RetrogeneDB ID: retro_cjac_1189

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:15038845..15041584(+)
• Located in intron of: ENSCJAG00000013507

Retrocopy information

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

Parental gene information

• Parental gene symbol: PKP4
• Ensembl ID: ENSCJAG00000015236
• Aliases: None
• Description: None

Sequence

>retro_cjac_1189
AGGACAAACACTGGTTCAGCTATATGGCAGATTGGGTCAGTCACCTCCAGGCAGACCTCCAATCCCAACGGACCAAACCC
TCAGTACCAAACCACCACCAGAGTGGGGTCCCCACTGGCCCTGAAGGATGCACAGACTCGACTAGCTTCCCCATCCCAAG
GCCAGGTGGGGTCATCGTCCCCCAAACGCTCAGGGATGACCGCCATACCACAGCATCTGGGACCTTTACTGCAAAGGACT
GTTCATGACATGGAGCAATTTGGACAGCAGCAGTATGACATTTATGAGAGGATGGTTCCACCCAGGCCAGACAGCCTGAC
AGGCTTACAGAGTTCCTATGCTAGTCAGCACAGTCAGTTTGGGCAAGACCTTCGTTCCGCTGTGTCTCCCGACTTGCACA
TTACTCCTACCTATGTGGGGAGGACCTATTACAGCCCCGTGTACCGCAGCCCAAACCACGGAACTGTGGAGCTCCAAGGA
TCGCAGAGGGCATTGTATCGCACAAGCTCAGTAGGTATTGGAAATCTACAAAGGACGTCCAGCCAACAAAGTACCCTTAC
ATACCAAAGAAATAATTATGCTCTGAACACAACAGCTACCTACACGGAGCCCTACAGGCCTATACAATATCGAGTGCAAG
AGTACAAGTACAACAGGCTTCAGCACACAGTGCCGGCTGATGATGGCACCACAAGATCCCCATCAATAGACAGCATTCAG
AAGGACCCTAGGGAGTTTGCCTGGCGTGATCCTGAGTTGCCTGAGGTCATTCACATGCTTCAGCACCAGTTCCCATCTGT
TCAGGCAAATGCAGCGGCCTACCTGCAGCACCTGTGCTTTGGCGACAACAAAGTGAAGATGGAGGTGTGTAGGTTAGGGG
GAGTCAAGAAGCATCTGGTTGACCTCTTGGACTACAGATTGTTGGAAGTTCAAAAGAATGCTGTGGTGCTCTTTGAAACC
TCGTTTTTGGCAAGTCTACAGATGAAAATGAAATAGCAATGAAGAATGTTGGTGGGATACCTGCCTTGTTGCAACTGTTG
AGAAAATCTATTGATGCAGAAGTAAGGGAGCTTGTTACAGGAGTTCTTTGTAATTTATCCTCATGTGATGCTGTAAAAAT
AATCATTCGAGATGCTCTCTCAACCTTAACAAACACTGTGATCGTTCCGCATTCTGAATGGAAGAACTCTTCTTTTGATG
ATCATCATAAAATTAAATTTCAGATTTCACTAGTTCTGCGTAACATGACAGGTTGCCTGAGGAACCTCAGCTCTGCCGGG
GAAGAAGCTCGGAAGCAAATGTGGTCCTGCGAGGGGCTGGTGGACTTGCTGTTGTACGTGATCCACACATGTGTGAACAT
ATCCGATTACGACAGCAAGACGGTGGAGAACTGTGTGTGCACCCTGAAGAACCTGTCCTATCGACTGGAGCTGGAGGTGC
CCCAGGCCCGGTTACTGGGACTGAACGAATTGGATGACTTACTGGGAAAAGAGTCTCCCAGCAAAGACTCTGAGCCAAGC
TGCTGGGGGAAGAAGAAGAAAAAGAAAAAGAGGACTCCGCAAGAAGATCAATGGGATGGAGTTGGTCCTATCCCAGGACT
GTCAAAGTCCCCCAAAGGGGTTGAGATGCTGTGGCACCCATCGGTGGTTAAACCATATCTGACTCTTCTAGCAGAAAGTT
CCAACTCAGCCACCTTGGAAGGCTCTGCCGGATCTCTCCAGAACCTCTCTGCAGGCAACTGGAAGTTTGCAGTATACATC
TGGGCAGCTGACCGAAAAGAAAAGGGGCTCCCCATCCTGTGGAACTTCTGAGAATGGACAACAATAGGGTTGTTTCTTCC
GTGGCAACTGCACTGAGGAATATGGCACTAGATGTTTGCAACAAGGAGCTCATAGGCAAATACGCCATGCGAGACCTGGT
CAACCAGTTTCCTGGTGGCAATGGTCCCAGTGTCTTGTCTGATGAGACCATGGCAGCCATCTGCTGTGCTCTACACGAGG
TCACCAGCAAAAACATGGAGAACGCCAAAGCCCTGGCCGACTTGGGAGGCATCGAGAAGCTGGTGAACATAACCAAAGGC
AGAGGCCACAGATCATCTCTGAAAGTGGTGAAGGCAGCAGCCCAGGTCTTGAATACATTATGGCAATATTGGGACCTCCG
GAGCATTTATAAAAAGGATGGGTGGAATCAGAACCATTTTATTACACCTGTGTCGACATTGGAGCAAGACCGATTCAAAT
AACATCCTTCCTTATCTACCACCAACCAACAGATGTCACCCATCATTCAGTCAGTCGGCAGCACCTCTTCCTCACCAGCA
TTGTTAGGAATCAGAGAGACCCTCGCTCTGAATATGATAGGACCCAGCCACCTATGCAGTATTACAATAGCCAACGGGAT
GCCACACATAAAGGCCTGTACCCTGGCTCCAGCAAACCTTCACCAATTTACATCAGTTCCTATTCCTCACCAGCAAGAGA
ACAAAATAGACGGCTACAGCATCAACACCTGTATTATAGTCAAGATGACTCCAACAGAAAGAACTTTGATGCATACAGAT
TTCATTTGCAGTCTCCTCATAGCTATGAAGACCCTTATTTTGATGACCGAGTTCACTTTCCAGCTTCTGCTGATTACTCA
ACACAGTATGGACTGAAATCAACCACAAATTATGTAGACTTTTATTCCACTAAACAACCTTCTTACAGAGCAGAACAGTA
CCCAGGGTCCCCAGACTCA

Alignment

ORF - retro_cjac_1189 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.74 %
• Parental protein coverage: 76.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RPASPTAIRRIGSVTSRQTSNPNGPTPQYQTTTRVGSPLTLTDAQTRVASPSQGQVGSSSPKRSGMTAVP
          R.....AI..IGSVTSRQTSNPNGP.PQYQTTTRVGSPL.L.DAQTR.ASPSQGQVGSSSPKRSGMTA.P
Retrocopy RTNTGSAIWQIGSVTSRQTSNPNGPNPQYQTTTRVGSPLALKDAQTRLASPSQGQVGSSSPKRSGMTAIP

Parental  QHLGPSLQRTVHDMEQFGQQQYDIYERMVPPRPDSLTGLRSSYASQHSQLGQDLRSTVSPDLHITPIYEG
          QHLGP.LQRTVHDMEQFGQQQYDIYERMVPPRPDSLTGL.SSYASQHSQ.GQDLRS.VSPDLHITP.Y.G
Retrocopy QHLGPLLQRTVHDMEQFGQQQYDIYERMVPPRPDSLTGLQSSYASQHSQFGQDLRSAVSPDLHITPTYVG

Parental  RTYYSPVYRSPNHGTVELQGSQTALYRTGSVGIGNLQRTSSQRSTLTYQRNNYALNTTATYAEPYRPIQY
          RTYYSPVYRSPNHGTVELQGSQ.ALYRT.SVGIGNLQRTSSQ.STLTYQRNNYALNTTATY.EPYRPIQY
Retrocopy RTYYSPVYRSPNHGTVELQGSQRALYRTSSVGIGNLQRTSSQQSTLTYQRNNYALNTTATYTEPYRPIQY

Parental  RVQEYNYNRLQHAVPADDGTTRSPSIDSIQKDPREFAWRDPELPEVIHMLQHQFPSVQANAAAYLQHLCF
          RVQEY.YNRLQH.VPADDGTTRSPSIDSIQKDPREFAWRDPELPEVIHMLQHQFPSVQANAAAYLQHLCF
Retrocopy RVQEYKYNRLQHTVPADDGTTRSPSIDSIQKDPREFAWRDPELPEVIHMLQHQFPSVQANAAAYLQHLCF

Parental  GDNKVKMEVCRLGGIK-HLVDLLDHRVLEVQKNA-CGALRNLVFGKSTDENKIAMKNVGGIPALLRLLRK
          GDNKVKMEVCRLGG.K.HLVDLLD.R.LEVQKNA.CGAL.NLVFGKSTDEN.IAMKNVGGIPALL.LLRK
Retrocopy GDNKVKMEVCRLGGVKKHLVDLLDYRLLEVQKNA<CGAL*NLVFGKSTDENEIAMKNVGGIPALLQLLRK

Parental  SIDAEVRELVTGVLWNLSSCDAVKMTIIRDALSTLTNTVIVPHSGWNNSSFDDDHKIKFQTSLVLRNTTG
          SIDAEVRELVTGVL.NLSSCDAVK..IIRDALSTLTNTVIVPHS.W.NSSFDD.HKIKFQ.SLVLRN.TG
Retrocopy SIDAEVRELVTGVLCNLSSCDAVKI-IIRDALSTLTNTVIVPHSEWKNSSFDDHHKIKFQISLVLRNMTG

Parental  CLRNLSSAGEEARKQMRSCEGLVDSLLYVIHTCVNTSDYDSKTVENCVCTLRNLSYRLELEVPQARLLGL
          CLRNLSSAGEEARKQM.SCEGLVD.LLYVIHTCVN.SDYDSKTVENCVCTL.NLSYRLELEVPQARLLGL
Retrocopy CLRNLSSAGEEARKQMWSCEGLVDLLLYVIHTCVNISDYDSKTVENCVCTLKNLSYRLELEVPQARLLGL

Parental  NELDDLLGKESPSKDSEPSCWGKKKKKKKRTPQEDQWDGVGPIPGLSKSPKGVEMLWHPSVVKPYLTLLA
          NELDDLLGKESPSKDSEPSCWGKKKKKKKRTPQEDQWDGVGPIPGLSKSPKGVEMLWHPSVVKPYLTLLA
Retrocopy NELDDLLGKESPSKDSEPSCWGKKKKKKKRTPQEDQWDGVGPIPGLSKSPKGVEMLWHPSVVKPYLTLLA

Parental  ESSNPATLEGSAGSLQNLSAGNWKFAAYIRAAVRKEKGLPIL-VELLRMDNDRVVSSVATALRNMALDVR
          ESSN.ATLEGSAGSLQNLSAGNWKFA.YI.AA.RKEKGLPIL.VELLRMDN.RVVSSVATALRNMALDV.
Retrocopy ESSNSATLEGSAGSLQNLSAGNWKFAVYIWAADRKEKGLPIL<VELLRMDNNRVVSSVATALRNMALDVC

Parental  NKELIGKYAMRDLVNRLPGGNGPSVLSDETMAAICCALHEVTSKNMENAKALADSGGIEKLVNITKGRGD
          NKELIGKYAMRDLVN..PGGNGPSVLSDETMAAICCALHEVTSKNMENAKALAD.GGIEKLVNITKGRG.
Retrocopy NKELIGKYAMRDLVNQFPGGNGPSVLSDETMAAICCALHEVTSKNMENAKALADLGGIEKLVNITKGRGH

Parental  RSSLKVVKAAAQVLNTLWQYRDLRSIYKKDGWNQNHFITPVSTLERDRFKSHPSL-STTNQQMSPIIQSV
          RSSLKVVKAAAQVLNTLWQY.DLRSIYKKDGWNQNHFITPVSTLE.DRFK.HPSL..T..Q....I....
Retrocopy RSSLKVVKAAAQVLNTLWQYWDLRSIYKKDGWNQNHFITPVSTLEQDRFK*HPSLSTTNQQMSPIIQSVG

Parental  GSTSSSPAL-LGIRDPRSEYDRTQPPMQYYNSQGDATHKGLYPGSSKPSPIYISSYSSPAREQNRRLQHQ
          ...SS...L....RDPRSEYDRTQPPMQYYNSQ.DATHKGLYPGSSKPSPIYISSYSSPAREQNRRLQHQ
Retrocopy STSSSPALL<RNQRDPRSEYDRTQPPMQYYNSQRDATHKGLYPGSSKPSPIYISSYSSPAREQNRRLQHQ

Parental  QLYYSQDDSNRKNFDAYRLYLQSPHSYEDPYFDDRVHFPASADYSTQYGLKSTTNYVDFYSTKRPSYRAE
          .LYYSQDDSNRKNFDAYR..LQSPHSYEDPYFDDRVHFPASADYSTQYGLKSTTNYVDFYSTK.PSYRAE
Retrocopy HLYYSQDDSNRKNFDAYRFHLQSPHSYEDPYFDDRVHFPASADYSTQYGLKSTTNYVDFYSTKQPSYRAE

Parental  QYPGSPDS
          QYPGSPDS
Retrocopy QYPGSPDS

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
SRP051959_colon	0.35 RPM	16.02 RPM
SRP051959_heart	0.89 RPM	24.01 RPM
SRP051959_kidney	2.68 RPM	108.89 RPM
SRP051959_liver	0.17 RPM	7.95 RPM
SRP051959_lung	0.70 RPM	22.32 RPM
SRP051959_lymph_node	0.21 RPM	9.52 RPM
SRP051959_skeletal_muscle	0.22 RPM	9.76 RPM
SRP051959_spleen	0.42 RPM	12.14 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1189 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1189 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1189 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015236	1 retrocopy	retro_cjac_1189 ,
Felis catus	ENSFCAG00000015402	1 retrocopy	retro_fcat_1721,