RetrogeneDB ID: retro_cjac_516

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:35688182..35689784(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT5
• Ensembl ID: ENSCJAG00000008977
• Aliases: None
• Description: None

Sequence

>retro_cjac_516
CTTGCCTTTGATGAATTTGGGCCCCTTTCCTCATCATCAAGGATCAGAACTACAAGTCACATTTTGTGGGACTTGAGGCC
CTCAGGTCTCATAAAATGGCAGTAAAGGCAGTAGGAAATACAATGAGAACATCCCATGGACCAAATGGGCTTGATAAGAT
GATAATGGATAAGGATGGCAATTTAACTGTAACTAATGATGACACCACCACCGTAAGCATGACGGATGTTGATCATCAGA
TTGCCAAACTGATGGTGGAACTGTCCAAGTCTCAAGATGATGAAATTGGAGATGGAAACACAGGAATGGTTGTCCTGGCT
GGCACCTTGTTAGAAGAAGCTCAGCAGTTGCTAGACTAAGGCATTCACCCAATCAGAGTAGCTGATGTCTATGAGTAGGC
TGTCCACGTTGCTACTGAACACCTGGACAAGATCAGCAATAGCATCCTTGTTTACATAAAGGACACCAAACCACTGATTC
GGACTGCAAAAACCATGCTGGGCTCTGAAGTGGTCAACAGTTGTCACTGACAAATGGCTGAGATTGCTGTGAATGCCTTC
CTTACTGTAGCAGATATGGAGCAGAGAGATGTTGACTTTGAGCTTATCAAAGTAGAAGGCAAAGTGGGCAGCAGACTGGA
GGACACTACATTGATTAAGGGGGTGATTGTGGACAAGGATTTCAGTCACCCACAGATACTGAAAGAAGTGGAAGATGCTA
AGATTGCAATCTTCACATGACCATTTGTGCCACCCAAACCAAAAACAAAGCATAAGTCGGATATGACCTCCGTAGAAGAT
TATAAATCCTTCAGAAATATGAAAAGAAGAAATTTGAAGAGATAATTCAACAAATTAAAGAGACTGGTGCTAACCTAGCC
ATTTGTCAGTGGGGCTTTGATGATGAAGCAAATCACTTACTTCTTCAGAACAACTGGCCTGCGGTTCGCTGGGTAGGAGG
ACCTGAAATTGAGCTGATTGCCATTGCAGCAGGAGGGTGCATCATCCCCAGGTTCTCAGAGCTCGCATCTGAGAAGCTGG
GCTTTTCTGGTCTTGTACAGGAAATCTCACTTGGGACAACTACAGATAAAGTGCTGGTCATCGAGCAGTGTAAGAACTCC
AGAGTTGTAACGATTTTTATTAGAAGAGGAAATAAGATGATCATTGAGGAGATGAAACAATCCCTTCCCTATGCTTTGTG
TGTCATCTGGAACCTCATCCACTATAATCACATGGTGTACAGAAGAGGGACTGTTGAGATATCCTGTACGCTGGCAGTTA
GCCAAGAGGTGGGTAAGTGCCCATCTTAGAACAGTACATCATGAGAGAGTTTGACAAAGTGCTGGAGGTCATCCCCATAA
CCCTGTCTGAAAACAGTGGCATGAATCCCATCCAGACTATGACCAAAGTCCAAGCCAGACAAGTGAAGGAGATAAATCCT
GCTGTTGGCGTCAACTGTTTGCACAAGGGGACAAATGACATGAAGCAACAGCATGTCATAGAAAGCTTGATTGGCAAAAG
GCAGAAGATATCTCTTGCAACACAAATGGTTAGAATGAGCTTGGAGATTGACAACATTTGTAAGCCGGGAGAATCTGAAG
AA

Alignment

ORF - retro_cjac_516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.93 %
• Parental protein coverage: 98.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LAFDEYG-RPFLIIKDQDRKSRLMGLEALKSHIMAAKAVANTMRTSLGPNGLDKMMVDKDGDVTVTNDGA
          LAFDE.G..PFLIIKDQ..KS...GLEAL.SH.MA.KAV.NTMRTS.GPNGLDKM..DKDG..TVTND..
Retrocopy LAFDEFG<APFLIIKDQNYKSHFVGLEALRSHKMAVKAVGNTMRTSHGPNGLDKMIMDKDGNLTVTNDDT

Parental  TILSMMDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALLEEAEQLLDRGIHPIRIADGYEQAARVAI
          T..SM.DVDHQIAKLMVELSKSQDDEIGDG.TG.VVLAG.LLEEA.QLLD.GIHPIR.AD.YE.A..VA.
Retrocopy TTVSMTDVDHQIAKLMVELSKSQDDEIGDGNTGMVVLAGTLLEEAQQLLD*GIHPIRVADVYE*AVHVAT

Parental  EHLDKISDSVLVDIKDTEPLIQTAKTTLGSKVVNSCHRQMAEIAVNAVLTVADMERRDVDFELIKVEGKV
          EHLDKIS.S.LV.IKDT.PLI.TAKT.LGS.VVNSCH.QMAEIAVNA.LTVADME.RDVDFELIKVEGKV
Retrocopy EHLDKISNSILVYIKDTKPLIRTAKTMLGSEVVNSCH*QMAEIAVNAFLTVADMEQRDVDFELIKVEGKV

Parental  GGRLEDTKLIKGVIVDKDFSHPQMPKKVEDAKIAILTCPFEPPKPKTKHKLDVTSVEDYKA-LQKYEKEK
          G.RLEDT.LIKGVIVDKDFSHPQ..K.VEDAKIAI.T.PF.PPKPKTKHK.D.TSVEDYK..LQKYEK.K
Retrocopy GSRLEDTTLIKGVIVDKDFSHPQILKEVEDAKIAIFT*PFVPPKPKTKHKSDMTSVEDYKS<LQKYEKKK

Parental  FEEMIQQIKETGANLAICQWGFDDEANHLLLQNNLPAVRWVGGPEIELIAIATGGRIVPRFSELTAEKLG
          FEE.IQQIKETGANLAICQWGFDDEANHLLLQNN.PAVRWVGGPEIELIAIA.GG.I.PRFSEL..EKLG
Retrocopy FEEIIQQIKETGANLAICQWGFDDEANHLLLQNNWPAVRWVGGPEIELIAIAAGGCIIPRFSELASEKLG

Parental  FAGLVQEISFGTTKDKMLVIEQCKNSRAVTIFIRGGNKMIIEEAKRSLHDALCVIRNLIRDNRVVYGGGA
          F.GLVQEIS.GTT.DK.LVIEQCKNSR.VTIFIR.GNKMIIEE.K.SL..ALCVI.NLI..N..VY..G.
Retrocopy FSGLVQEISLGTTTDKVLVIEQCKNSRVVTIFIRRGNKMIIEEMKQSLPYALCVIWNLIHYNHMVYRRGT

Parental  AEISCALAVSQEADKCPT-LEQYAMRAFADALEVIPMALSENSGMNPIQTMTEVRARQVKERNPALGIDC
          .EISC.LAVSQE..KCP..LEQY.MR.F...LEVIP..LSENSGMNPIQTMT.V.ARQVKE.NPA.G..C
Retrocopy VEISCTLAVSQEVGKCPS<LEQYIMREFDKVLEVIPITLSENSGMNPIQTMTKVQARQVKEINPAVGVNC

Parental  LHRGTNDMKQQHVIETLIGKKQQISLATQMVRMILKIDDIRKPGESEE
          LH.GTNDMKQQHVIE.LIGK.Q.ISLATQMVRM.L.ID.I.KPGESEE
Retrocopy LHKGTNDMKQQHVIESLIGKRQKISLATQMVRMSLEIDNICKPGESEE

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	53.89 RPM
SRP051959_heart	0.00 RPM	51.11 RPM
SRP051959_kidney	0.00 RPM	62.52 RPM
SRP051959_liver	0.00 RPM	83.03 RPM
SRP051959_lung	0.00 RPM	58.90 RPM
SRP051959_lymph_node	0.00 RPM	69.93 RPM
SRP051959_skeletal_muscle	0.00 RPM	66.41 RPM
SRP051959_spleen	0.00 RPM	63.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_516 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_516 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017889	1 retrocopy	retro_btau_1432,
Callithrix jacchus	ENSCJAG00000008977	1 retrocopy	retro_cjac_516 ,
Homo sapiens	ENSG00000150753	2 retrocopies	retro_hsap_1219, retro_hsap_3230,
Gorilla gorilla	ENSGGOG00000024064	1 retrocopy	retro_ggor_2197,
Myotis lucifugus	ENSMLUG00000007977	1 retrocopy	retro_mluc_1735,
Macaca mulatta	ENSMMUG00000020112	2 retrocopies	retro_mmul_1294, retro_mmul_2033,
Monodelphis domestica	ENSMODG00000002356	1 retrocopy	retro_mdom_861,
Pan troglodytes	ENSPTRG00000016725	2 retrocopies	retro_ptro_2182, retro_ptro_834,
Tupaia belangeri	ENSTBEG00000001201	2 retrocopies	retro_tbel_1618, retro_tbel_4389,