RetrogeneDB ID: retro_cpor_17

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_33:4853948..4857008(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000021881
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000006442
• Aliases: None
• Description: None

Sequence

>retro_cpor_17
ATGGCTTCCTCATATTACAGCAGTCTGAATCGAGCTCAGTTAACCTTTGAATATCTGCACACAAATTCAACCACACATGA
ATTCTTATTTGGAGCTCTTGCTGAACTGGTTGATAATGCAAGAGATGCACATGCCACCAGAATAGATATTTATGCAGAAA
GACGAGAGAACCTTCAAGGGGGATTTATGCTCTGTTTTTTGGATGATGGAGTAGGAATGAATCCCAATGAGGCTGCCGGT
GTTACTCAGTTTGGGAGATCAACCAAACGAGCACCAGAGTCCACCCAGATTGGGCAGTACGGGAATGGGTTAAAATCTGG
CTCAATGCGCATTGGGAAGGATTTTATTCTTTTCACCAAGAAGAAAGATACCATGACCTGTCTCTTCCTCTCTCGAACTT
TTCACGAGGAAGAAGGCATTGATGAAGTGATAGTCCCATTGCCTTCCTGGAATGCTCAGACCCAGGAAGCTGTTACAGAA
AATATGGAGAAGTTTTCCATTGAGACAGAACTCATTTACAAGTATTCTCCCTTCCACACTGAGGAGGAAGTAATGAGACA
GTTCATGAAGATTTCTGGGGACAGTGGAACACTAGTGATCATCTTTAATCTCAAACTCATGGATAATGGAGAGCCTGAGC
TAGACATAGTCTCAAATCCAAAAGATATCCAGATGGCAGAGGCCTCCCCCGTGGGCACAAAGCCAGAACGCTGGTCCTTC
AGAGCTTACACATCTGTGCTCTACATTGATCCCCGGATGAGGATCTTCATCCACGGGCACAAGGTGCAGACCAAGAGGCT
TGCCTGTTGTCTATACAAGCCCAGGATGTACAAGTACACATCCAACCGTTTCAAGACCCGCGCAAAGCAGGAGGTGGAGA
AAGCAGAGCATGTAGCATGGATTGCTCAAGAGAAGGCCTGGGAAGCCGAGAGCAAAGCTCGAACATTAGAAGTACGCATA
GGTGGCAATCTTACTCGGGAATCCAAGATGATGTTAAGGCAGGTTCAGAACACTGCCATAAACCTGCGCAGAGAAGCCAA
TATCAAGAAGAGGGTCAAGGAAGCCAAGGAGCAAGCGCTCAAGGAACCTAAGGAACTGAATTTTGTTTTTGGGGTCAACA
TTGAACATCGGGAGCTAGATGGCATGTTCATCTACAACTGTAGCCGCCTGATCAAGATGTATGAGAAAGTGGGCCCACAG
CTGGAAGGGGGCATGGCCTGTGGTGGAGTTGTTGGGGTTGTTGATGTGCCCTACCTGGTCCTGGAGCCTACACACAACAA
GCAGGACTTTGCTGATGCCAAGGAGTTCCGGTACCTGTTGAAGGCAATGGGGGAGCATTTGGCACAGTACTGGAAGGACA
CTGCCATTGCCCAACGTGGAATCATCAGGTTTTGGGATGAGTTTGGTTATCTTTCTGCCAACTGGAACCAGCCCCCGTCC
AATGAGCTACATTACAAACGCAAGAGAGCAATGCAAATCCCAACCACCATCCAGTGTGATTTGTGTCTGAAGTGGAGGAC
CCTCCCCTTCCAGTTGAACTCAGTAGAAAAAGATTATCCTAACACCTGGGTTTGTTCCATGAACATTGATCCTGAGCAAG
ATCATTGTGAAGCTCCTGAACAAAATCAGAAGTTTCCGATGGGCACATACAAAAAAGTTGCAAAGACACAGGAAAAGAAG
CAAAAGGAGCTAGCAGAGAAAATTCGCCAGCAGCAGGAAAAGCTGGATGCCCTTCAGAAAATCACCCCCATCCGCTCCCA
AGCAGACTTGAAGAAATTGCCCTTGGAGGTGACAACCAGACCTTCCTCTGAGGAACCTGCTTGTAAATCACAGCGTCGTT
GGCCACCACCTTTATCTCCTGAGATCAGAAAACCCCCAAGCAGATCTTCTTCTCTGCAAGTTCCCAAAACTCCACCCCAA
AAGGTTCCGATCATCAGAATCCCAAAGATTCCTGTACTAACAGCCCGGGGAAAGCCTAGTACCTTCAGCCCACTCCAGTC
ACCTGAGGCATCCCAAAAGTGTGTCGCTACCCCAGTCAAGACTGCATCCTTGACCACTCCTCTGGTGCAGCCACTGTTAT
CATCTCCACTGCCCAACTCCAAGACTTCTTGGAAGCCCCCCAAACCCAAAGCCATCAAGACTCCAATGGTTAGGATGTTA
GAGTCACCTGTTAAACTCTCCAGAGATACCACTGGTCGGAAGCGGAGTCTTCAGGACTCTGATGAGGAAGAGCCTGGAAG
AAGGAAGAAGTGCAAGAAGGGCAAATTTGCTGTGAAGAAGGAAAAGAAATCAAAAGAACTTTCACACAGTGCTGGGAAAG
AGGACTCAGCTGACCTCAAAAGGGCTGAGGAAGATTTAGGGCTTCCTGTGGAAGTACAGGTGAACAAAGAGTGGTATACA
GGCCATGTCACAGCCACAGAGGTGGAAAAGAATGTGGTGTGGTGGAAAGTGGAGTTTGACCATGAGACTGCAGATGCAAC
TCCAGGAAATCATTGGGTGGAGAAATGTAGTGACAGTGTGCGGCTGATGAAGCCACCTTTTGCAGAGTATCAACCCCCCA
CCACACAGCTGGAAAACAGAGAAGAAAAAGCAGCTGTGGTGGGTCAGCAGACTACAGCCATGGCAGAGCCCTCTGCCCCT
GACTGCATCCATGTCAAGCCTGACACCACTACTGTGAATAAAAAGTGTGAAACCATAGATTTCCTGGTACAGCTTCTCCG
GGACTGCTTACAGTATTTCCGGCCTCCAAAGTTTCCCATGTCCAAAAAGGAGCTGAAAACTATGAATTTAGACAAGATAT
TATCTTTTCCTATGGAACAATACTTTAAGCATTATGAAGAGCATTTGCAGAACCTGTGCCATTTCTACCAGAGCCAAGCC
GACTCCAGGGTCAGGGCCTCTGAGGAAAGCCTACATGCATCTGAGAGGAAGCTCCAAGAGGTCCAGGAGAAGCTGCAGAA
GCTGAGGACCAACATCATGGTGTTCTTGGGAAAAGACCCAGACTTCAAAACTGGGGATGACCTGGATGCGTACATTGAAC
ACCTTGTCACCACAGGGAAT

Alignment

ORF - retro_cpor_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFTYYSSLNRAQLTFEYLHTNSTTHEFLFGALAELVDNARDADATRIDIYAERREDLRGGFMLCFLDDG
          MA..YYSSLNRAQLTFEYLHTNSTTHEFLFGALAELVDNARDA.ATRIDIYAERRE.L.GGFMLCFLDDG
Retrocopy MASSYYSSLNRAQLTFEYLHTNSTTHEFLFGALAELVDNARDAHATRIDIYAERRENLQGGFMLCFLDDG

Parental  AGMDPSDAASVIQFGKSAKRTPESTQIGQYGNGLKSGSMRIGKDFILFTKKEDTMTCLFLSRTFHEEEGI
          .GM.P..AA.V.QFG.S.KR.PESTQIGQYGNGLKSGSMRIGKDFILFTKK.DTMTCLFLSRTFHEEEGI
Retrocopy VGMNPNEAAGVTQFGRSTKRAPESTQIGQYGNGLKSGSMRIGKDFILFTKKKDTMTCLFLSRTFHEEEGI

Parental  DEVIVPLPTWNAQTREPVTDNVEKFAIETELIYKYSPFRTEEEVMNQFMKIPGNSGTLVIIFNLKLMDNG
          DEVIVPLP.WNAQT.E.VT.N.EKF.IETELIYKYSPF.TEEEVM.QFMKI.G.SGTLVIIFNLKLMDNG
Retrocopy DEVIVPLPSWNAQTQEAVTENMEKFSIETELIYKYSPFHTEEEVMRQFMKISGDSGTLVIIFNLKLMDNG

Parental  EPELDIISNPRDIQMAETSPEGTKPERRSFRAYAAVLYIDPRMRIFIHGHKVQTKRLSCCLYKPRMYKYT
          EPELDI.SNP.DIQMAE.SP.GTKPER.SFRAY..VLYIDPRMRIFIHGHKVQTKRL.CCLYKPRMYKYT
Retrocopy EPELDIVSNPKDIQMAEASPVGTKPERWSFRAYTSVLYIDPRMRIFIHGHKVQTKRLACCLYKPRMYKYT

Parental  SSRFKTRAEQEVKKAEHVARIAEEKAREAETKARTLEVRLGGDLTRDSRVMLRQVQNTAITLRREADVKK
          S.RFKTRA.QEV.KAEHVA.IA.EKA.EAE.KARTLEVR.GG.LTR.S..MLRQVQNTAI.LRREA..KK
Retrocopy SNRFKTRAKQEVEKAEHVAWIAQEKAWEAESKARTLEVRIGGNLTRESKMMLRQVQNTAINLRREANIKK

Parental  RIKEAKQRALKEPKELNFVFGVNIEHRDLDGMFIYNCSRLIKMYEKVGPQLEGGMACGGVVGVVDVPYLV
          R.KEAK..ALKEPKELNFVFGVNIEHR.LDGMFIYNCSRLIKMYEKVGPQLEGGMACGGVVGVVDVPYLV
Retrocopy RVKEAKEQALKEPKELNFVFGVNIEHRELDGMFIYNCSRLIKMYEKVGPQLEGGMACGGVVGVVDVPYLV

Parental  LEPTHNKQDFADAKEYRHLLRAMGEHLAQYWKDIAIAQRGIIKFWDEFGYLSANWNQPPSSELRYKRRRA
          LEPTHNKQDFADAKE.R.LL.AMGEHLAQYWKD.AIAQRGII.FWDEFGYLSANWNQPPS.EL.YKR.RA
Retrocopy LEPTHNKQDFADAKEFRYLLKAMGEHLAQYWKDTAIAQRGIIRFWDEFGYLSANWNQPPSNELHYKRKRA

Parental  MEIPTTIQCDLCLKWRTLPFQLNSVEKDYPDTWVCSMNPDPEQDRCEASEQKQKVPLGTFKKDPKTQEEK
          M.IPTTIQCDLCLKWRTLPFQLNSVEKDYP.TWVCSMN.DPEQD.CEA.EQ.QK.P.GT.KK..KTQE.K
Retrocopy MQIPTTIQCDLCLKWRTLPFQLNSVEKDYPNTWVCSMNIDPEQDHCEAPEQNQKFPMGTYKKVAKTQEKK

Parental  QKQLSEKIRQQQEKLEALQKTTPIRSQADLKKLPLEVTARPSNEEPARRPQRPRSPPLPAVIKNAPSRPP
          QK.L.EKIRQQQEKL.ALQK.TPIRSQADLKKLPLEVT.RPS.EEPA...QR...PPL...I...PSR..
Retrocopy QKELAEKIRQQQEKLDALQKITPIRSQADLKKLPLEVTTRPSSEEPACKSQRRWPPPLSPEIRKPPSRSS

Parental  SLQAPRLVSQPQKAPIISNPPKPPALVARVEASTSRLLQPPEAPRKPVNTSIKIVPRTPSLVQPLSSSLL
          SLQ.P.....PQK.PII...PK.P.L.AR...ST...LQ.PEA..K.V.T..K....T..LVQPL.SS.L
Retrocopy SLQVPK--TPPQKVPII-RIPKIPVLTARGKPSTFSPLQSPEASQKCVATPVKTASLTTPLVQPLLSSPL

Parental  PNSKSSREIPAPKVIKTPVVKKPEPPVKPSLATTGRKRSLGVSDEEEAEEEAERKKEKCKRGKFAVKEEK
          PNSK.S...P.PK.IKTP.V...E.PVK.S..TTGRKRSL..SDEEE......RKK..CK.GKFAVK.EK
Retrocopy PNSKTSWKPPKPKAIKTPMVRMLESPVKLSRDTTGRKRSLQDSDEEE---PGRRKK--CKKGKFAVKKEK

Parental  KESNELSDSAGEEDPADLKKAQKDKGLHVEVRVNREWYTGRVTAVEVGKNVVRWKVKFDYVPTDTTPRDR
          K.S.ELS.SAG.ED.ADLK.A..D.GL.VEV.VN.EWYTG.VTA.EV.KNVV.WKV.FD....D.TP...
Retrocopy K-SKELSHSAGKEDSADLKRAEEDLGLPVEVQVNKEWYTGHVTATEVEKNVVWWKVEFDHETADATPGNH

Parental  WVEKGSEDVRLMKPPSPEYQTPDTQQEEEEEE-AVVAQQAVAMAEPSTSDCIRIEPDTTAPSTNHETIDL
          WVEK.S..VRLMKPP..EYQ.P.TQ.E..EE..AVV.QQ..AMAEPS..DCI...PDTT......ETID.
Retrocopy WVEKCSDSVRLMKPPFAEYQPPTTQLENREEKAAVVGQQTTAMAEPSAPDCIHVKPDTTTVNKKCETIDF

Parental  LVQILRNCLRYFLPPSFPISKKELSVMNSDELISFPLKEYFKQYEVGLQNLCHSYQSRADSRAKASEESL
          LVQ.LR.CL.YF.PP.FP.SKKEL..MN.D...SFP...YFK.YE..LQNLCH.YQS.ADSR..ASEESL
Retrocopy LVQLLRDCLQYFRPPKFPMSKKELKTMNLDKILSFPMEQYFKHYEEHLQNLCHFYQSQADSRVRASEESL

Parental  RTSERKLRETEEKLQKLRTNIVALLQKVQEDIDINTDDELDAYIEDLITKGD
          ..SERKL.E..EKLQKLRTNI...L.K...D.D..T.D.LDAYIE.L.T.G.
Retrocopy HASERKLQEVQEKLQKLRTNIMVFLGK---DPDFKTGDDLDAYIEHLVTTGN

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	35.49 RPM
SRP017611_kidney	0.00 RPM	54.33 RPM
SRP017611_liver	0.00 RPM	33.30 RPM
SRP040447_lung	0.08 RPM	45.62 RPM
SRP040447_skeletal_muscle	0.08 RPM	19.25 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_17 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_17 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006442	1 retrocopy	retro_cpor_17 ,
Monodelphis domestica	ENSMODG00000009557	1 retrocopy	retro_mdom_1757,
Mus musculus	ENSMUSG00000034543	1 retrocopy	retro_mmus_49,
Otolemur garnettii	ENSOGAG00000009971	2 retrocopies	retro_ogar_2044, retro_ogar_282,
Rattus norvegicus	ENSRNOG00000019624	1 retrocopy	retro_rnor_412,