACCACCTCATGTTATGAAAGTACCAGCATCACAG
CCCCGGCAGAGTCTAAACCTGAATCTCAGATTCCACCACAGAGGCCTCACAGGGATCAACAAGTGTGAGAACAATGAATA
AATATTCCTCCCCAGAGGGGACCCAGACCAGTTCATGAGCCTGGGGAGCAAGGTGAGGTTGAACCCCGGAGAAGTTGAGA
CATCCTGACAGCCACCAGCTCTTCATCGGTGAGGTAGACAAATTAGAACTTAAAGATTTCTTTCAAAATCATGGGAATGT
GAGGGAGCTATGCATAAATGGTGGCAGGAAGTTACCCAATTTTGGTTTTGTGGCATTTAATGATTCTAACAATGTGCAGA
AGGTCCTTAGCAACAGGCTCATCGTGTTCAGAGGTGAAGCCCAACTGAATGTGGAAGAGAAGAAGACCCGCGCTGCCAGG
GAAGGGGACCATTAAGACAACCACCTGCAGGGACCTGCAGACCCTCGAGGTAGGCTGGGCAGTGGCATGCAAGGCCCTCC
TTGTGGAGGAAGGGTGCAGGAGCCCAGCTTCAGGGTAGGTGGGGGGGGTGCTCCCTAGCAG

Alignment

ORF - retro_cpor_464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.37 %
• Parental protein coverage: 50.32 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KSSSPAPADPAQTAQED-LRTFSWASVTSKNLPPSGAVPVTGIPPHVVKAPASQPRP-ESKPESQLPPQR
          KSSSPAPAD.AQT..ED.LRTF.W.S.T.KNL.PS.AV.VT..PPHV.K.PASQPR..ESKPESQ.PPQR
Retrocopy KSSSPAPADIAQTVRED>LRTFCWVSMTTKNLHPSRAVSVTVTPPHVMKVPASQPRQ<ESKPESQIPPQR

Parental  PQRDQRVREQRINIPPQRGPRPIREAGEQGDAEPRRI-VRHPDSHQLFIGNLPHEVDKSELKDFFQSYGN
          P.RDQ.V.EQ.INIPPQRGPRP..E.GEQG..EPRR...RHPDSHQLFIG....EVDK.ELKDFFQ..GN
Retrocopy PHRDQQV*EQ*INIPPQRGPRPVHEPGEQGEVEPRRS<LRHPDSHQLFIG----EVDKLELKDFFQNHGN

Parental  VVDLRINSGGKLPNFGFVVFDDSEPVQKVLSNRPIMFRGEVRLNVEEKKTRAAREGDRRDNRLRGPGGPR
          V..L.IN.G.KLPNFGFV.F.DS..VQKVLSNR.I.FRGE..LNVEEKKTRAAREGD..DN.L.GP..PR
Retrocopy VRELCINGGRKLPNFGFVAFNDSNNVQKVLSNRLIVFRGEAQLNVEEKKTRAAREGDH*DNHLQGPADPR

Parental  GGLGGGLRGPPRGGMVQKPGFGVGRGLAPRQ
          G.LG.G..GPP.GG.VQ.P.F.VG...AP.Q
Retrocopy GRLGSGMQGPPCGGRVQEPSFRVGXXXAP*Q

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	18.92 RPM
SRP017611_kidney	0.00 RPM	38.11 RPM
SRP017611_liver	0.00 RPM	29.03 RPM
SRP040447_lung	0.00 RPM	37.18 RPM
SRP040447_skeletal_muscle	0.00 RPM	60.51 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_464 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_464 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 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006626	2 retrocopies	retro_cpor_1119, retro_cpor_464 ,
Dasypus novemcinctus	ENSDNOG00000018758	3 retrocopies	retro_dnov_1492, retro_dnov_1632, retro_dnov_526,
Echinops telfairi	ENSETEG00000017447	1 retrocopy	retro_etel_1488,
Homo sapiens	ENSG00000145907	1 retrocopy	retro_hsap_2322,
Microcebus murinus	ENSMICG00000012235	2 retrocopies	retro_mmur_1247, retro_mmur_1469,
Mustela putorius furo	ENSMPUG00000013661	1 retrocopy	retro_mputfur_625,
Mus musculus	ENSMUSG00000018583	3 retrocopies	retro_mmus_1389, retro_mmus_3229, retro_mmus_3688,
Nomascus leucogenys	ENSNLEG00000016470	1 retrocopy	retro_nleu_1814,
Oryctolagus cuniculus	ENSOCUG00000022143	1 retrocopy	retro_ocun_1352,
Otolemur garnettii	ENSOGAG00000001726	2 retrocopies	retro_ogar_3156, retro_ogar_3183,
Pongo abelii	ENSPPYG00000015968	1 retrocopy	retro_pabe_2104,
Pan troglodytes	ENSPTRG00000017438	1 retrocopy	retro_ptro_1696,
Pteropus vampyrus	ENSPVAG00000017250	2 retrocopies	retro_pvam_1188, retro_pvam_188,
Rattus norvegicus	ENSRNOG00000013186	1 retrocopy	retro_rnor_1282,
Tupaia belangeri	ENSTBEG00000004386	12 retrocopies	retro_tbel_2177, retro_tbel_2295, retro_tbel_2296, retro_tbel_2327, retro_tbel_2352, retro_tbel_2460, retro_tbel_2461, retro_tbel_3889, retro_tbel_3928, retro_tbel_4180, retro_tbel_4190, retro_tbel_4246,
Tarsius syrichta	ENSTSYG00000004570	1 retrocopy	retro_tsyr_1391,
Tursiops truncatus	ENSTTRG00000009072	1 retrocopy	retro_ttru_70,