RetrogeneDB ID: retro_cpor_681

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_23:9057137..9060293(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000000211
• Aliases: None
• Description: None

Sequence

>retro_cpor_681
ATGAAGGAAGAGGTAAAGAGAATCCCTGTAAAAGTAGCACTACGTTGTCGCCCTCTGGTCGCTAAAGAGATCAGTGAGGG
CTGCCACATGTGCCTTTCCTTTGTGCCAGGGGAACCTCAGGTACTGGTCGGTAAGGACAAATGCTTTACTTATGATTTTG
TGTTTGACCCCTCTGCTGAGCAGGAAGAGGTCTTTAATACCGCGGTTGCACCACTCATTAGGGGTGTATTTAAAGGATAC
AATGCAACTGTCCTGGCCTACGGGCAGACTGGCTCTGGGAAAACCTATTCAATGGGAGGTGCGTACACTGCAGAGCAAGA
GAATGAGCCCACGATTGGGGTCATTCCTAGGGCCATAGACCTGCTCTTCAAAGAAATTGATAAAAAGCATGACTTTAAAT
TTACTCTGAAAGTATCTTACTTGGAGATTTACAATGAAGAAATTTTAGACCTTCTGTGCTTGTCTCAAGGGAAAACTCCT
CACATAAATATCCGGGAAGATCCCAAGGAAGGCATAAAGATGATAGGACTCACCGAGAAGACTGTTGTTGTTGCCTTGGA
CACTATTTCCTGTTTGGAGCAGGGCAACAACTGTAGGACTGTGGCCTCTACGGCTATGAACGCCCAGTCCTCCCGATCTC
ATGCTATCTTCACCATTTCCATAGAGCAAAGAAAGAAAAACGACAAGAACAGCAGCTTTCACTCCAAGCTGCACCTTGTA
GACCTCGCTGGATCAGAAAGACAGAAGAAAACCAAAGCAGAAGGAGATCGTCTAAAAGAAGGGATTAATATTAACCGAGG
TCTCCTATGCTTGGGGAATGTAATCCGTGCTCTTGGAGATGACAGAAAGGGAAGCTTTGTGCCCTACAGAGATTCCAAAC
TGACTCGACTGCTTCAGGATTCTCTAGGAGGTAACAGCCATACACTCATGATAGCCTGTGTAAGTCCTGCTGATTCCAAT
CTGGAGGAAACATTAAATACCCTTCAGTATGCTGACAGAGCAAGGAAAATAAAAAACAAACCTGTTATTAACATTGATCC
CCAGACAGCTGAACTTAATCAACTTAAGCAACAGGTACAACAGCTTCAGGTTTTGTTGCTGCAAGCCCGTGGAGGTGCCC
TGCCTGGGTCTCTAAATATGGAACCATCAGAGAACCTACAATCCCTGATAGAGAAGAATCAGTCCCTAGTAGAGGAGAAC
GTGAAACTAAGCCGTAGTCTGAGCGAGGCAACTGGTGAGACCGTACAAATGTTGGAAAGGATCATTTTGATGGAACAAAC
AAATGAAAAACTGAATATGAAATTAGAAGAGCTCAGACAGCATGCAGCCTGTAAGCTGGACCTTCAAAACCTAGTGGAGA
ATCTGGAAGACCAGGAATTAAAAGAAAATGTAGAGGTAATTTGCCATCTGCAACAAGTGATTCTCCAGCTGTCCAAAGAA
ACTGTACCTTGCATAGCTACAGCCACTAATACTACATTAGAAGAAGAAGCTCAAATGCAAAGCAGTTCAGAGACTAGCAG
CGGGTCTTCTGATGCTTTCACTACCCATCACGCTTTGCGACAAGCCCAGATGTCAAAGCAGCTGCTTGAGTTGAACAAAG
CTCTGGCACTGAAAGAGGCCTTGGCCAAGAAGATGACTCAGAATGACAGTGAACTAAACCCCATTCAGTTAATGTACCAG
GATAACATAAAAAATCTAGAATTGGAAGTGAGTCAGCTGCAAAGAAAAAAAGAAGACTTAATTCTCGAACTTCAGACAGC
AAAAAAGGACATTAACCAGGCCAAGCTGAGTGAGTGCCGTCGCAAACGTCTCCAAGAGCTTGAGAGTCAAATAGCTGATT
TGAAAAAGAAGCTACATGAACATTTCAAGCTTCTGAAAATGAAGGAATCCACAGAGCACACTGTGACCAAACTGAACCAG
GAGATAGCAATAATGAAAAACCAGCGAGTCCAGTTAATGCACCAGATGAAGGAGGATGCAGAAAAGTTTAGACAGTGGAA
GCAACAAAAAGACAAAGAAGTAATCCAGTTAAAAGAACAGGACCGTAAGAGGCAATATGAGCTTCTCAAACTTGAGAGAA
ACTTCCAGAAACAGTCCAGTGTACTCAGACGTAAAGCTGAAGAGGCAGCAGCTGCCAACAAGCGTCTCAGAGATGCTCTC
CAGAGGCAACAGGAGGGTGCAGATAAGCGAAAACAGACTCAGAGCCGTGGAATGGAAGGCACCGCAGCACGAGTGAAAAG
TTGGCTTGGGAGTGAAATCGAGGTTATGGTGAGTATTGAGGAAGCCAAACGTCATTTGAATGACCTCCTTCAAGACAGAA
AGATCCTGGCTCAGGACCTGGCTCAGCTTAAGTCAAAAAAAGAATCTGAGGAGAATCCACCTCCTAAACTTCAAAGGCGT
ACAATCTCACTTGCTGAAATGCCTGCTCAAGTTTCAGAGTCAGAGGATTCTACTAAAAAGCAGATTGAAAGCTTAGAGAC
TGAAATAAAACTCAGGAGCGCTCAGATTGCCGACTTCCAACAGAAGCTTCTGGATGCAGAAAGTGAAGACAGGCCCCCCA
AAACCTGGGAGAACATTACTACGATTCTGGAAGCCAAGTGCGCCCTGAAATACTTAATTGGAGAGCTGGTCTCTTCCAAA
TTACAGGTCAGCAGTCTTGAAAGTAGCCTGAAACAGAGCAAGGCCAGCTGTGCTGACGTGCAGAAGATACTGTTTGAGGA
ACGAAATCGTTTTGCTGAGATAAAGACAGAGTTTCAAGCTGACCTGGTCAGAGTGGAGCAGCAGAACCAGGAGAAGGTGC
TGTATCTCCTCAGCCAGCTGCCGCAAAGCCGGGCAGCTGAGAAGCAGCTGGAGGAGACAGGTAGCGTGACAGAACAACAG
CTGCTGAGCACTCTACACTGTCAGGAGGAAGAGCTTAAGAAGATGCAAGAAGTATGCGAGCAAAATCGGAAGCTTCTCCA
GGAAAATGAAAAACTCAAGCAGAAACTGCACCTATTTCACGCAGTCAACAGGCAGAAATCTCATGTTCCTGAGGAAATGT
CCTCCTCCTCAGACTCCTCCTTTGACTATATCCCTCCTAAGCCAAAACCATCCCATGGTAAAGTAAAGATCCCAGAACAA
AGCATGGACATGGAGGATCTAAAATGTTATTCAGAG

Alignment

ORF - retro_cpor_681 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.98 %
• Parental protein coverage: 85.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKEEVKGIPVRVALRCRPLVPKEISEGCQMCLSFVPGKPQVVVGNDKSFTYDFVFDPSAEQEEVFNTAVA
          MKEEVK.IPV.VALRCRPLV.KEISEGC.MCLSFVPG.PQV.VG.DK.FTYDFVFDPSAEQEEVFNTAVA
Retrocopy MKEEVKRIPVKVALRCRPLVAKEISEGCHMCLSFVPGEPQVLVGKDKCFTYDFVFDPSAEQEEVFNTAVA

Parental  PLIKGIFKGYNATVLAYGQTGSGKTYSMGGAYTAEQENEPTVGVIPRVIQLLFNEIDKKSDFEFTLKVSY
          PLI.G.FKGYNATVLAYGQTGSGKTYSMGGAYTAEQENEPT.GVIPR.I.LLF.EIDKK.DF.FTLKVSY
Retrocopy PLIRGVFKGYNATVLAYGQTGSGKTYSMGGAYTAEQENEPTIGVIPRAIDLLFKEIDKKHDFKFTLKVSY

Parental  LEIYNEEILDLLCSSREKASQINIREDPKEGIKIIGLTEKTVFVALDTVSCLEQGNNCRTVASTAMNSQS
          LEIYNEEILDLLC.S..K...INIREDPKEGIK.IGLTEKTV.VALDT.SCLEQGNNCRTVASTAMN.QS
Retrocopy LEIYNEEILDLLCLSQGKTPHINIREDPKEGIKMIGLTEKTVVVALDTISCLEQGNNCRTVASTAMNAQS

Parental  SRSHAIFTISIEQRKKNDKNSSFRSKLHLVDLAGSERQKKTKAEGDRLKEGININRGLLCLGNVISALGD
          SRSHAIFTISIEQRKKNDKNSSF.SKLHLVDLAGSERQKKTKAEGDRLKEGININRGLLCLGNVI.ALGD
Retrocopy SRSHAIFTISIEQRKKNDKNSSFHSKLHLVDLAGSERQKKTKAEGDRLKEGININRGLLCLGNVIRALGD

Parental  DKKGGFVPYRDSKLTRLLQDSLGGNSHTLMIACVSPADSNLEETLNTLRYADRARKIKNKPVINFDPQTA
          D.KG.FVPYRDSKLTRLLQDSLGGNSHTLMIACVSPADSNLEETLNTL.YADRARKIKNKPVIN.DPQTA
Retrocopy DRKGSFVPYRDSKLTRLLQDSLGGNSHTLMIACVSPADSNLEETLNTLQYADRARKIKNKPVINIDPQTA

Parental  ELNHLKQQVQQLQVLLLQAHGGTLPTSINVEPSENLQSLMEKNQSLIEENEKLSRGLSEAAGQIAQMLER
          ELN.LKQQVQQLQVLLLQA.GG.LP.S.N.EPSENLQSL.EKNQSL.EEN.KLSR.LSEA.G...QMLER
Retrocopy ELNQLKQQVQQLQVLLLQARGGALPGSLNMEPSENLQSLIEKNQSLVEENVKLSRSLSEATGETVQMLER

Parental  IILTEQANEKMSTKLEELRQHAACKLDLQKLIETLEDQELKENVEIIRNLQQVIIQLSDETVACMAAAID
          IIL.EQ.NEK...KLEELRQHAACKLDLQ.L.E.LEDQELKENVE.I..LQQVI.QLS.ETV.C.A.A..
Retrocopy IILMEQTNEKLNMKLEELRQHAACKLDLQNLVENLEDQELKENVEVICHLQQVILQLSKETVPCIATATN

Parental  TAVEPEAQLETSPETSR-SSDVFTTQHALRQAQMSKELTELNKALALKEALARKMTQNNSQLQPIQFQYQ
          T..E.EAQ...S.ETS..SSD.FTT.HALRQAQMSK.L.ELNKALALKEALA.KMTQN.S.L.PIQ..YQ
Retrocopy TTLEEEAQMQSSSETSSGSSDAFTTHHALRQAQMSKQLLELNKALALKEALAKKMTQNDSELNPIQLMYQ

Parental  DNIKNLELEVINLQKEKEELLLELQTAKKDVNQAKLSERRRKRLQELESQIADLKKKLNEQSKLLKLKES
          DNIKNLELEV..LQ..KE.L.LELQTAKKD.NQAKLSE.RRKRLQELESQIADLKKKL.E..KLLK.KES
Retrocopy DNIKNLELEVSQLQRKKEDLILELQTAKKDINQAKLSECRRKRLQELESQIADLKKKLHEHFKLLKMKES

Parental  TEHTVTKLNQEIRMMKNQRVQLMRQMKEDAEKFRQWKQQKDKEVIQLKERDRKRQYELLKLERNFQKQSS
          TEHTVTKLNQEI..MKNQRVQLM.QMKEDAEKFRQWKQQKDKEVIQLKE.DRKRQYELLKLERNFQKQSS
Retrocopy TEHTVTKLNQEIAIMKNQRVQLMHQMKEDAEKFRQWKQQKDKEVIQLKEQDRKRQYELLKLERNFQKQSS

Parental  VLRRKTEEAAAANKRLKDALQKQREVADKRKEVQSRGMEGTTARVKSWLGNEIEVMVSTEEAKRHLNDLL
          VLRRK.EEAAAANKRL.DALQ.Q.E.ADKRK..QSRGMEGT.ARVKSWLG.EIEVMVS.EEAKRHLNDLL
Retrocopy VLRRKAEEAAAANKRLRDALQRQQEGADKRKQTQSRGMEGTAARVKSWLGSEIEVMVSIEEAKRHLNDLL

Parental  EDRKILAQDLAQLKEKKESGENPPPKLRRRTFSLAEMPGQVSESEDSITKQIESLETEMELRSAQIADLQ
          .DRKILAQDLAQLK.KKES.ENPPPKL.RRT.SLAEMP.QVSESEDS..KQIESLETE..LRSAQIAD.Q
Retrocopy QDRKILAQDLAQLKSKKESEENPPPKLQRRTISLAEMPAQVSESEDSTKKQIESLETEIKLRSAQIADFQ

Parental  QKLLDAESEDRPKQRWENIATILEAKCAMKYLIGELVSSKIQFSKLESSLKQSKASCADMQKMLFEERNR
          QKLLDAESEDRP...WENI.TILEAKCA.KYLIGELVSSK.Q.S.LESSLKQSKASCAD.QK.LFEERNR
Retrocopy QKLLDAESEDRPPKTWENITTILEAKCALKYLIGELVSSKLQVSSLESSLKQSKASCADVQKILFEERNR

Parental  FADIEAELQDEMVKLEQQHQEKVLYLLSQLKQSQMIEKQLEESVSGKEQQLLSTLKYQDEELKKMQEICE
          FA.I..E.Q...V..EQQ.QEKVLYLLSQL.QS...EKQLEE..S..EQQLLSTL..Q.EELKKMQE.CE
Retrocopy FAEIKTEFQADLVRVEQQNQEKVLYLLSQLPQSRAAEKQLEETGSVTEQQLLSTLHCQEEELKKMQEVCE

Parental  QNQQLLQENEIIKQKLMLLQVANREKPHLSKDILLSPDSSFEYIPPKPKPSRVKEKFLEQSMDIEDLKYY
          QN..LLQENE..KQKL.L....NR.K.H.......S.DSSF.YIPPKPKPS..K.K..EQSMD.EDLK.Y
Retrocopy QNRKLLQENEKLKQKLHLFHAVNRQKSHVPEEMSSSSDSSFDYIPPKPKPSHGKVKIPEQSMDMEDLKCY

Parental  SE
          SE
Retrocopy SE

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	0.69 RPM
SRP017611_kidney	0.00 RPM	0.73 RPM
SRP017611_liver	0.00 RPM	0.70 RPM
SRP040447_lung	0.00 RPM	3.13 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.63 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_681 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_681 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015566	1 retrocopy	retro_cjac_2142,
Cavia porcellus	ENSCPOG00000000211	1 retrocopy	retro_cpor_681 ,
Homo sapiens	ENSG00000090889	1 retrocopy	retro_hsap_18,
Gorilla gorilla	ENSGGOG00000006631	1 retrocopy	retro_ggor_2218,
Myotis lucifugus	ENSMLUG00000011048	1 retrocopy	retro_mluc_114,
Mus musculus	ENSMUSG00000034311	1 retrocopy	retro_mmus_268,
Pongo abelii	ENSPPYG00000020438	1 retrocopy	retro_pabe_2700,
Rattus norvegicus	ENSRNOG00000038035	1 retrocopy	retro_rnor_2330,