RetrogeneDB ID: retro_cjac_564

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:81879828..81881389(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000021566
• Aliases: None
• Description: None

Sequence

>retro_cjac_564
AAGGTGGTAAAGCGGAAAGCAGATACTACCACCCCTACACCTATAGCCATCCTGGCTCCTGGTTCCCCAGCTAGCCCTCC
TGGGAGTCTTGAGCCTGAGGCAGCATGGCTTCCCCCTATGCGCAGAGAGAGTGGTCACCCCATCAAGCCCCCATGCAAAG
ACTTGCCTGATTCTCAGCAACAACACTGAGCTCTAAGAAAGGAAAGCTTTCAGAACAATTGAAACATTGCAGCAGCATTT
TGAAGGAGTTACTCTCTAAGAAGCATGCTGCTTATGCTTGGCCTTTCTATAAACCAGTGGACGCTTCTGCACTTGGCCTG
CATGACTACCTTGACATCATTAAGCACCCCATGGATTTCAGCACTGTCAAGCGGAAGATGGAGAACTGTGATTAACAGGA
TGCACAGGAGTTTGCTGCTAAAGTATGGCTTATGTTCTCTAACTCTGTAAGTACAATCCCCCAGATCACAATGTTGTGGC
AATGGCACGAAAGCTACAGGATGTACTTGAGTTCTGTTATGCCAAGATACCAGATGAACCACTGGAACCAGGGCCTCTAC
CAGTCTCTACTGCCATTCCCCCTGGCTTGGCCAAACCATCTTCAGAGTCCTCCAGTGAGGAAAGTAGCAGTGAGAGCTCC
TCTGAGGAGGAAGATGAGGAGGATGAGGAAGAAGAGAGGTGAAAGCTCAGACTCAGAGGAAGAAAGGGCTCATCGCTTGG
CAGAACTGCAGGAACAGCTTCGGGCAGTACATGAACAACTGGCTGTTCTGTCCCATGGTCCAATATCCAAGCCCAAGAGG
AAAAGAGAGAAAAAAGAGAAAAAGAAGAAACAGAAGGCAGAGAAGCATCGAGGATGAGCTGGGGCGATGAAGAAGACAAG
GGGCCTGAAGCACCCTGCCCACCTCAGCCCAAGAAGTCCAAGAAAGCAAGTGGCAGTGGATGTGGCAGTGCTGCTTTAGG
CCCTTCAGGCTTTGGACCTTCTGGAGGAAGTGGCACCAAGCTCCCCAAAGAGGCCACAAAGACAGCCCCACCTGCCCTGC
CTATGGATTATGATTCAGAGGAGGAGGAAGAGAGCAGGCCCATGAGTTATGATGAAAAGCTGCAGCCGAGCCTGGACATC
AACAAATTACCTGGAGAGAAGCTGGGCCGAGTTGTGCACATAATCCAAGCCAGGGAACCCTCTTTACGTGATTCAAACTC
AGAAGAGATTGAGGTTGATTTTGAAACACTCAAGCAATCCACACTTAGAGAGTTTGAGCGCTATGTCCTTTCTTGCCTAT
GTAAGAAAACCCGGAAGCCCTATACCATTAAGAAGCCTGTGGGAAAGACAAAGGAAGAACTGGCTTTGGAGAAAAAGCGG
GAATTAGAAAAGCAGTTACAAGATGCCAGCGGACAGTTCAATTCCACTAAAAAGCCCCCCAAGAGAGCAAGTGAGAAAAC
AGAGTCATCCTCTGCACAGCAAGTAGTAGTGTCACGCCTCAGTGCTTCCAGCTCCAGCTCAGATTCCAGCTCCTCCTCTT
GATCATCATCTTCTTCAGACACCAGTGATTCAGACTTAGGC

Alignment

ORF - retro_cjac_564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.31 %
• Parental protein coverage: 65.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KGVKRKADTTTPTPTAILAPGSPASPPGSLEPKAARLPPMRRESGRPIKPPRKDLPDSQQQH-QSSKKGK
          K.VKRKADTTTPTP.AILAPGSPASPPGSLEP.AA.LPPMRRESG.PIKPP.KDLPDSQQQH..SSKKGK
Retrocopy KVVKRKADTTTPTPIAILAPGSPASPPGSLEPEAAWLPPMRRESGHPIKPPCKDLPDSQQQH<LSSKKGK

Parental  LSEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFA
          LSEQLKHC..ILKELLSKKHAAYAWPFYKPVDASALGLHDY.DIIKHPMD.STVKRKMEN.D..DAQEFA
Retrocopy LSEQLKHCSSILKELLSKKHAAYAWPFYKPVDASALGLHDYLDIIKHPMDFSTVKRKMENCD*QDAQEFA

Parental  ADVRLMFSNCY-KYNPPDHDVVAMARKLQDVFEFRYAKMPDEPLEPGPLPVSTAIPPGLAKSSSESSSEE
          A.V.LMFSN...KYNPPDH.VVAMARKLQDV.EF.YAK.PDEPLEPGPLPVSTAIPPGLAK.SSESSSEE
Retrocopy AKVWLMFSNSV<KYNPPDHNVVAMARKLQDVLEFCYAKIPDEPLEPGPLPVSTAIPPGLAKPSSESSSEE

Parental  SSSESSSEEEEEEDEEDEEEE-SESSDSEEERAHRLAELQEQLRAVHEQLAALSQGPISKPKRKREKKEK
          SSSESSS...EEEDEEDEEEE..ESSDSEEERAHRLAELQEQLRAVHEQLA.LS.GPISKP.........
Retrocopy SSSESSS---EEEDEEDEEEE>GESSDSEEERAHRLAELQEQLRAVHEQLAVLSHGPISKPXXXXXXXXX

Parental  KKKRKAEKHRGRAGA-DEDDKGPRAPRPPQPKKSKKASVSGGGSAALGPSGFGPSGGSGTKLPKKATKTA
          .KK.KAEKHRG.AGA.DE.DKGP.AP.PPQPKKSKKAS.SG.GSAALGPSGFGPSGGSGTKLPK.ATKTA
Retrocopy XKKQKAEKHRG*AGA<DEEDKGPEAPCPPQPKKSKKASGSGCGSAALGPSGFGPSGGSGTKLPKEATKTA

Parental  PPALPTGYDSEEEEESRPMSYDEKRQLSLDINKLPGEKLGRVVHIIQAREPSLRDSNPEEIEIDFETLKP
          PPALP..YDSEEEEESRPMSYDEK.Q.SLDINKLPGEKLGRVVHIIQAREPSLRDSN.EEIE.DFETLK.
Retrocopy PPALPMDYDSEEEEESRPMSYDEKLQPSLDINKLPGEKLGRVVHIIQAREPSLRDSNSEEIEVDFETLKQ

Parental  STLRELERYVLSCLRKKPRKPYTIKKPVGKTKEELALEKKRELEKRLQDVSGQLNSTKKPPKKASEKTES
          STLRE.ERYVLSCL.KK.RKPYTIKKPVGKTKEELALEKKRELEK.LQD.SGQ.NSTKKPPK.ASEKTES
Retrocopy STLREFERYVLSCLCKKTRKPYTIKKPVGKTKEELALEKKRELEKQLQDASGQFNSTKKPPKRASEKTES

Parental  SSAQQVVVSRLSASSSSSDSSSSSSSSSSSDTSDSDSG
          SSAQQVVVSRLSASSSSSDSSSSS.SSSSSDTSDSD.G
Retrocopy SSAQQVVVSRLSASSSSSDSSSSS*SSSSSDTSDSDLG

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	0.00 RPM	53.38 RPM
SRP051959_heart	0.05 RPM	53.22 RPM
SRP051959_kidney	0.09 RPM	73.99 RPM
SRP051959_liver	0.02 RPM	46.18 RPM
SRP051959_lung	0.00 RPM	81.14 RPM
SRP051959_lymph_node	0.07 RPM	77.87 RPM
SRP051959_skeletal_muscle	0.00 RPM	37.74 RPM
SRP051959_spleen	0.02 RPM	74.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_564 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_564 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_564 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021566	2 retrocopies	retro_cjac_2409, retro_cjac_564 ,
Oryctolagus cuniculus	ENSOCUG00000003097	1 retrocopy	retro_ocun_710,