RetrogeneDB ID: retro_cjac_830

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:12136416..12137831(+)
• Located in intron of: ENSCJAG00000012468

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC1
• Ensembl ID: ENSCJAG00000000970
• Aliases: None
• Description: histone deacetylase 1 [Source:HGNC Symbol;Acc:4852]

Sequence

>retro_cjac_830
CAGAAAGTCTGTTACTACTGTGACAGTGATGTTGGAAATTACTGTTATGGACAGGCCCACTCAAAAAAGCCTCACTGAAT
CTACACAACTCACAGTTTGTTGCTCAACTATGGTTTCTACTGAAAAAGGAAACCCGTCACCCTCACAAAGCCAATGCTGA
GGAGATGACCGAGTACCACAGTGATGAATACATTAAATTTTTGTGTTCGTCTGTCCAGATTACATGTCTGAGTACAGCAA
GCAGATGCAGAGATTCAACGTTAGTGAGGACTGTCCAATATTTGATGGCCTGTTTGAATTCTGTCATTTGTCTTCTGGTG
GCTCTGTGGCAAGTGCTGTGAAACTTAATAAGCAGCAGATGGACATTGCTGTAACTTGGGCTGGGGGCCTGCACGATGCA
AAGAAGTTCAAGGCATCTGCCTTCTGTTATATCAATGATACAATCTGGGCCACTCTGGAACTGTTAAAATATCACCAGAG
GATGCTGCATGTTGACATTGATATTCACCAGGATGATGGCATGGAAGAGGCCTTCTATATTACAGGCCAGGTCAGGACTG
CATCCTGTCATAAATATGGAGAGTACTTCCCAGGAAATGGGGACCTATGGGATACTGGGGCTGGCAAAGGCAGATATTAT
GCTGTTAACTACCTGCTCCTAGATGGGATTGATGATGAGTCCTATGACGACATTTTCAAACTGGTAATGTCCAAAGTAAT
AGAGATGTTTCTGTCCAGTGTCATGGTCTTACAGCATGGCTTGGATGCCTTGTCTAGAGATCAGTTATATTGCTTTATCT
GACTATCAAAGGGCATGCCGAGTGTGTGGAATTTGTCAAGAGCTTCAACCTGCCTATGCTGATGATGGCAGAAGGTGTTT
ACACCATTTATAATGTTGCTCAGTGCTGGAAATAAGAAATAGTCATGGCTCTGGATATGGAGATCCCTAATGAGCCTTCA
TAAAATGACTACTTTGAATACTTTGGATCATATTTCAAGCCCTACATCAGTCCTTCCAATATGACTAACCAGAACACTAA
TGACTACTTGAGAAGATCAAACAACGGCTGTTTGAGAACTTGGTAATTCAGCCCCATCCATCTACAGTCCAAATGTGTGT
GATTCCTGAGGATGCCATCCCTGAAGAGGGTGGCGATGAGACTGAAGAAGACCTTGACAAGCTCATCTCCATCTGTTTCT
CAGACAGATAAATTTCCTGTGATGAAGAGTTCTTCAGCTCTGATGAGGAGGGAGAGGGCGGCCTCAAGATCTCTCCCATG
ATCACAAAATACAAGGAGGTTAAAACAGGATGAAAAAGAGAGATTCAGAGATGAAGAAAGAAGTCACAGAAGAGCAGAAA
AACCAAGGAGGAGAAGCCAGAGGTCAAAGAGGTCACGGAGGAGGTCAAACTGGCC

Alignment

ORF - retro_cjac_830 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.29 %
• Parental protein coverage: 98.34 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLY-RKMEIYRPHKANAEEMTKYHSDDYIKFLR
          .KVCYY.D.DVGNY.YGQ.H..KPH.I..TH.LLLNYG.Y..K.E...PHKANAEEMT.YHSD.YIKFL.
Retrocopy QKVCYYCDSDVGNYCYGQAHSKKPH*IYTTHSLLLNYGFY<LKKETRHPHKANAEEMTEYHSDEYIKFLC

Parental  S-IRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLHHAKKSE
          S...PD.MSEYSKQMQRFNV.EDCP.FDGLFEFC.LS.GGSVASAVKLNKQQ.DIAV.WAGGLH.AKK..
Retrocopy S<VCPDYMSEYSKQMQRFNVSEDCPIFDGLFEFCHLSSGGSVASAVKLNKQQMDIAVTWAGGLHDAKKFK

Parental  ASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGA
          AS.FCY.ND...A.LELLKYHQR.L..DIDIH..DG.EEAFY.T..V.T.S.HKYGEYFPG.GDL.D.GA
Retrocopy ASAFCYINDTIWATLELLKYHQRMLHVDIDIHQDDGMEEAFYITGQVRTASCHKYGEYFPGNGDLWDTGA

Parental  GKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCF-NLTIKGHAKCV
          GKG.YYAVNY.L.DGIDDESY..IFK.VMSKV.EMF..S..VLQ.G.D.LS.D.L.CF..LTIKGHA.CV
Retrocopy GKGRYYAVNYLLLDGIDDESYDDIFKLVMSKVIEMFLSSVMVLQHGLDALSRDQLYCF<YLTIKGHAECV

Parental  EFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNT
          EFVKSFNLPMLM...G.YTI.NVA.CW..E...ALD.EIPNE...NDYFEYFG..FK..ISPSNMTNQNT
Retrocopy EFVKSFNLPMLMMAEGVYTIYNVAQCWK*EIVMALDMEIPNEPS*NDYFEYFGSYFKPYISPSNMTNQNT

Parental  NEY-LEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKRISICSSDKRIACEEEFSDSE
          N.Y.LEKIKQRLFENL...PH...VQM..IPEDAIPEE.GDE.EED.DK.ISIC.SD..I.C.EEF..S.
Retrocopy NDY<LEKIKQRLFENLVIQPHPSTVQMCVIPEDAIPEEGGDETEEDLDKLISICFSDR*ISCDEEFFSSD

Parental  EEGEGGRKNSSNFKKAKRVKTEDEKEKEPEEKKEVTEEEKTKEEKPEAKGVKEEVKLA
          EEGEGG.K.S....K.K.VKT....E.....KK......KTKEEKPE.K.V.EEVKLA
Retrocopy EEGEGGLKISPMITKYKEVKTG*KREIQR*RKKS-QKSRKTKEEKPEVKEVTEEVKLA

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	14.64 RPM	31.55 RPM
SRP051959_heart	0.09 RPM	12.61 RPM
SRP051959_kidney	0.04 RPM	22.72 RPM
SRP051959_liver	0.13 RPM	11.91 RPM
SRP051959_lung	0.18 RPM	25.56 RPM
SRP051959_lymph_node	0.02 RPM	39.47 RPM
SRP051959_skeletal_muscle	0.24 RPM	6.31 RPM
SRP051959_spleen	0.04 RPM	27.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_830 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_830 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_830 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Callithrix jacchus	ENSCJAG00000000970	2 retrocopies	retro_cjac_2490, retro_cjac_830 ,
Homo sapiens	ENSG00000116478	1 retrocopy	retro_hsap_826,
Gorilla gorilla	ENSGGOG00000011741	1 retrocopy	retro_ggor_676,
Myotis lucifugus	ENSMLUG00000013837	1 retrocopy	retro_mluc_283,
Macaca mulatta	ENSMMUG00000009948	2 retrocopies	retro_mmul_1085, retro_mmul_2518,
Mus musculus	ENSMUSG00000028800	1 retrocopy	retro_mmus_153,
Nomascus leucogenys	ENSNLEG00000002473	1 retrocopy	retro_nleu_259,
Pelodiscus sinensis	ENSPSIG00000004134	1 retrocopy	retro_psin_44,
Pteropus vampyrus	ENSPVAG00000013325	1 retrocopy	retro_pvam_1339,
Rattus norvegicus	ENSRNOG00000009568	3 retrocopies	retro_rnor_1091, retro_rnor_1098, retro_rnor_2457,
Sarcophilus harrisii	ENSSHAG00000008787	1 retrocopy	retro_shar_573,