RetrogeneDB ID: retro_cpor_1272

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_62:698143..700189(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000014231
• Aliases: None
• Description: None

Sequence

>retro_cpor_1272
ATGAATGCTCTCCAAACTATAGAGGGTCTCTTGACTTTAAGCCAGCAGGAAGAACTTGTGGATTTACCAAATAGCTATCC
CTTGAGTGCTAGTGAAGATGAGGGGGACAGTGATGGAGAGAGAAAACATCAAAAGCTTCTGAAAGCCATCAGTTGTCTCG
ATGAAAAGAATAGATGGAAATGGACTGAGCGGTCTGAGGCTAGTTTACAGGTCTCAGAATTCAACATGAGTTCTGAAGGA
TCAGGAGAAAAGCTGGTCCTTTCCGATCTTCTTGAGCCTGTTAGAACTTCATCTGCATTGGCTGCTGTGAAAAAGCAACT
GAATAAAGTTAAATCCAAAAAGACTATGGAATTACCCCTTAACAAAGAAGAAGTTAAACAGATCCACAGAGAAATAGCAT
TCAATAAGACATCACAAACCCTCTCCAAGTGGGACCCTATTGTTCTCAGGAACTGGCAAGCAGAGCAGCTGGTATTTCCC
TTGGAGAAGAAACAGCCAGCCTTTGTTCCCATTGAACTTGTCCTCAGTGGTTGGAAGGCAAGAACCCCCCTGGAGCAGGA
AATCTTTAACCTCCTTCATAAAAACAGGCAGCCAGTGACAGATCCTTTATTGGCTCCCATGGAAAAGGCTGCTCTCAAAG
CTATGAGCCTGGAAGAGGCCAAGATGCACCGAGCAGAGCTTCAGAGGGCCCGGGTTTTGCAGTCCTATTATGAAGCCAGA
GCAAAAAGAGAGAAGAAAATCAAAAGTAAAATGTTTCACAGAAACATGAAGAAAGAAAAGGCCAGGAAAGCCCTGAAAGA
CTTTGATCATCTGTGGAAGGTAAATCCTACTGCTGCATTGGATGAACTGCAAAAAATGGAAAAGGCCAGAGTGATGGAGC
GAATGAGCCTGAAGCACCAGAACAGTGGGAAATGGGCCAAGTCAAAGATGGTTATGGCCAAATATGACTTGGAAGCTCGC
CAAGCTGTGCAAGAACAATTGGCTAAGAACAAAGAACTGACACACAAACTCCAGATAATCTCAGAGAGTGAAGAAGAGAA
GAGGGGTACCAAAGAGGAAGAATCTCTTGTCCCTGATGTACTGAATGAGGTACAGATGTGTACAGATGGACCAAATCCTT
GGCTGCTTAGGGGTTGTAACAGTGATACAAAAGAGAGTGAAATCCAGCCAGACCCTGAACAACAGCCTGAGCCTGTCATC
CCAAAGTTTCCTAAAACTGAGGAAGATGAAAGACCAGCAGCAGAGGAAGAAATTTTGTTGAAAGGATTTGGGGAAAGTCG
ATCCCTTAGAGAAAGATTTCAGCTCAACCGTGACACTGAGTCAGTGGGCTGCCAAGAAACAAAAGATTCTAGCACCCAGG
ACATACTGGCCAAATTGAAGGCATTGAATCAGAAACTAGAAAACCGTCACTCCAGCAAGCAAACAGTGAGTCCAGCAGGG
ACTGTTCTCCAGGTGCAGAGAGAGGAATGTATCCCAGAAGAAGAGGAATCTCTGTTGTTGCAGAGGCCAGAGAGAGTGCA
AATTCTGGAAGAACTAGAAGGTCTGGGCAAAGAAGAATATTTTCAAAATAAGGAGCTTCCTAGACCTTTGTTAAAATGGA
AGCAAATGAAGAGAAACCCAAATAACCAGACTGATTCCCCTAAGGGGAAGAAAAAGGAGCAAATGATTGATCTCCAGAAT
CTTCTAACTACAGAACCTCCTTCCGTGAAATCTTTGGCCATTCCCACAGCAATAGAGGAGTTGGAAGATGAAGAGAAGCA
AAATCTAAAGCAGATGATAAAGGAAGCTTTTTCTGGAGATGATGTCATCAGCGATTTTTTGAAAGAGAAGAGAGAGGCTA
TGAAGGCAAGTAAGCCAAAGGCTGTGGACCTGATGCTGCCAGGCTGGGGCAAGTGGGGAGGTGCAGGTCTGAAGCCCAGT
GCCAAGAAAGGACGCCGGTTCCTCATTAAAGCCCCTGAAGGTCCTCCAAGAAAAGACAAGGATTTGCCAAATGTAATTGT
CAGTGAGAAGCGCAACATCCATGCAGCAGCTCATCAAGTACAGGTG

Alignment

ORF - retro_cpor_1272 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNAMRAAEGLLALSQQEELVDLQD-YPLSASEDEGDSDGERKHQKLLESIGSLDGKKRWKLAERSEASLK
          MNA....EGLL.LSQQEELVDL...YPLSASEDEGDSDGERKHQKLL..I..LD.K.RWK..ERSEASL.
Retrocopy MNALQTIEGLLTLSQQEELVDLPNSYPLSASEDEGDSDGERKHQKLLKAISCLDEKNRWKWTERSEASLQ

Parental  VSEFNVSSEGSGEKLLLSDLLEPAKTSSSLAAVKKQLSRVKSKKAVELPLNKQEVERINREVAFNKTSQT
          VSEFN.SSEGSGEKL.LSDLLEP..TSS.LAAVKKQL..VKSKK..ELPLNK.EV..I.RE.AFNKTSQT
Retrocopy VSEFNMSSEGSGEKLVLSDLLEPVRTSSALAAVKKQLNKVKSKKTMELPLNKEEVKQIHREIAFNKTSQT

Parental  LSKWDPIVLKNRQAEQLVFPLEKEPASFVPIEHVFGSWKARTPLEQEIFNILYKNKQPVTDPLLTPMEKA
          LSKWDPIVL.N.QAEQLVFPLEK....FVPIE.V...WKARTPLEQEIFN.L.KN.QPVTDPLL.PMEKA
Retrocopy LSKWDPIVLRNWQAEQLVFPLEKKQPAFVPIELVLSGWKARTPLEQEIFNLLHKNRQPVTDPLLAPMEKA

Parental  SLKAMSLEEAKMRRAELQRARALQSYYEAKARRMFKKRDSKYHKIVKKGKVKKALKEFEQLQKVNPAAAL
          .LKAMSLEEAKM.RAELQRAR.LQSYYEA.A.R..K......H...KK.K..KALK.F..L.KVNP.AAL
Retrocopy ALKAMSLEEAKMHRAELQRARVLQSYYEARAKREKKIKSKMFHRNMKKEKARKALKDFDHLWKVNPTAAL

Parental  EELEKIEKARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQLAKNKELTQKLQVVSESEEEEKGT
          .EL.K.EKAR.MERMSLKHQNSGKWAKSK..MAKYDLEARQA.QEQLAKNKELT.KLQ..SESEEE..GT
Retrocopy DELQKMEKARVMERMSLKHQNSGKWAKSKMVMAKYDLEARQAVQEQLAKNKELTHKLQIISESEEEKRGT

Parental  EEEELLVPDAVNEIQMCTDGPNPWMLRNCNSDAK-GEIQKDPEQPPEPMVQEVSESEEEEKPGGEEEVLL
          .EEE.LVPD..NE.QMCTDGPNPW.LR.CNSD.K..EIQ.DPEQ.PEP........EE.E.P..EEE.LL
Retrocopy KEEESLVPDVLNEVQMCTDGPNPWLLRGCNSDTKESEIQPDPEQQPEPVIPKFPKTEEDERPAAEEEILL

Parental  QEFEERRSLRKSSELSKNAEPVGSQKTKDSSSQEVLSELKALTQKLNQKNCQSKKQNVNLVKTVLQGQRE
          ..F.E.RSLR....L....E.VG.Q.TKDSS.Q..L..LKAL.QKL...N..S.KQ.V....TVLQ.QRE
Retrocopy KGFGESRSLRERFQLNRDTESVGCQETKDSSTQDILAKLKALNQKL--ENRHSSKQTVSPAGTVLQVQRE

Parental  ECAPEEEEPLLLQRPERVQTLEDLEDLDHEEYSQIRELSRPVLEGERTERTTDNQTDASKGKKKEQMIDL
          EC.PEEEE.LLLQRPERVQ.LE.LE.L..EEY.Q..EL.RP.L......R...NQTD..KGKKKEQMIDL
Retrocopy ECIPEEEESLLLQRPERVQILEELEGLGKEEYFQNKELPRPLLKWKQMKRNPNNQTDSPKGKKKEQMIDL

Parental  QNLLTTKSPSVKSLAVPTAIEELEDEEEKHQKQIIKEAFAGDDVIRDFLKEKKEAVKASKPKDVDLTLPG
          QNLLTT..PSVKSLA.PTAIEELEDEE....KQ.IKEAF.GDDVI.DFLKEK.EA.KASKPK.VDL.LPG
Retrocopy QNLLTTEPPSVKSLAIPTAIEELEDEEKQNLKQMIKEAFSGDDVISDFLKEKREAMKASKPKAVDLMLPG

Parental  WGEWGGIGLKPSAKKRRRFLIKAPEGPPRKDKNLPNVIISEKRNIQAAAHQVRL
          WG.WGG.GLKPSAKK.RRFLIKAPEGPPRKDK.LPNVI.SEKRNI.AAAHQV..
Retrocopy WGKWGGAGLKPSAKKGRRFLIKAPEGPPRKDKDLPNVIVSEKRNIHAAAHQVQV

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	7.71 RPM	14.32 RPM
SRP017611_kidney	4.82 RPM	15.91 RPM
SRP017611_liver	0.57 RPM	8.66 RPM
SRP040447_lung	4.67 RPM	15.84 RPM
SRP040447_skeletal_muscle	3.20 RPM	11.33 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1272 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1272 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013671	2 retrocopies	retro_btau_133, retro_btau_1706,
Cavia porcellus	ENSCPOG00000014231	2 retrocopies	retro_cpor_1272 , retro_cpor_242,
Dasypus novemcinctus	ENSDNOG00000002180	1 retrocopy	retro_dnov_1479,
Homo sapiens	ENSG00000156697	1 retrocopy	retro_hsap_29,
Gorilla gorilla	ENSGGOG00000014930	1 retrocopy	retro_ggor_163,
Loxodonta africana	ENSLAFG00000016653	1 retrocopy	retro_lafr_110,
Myotis lucifugus	ENSMLUG00000001984	2 retrocopies	retro_mluc_1643, retro_mluc_308,
Macaca mulatta	ENSMMUG00000020700	1 retrocopy	retro_mmul_35,
Mus musculus	ENSMUSG00000063785	1 retrocopy	retro_mmus_261,
Nomascus leucogenys	ENSNLEG00000015258	1 retrocopy	retro_nleu_2091,
Procavia capensis	ENSPCAG00000006070	1 retrocopy	retro_pcap_127,
Pan troglodytes	ENSPTRG00000022262	1 retrocopy	retro_ptro_824,
Tarsius syrichta	ENSTSYG00000009415	1 retrocopy	retro_tsyr_2104,
Tursiops truncatus	ENSTTRG00000003794	1 retrocopy	retro_ttru_1687,