RetrogeneDB ID: retro_cpor_813

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_29:10865144..10865948(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT3
• Ensembl ID: ENSCPOG00000009131
• Aliases: None
• Description: None

Sequence

>retro_cpor_813
CCCATGCCTGTGCTCAGCCAGAATGCAAATGTGAATCTGGAAGAAAAGTTAGATCTGGAAACAGCAATGCTGCTGAGACC
ACTGCAGAAATCATTCAAGTATGTTTGGGACCCAAGTACATGAGGAAGATGCTTTGGGACCCAAAGGAAAGCATTGCAAT
GACCAAGAATGGTAATGCTACTCTTCAAGAGATTCAAATCAAGCATCCAGGGTCCAAGTCCATGATTGAAATTAGCTGGA
CATGGGATAATGTATTTGGAGATGGGATCCTATCAGTAATTATTCATATGGGAAAGATGTCATCTATGGTTGAACATTTA
GTAAGTCATCAGATGCACTGAACAGTGGTGATTAGTGCTTATTGCAAGGCACTGGATGATATGATCAGCCCTGTAGATAA
AATCAGTAGGCACATCCACGCCAATAACTATGATATGGTGCTACACACTATCAATAGCTCAATTACTATCAAAGCAATCA
GTCATTGTCCTTTCTAACTTGCAACATTGTCCTGGATTCTGTCAAGACCATACCACTTAAGAATTGTAGGAAGGAGACTG
ACATCAAAAAATACATATGAATAGAAAAGATAACTAGGACACCATTGAAGGCTCATGTGTTTTGCATGGAATCATGATTA
ACAAAGATGTGATACATTCACAACAGTAGCACTATTTAAAGGACCCTCCCAGTGTGGTACTGAATTCTCTGGCATACAAG
AAAGAAGACCAGACTGTCACTGAGATTGCACAAGAGGAAGACTGCACCCAAATCCTTCAAGTGGAAAAATATAACCAGCA
ACTG

Alignment

ORF - retro_cpor_813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.42 %
• Parental protein coverage: 50.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PVLVLSQNT-KRESGRKVQSGNISAAKTIADIIRTCLGPKSMMKMLLDPMGGIVMTNDGNAILREIQVQH
          P..VLSQN..K.ESGRKV.SGN..AA.T.A.II..CLGPK.M.KML.DP...I.MT..GNA.L.EIQ..H
Retrocopy PMPVLSQNA<KCESGRKVRSGNSNAAETTAEIIQVCLGPKYMRKMLWDPKESIAMTKNGNATLQEIQIKH

Parental  PAAKSMIEISRTQDEEVGDGTTSVIILAGEMLSVAEHFLEQQMHPTVVISAYRKALDDMISTLKKISTPV
          P..KSMIEIS.T.D...GDG..SVII..G.M.S..EH....QMH.TVVISAY.KALDDMIS...KIS...
Retrocopy PGSKSMIEISWTWDNVFGDGILSVIIHMGKMSSMVEHLVSHQMH*TVVISAYCKALDDMISPVDKISRHI

Parental  DINNRDTMLNIINSSITTKAISR-WSSLACNIALDAVKTVQFEENGRKEIDIKKYARVEKIPG-GIIEDS
          ..NN.D..L..INSSIT.KAIS...S.L.CNI.LD.VKT.....N.RKE.DIKKY...EKI.....IE.S
Retrocopy HANNYDMVLHTINSSITIKAISH<LSFLTCNIVLDSVKTIPL-KNCRKETDIKKYI*IEKITR<DTIEGS

Parental  CVLRGVMINKDVTHSRMRRYIKNPRIVLLDSSLEYKKGESQTDIEITREEDFARILQMEEEYIQQL
          CVL.G.MINKDV.HS....Y.K.P..V.L..SL.YKK.E.QT..EI..EED...ILQ..E.Y.QQL
Retrocopy CVLHGIMINKDVIHSQQ*HYLKDPPSVVL-NSLAYKK-EDQTVTEIAQEEDCTQILQV-EKYNQQL

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	0.06 RPM	93.81 RPM
SRP017611_kidney	0.00 RPM	148.34 RPM
SRP017611_liver	0.00 RPM	121.27 RPM
SRP040447_lung	0.00 RPM	161.01 RPM
SRP040447_skeletal_muscle	0.00 RPM	127.95 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_813 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_813 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005776	1 retrocopy	retro_cjac_1243,
Cavia porcellus	ENSCPOG00000009131	1 retrocopy	retro_cpor_813 ,
Mus musculus	ENSMUSG00000001416	2 retrocopies	retro_mmus_2352, retro_mmus_824,
Otolemur garnettii	ENSOGAG00000008967	1 retrocopy	retro_ogar_2017,
Rattus norvegicus	ENSRNOG00000019090	2 retrocopies	retro_rnor_1450, retro_rnor_2823,
Ictidomys tridecemlineatus	ENSSTOG00000001798	1 retrocopy	retro_itri_788,