RetrogeneDB ID: retro_cjac_1437

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:95192345..95193018(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC7
• Ensembl ID: ENSCJAG00000004119
• Aliases: None
• Description: zinc finger, DHHC-type containing 7 [Source:HGNC Symbol;Acc:18459]

Sequence

>retro_cjac_1437
GTCATATTTAACTGATTGGCTATGCTCGCCCTGTTATCCCACCTGAGAACCATGCTCAGTGACCCTGGGCAGTACTCAAA
GGAAACACTACAAAAGAATACATGGATAGCCTGCAGCTGAAGCCTGAAAGGTGATCTACAAGTGCTCCAAGTGCTGCTAC
ATTAAACCAGAGTGTGCCCACCACTGCAGTATTTGCAAAAGATATATTCAGAAAATGGATTATCACTGCCTGTGGGAGAA
CAATTATGTAGGAAAAAAGAATCAAAGGTTTTTTGTGCTCTTCACTGTGTATGTAGCTCTGTCTTCAGTCCATGCTCTGA
TCCTCTGTGGATTCAGTTTATCTCCTGCGTCCAAGGGCAGTGGACTAAATGCAGTGACTTTTCACCTCCGATAACTGTAA
TTCTGTTGATCTTCCTGTGCCTTAAAAGTCTTCTGTTTTTCACTTTTATTACAGTTATGTTTGGCACTCAAATCCACTCC
ATAAGCAATGATGAGACGGAAATTGAGCAATTGAAAAGTGAGAAGCTCACATGAGGGCAGAGACTGTGATGGGAAGGGAT
GAAGTCTGTGCTTGGGGAATCCCCCCTCACTCCTCTGGATGAATCCCTTTGTCGGCTTCCACTTTAGGTGGCTGCCCACG
AGACCCAGAAAAGGTGGCCCAGAGTTCTCAGTG

Alignment

ORF - retro_cjac_1437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.48 %
• Parental protein coverage: 73.05 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VIFNFLAVLALSSHLRTMLTDPG-AVPKGNATKEYMESLQLKPG-EVIYKCPKCCCVKPERAHHCSICKR
          VIFN.LA.LAL.SHLRTML.DPG.AV.KGN.TKEYM.SLQLKP...VIYKC.KCC..KPE.AHHCSICKR
Retrocopy VIFN*LAMLALLSHLRTMLSDPG<AVLKGNTTKEYMDSLQLKPE<KVIYKCSKCCYIKPECAHHCSICKR

Parental  CIRKMDHHCPWVNNCVGEKNQRFFVLFTMYIALSSVHALILCG-LQFISCVRGQWTECSDFSPPVTVILL
          .I.KMD.HC.W.NN.VG.KNQRFFVLFT.Y.ALSSVHALILCG..QFISCV.GQWT.CSDFSPP.TVILL
Retrocopy YIQKMDYHCLWENNYVGKKNQRFFVLFTVYVALSSVHALILCG<IQFISCVQGQWTKCSDFSPPITVILL

Parental  TFLCLEGLLFFTFTAVMFGSQIHSICNDETEIERLKSEKPTWERRLRWEGMKSV-FGGPPSLLWMNPFVG
          .FLCL..LLFFTF..VMFG.QIHSI.NDETEIE.LKSEK.T...RL.WEGMKSV..G.PPSLLWMNPFVG
Retrocopy IFLCLKSLLFFTFITVMFGTQIHSISNDETEIEQLKSEKLT*GQRL*WEGMKSV>LGNPPSLLWMNPFVG

Parental  FHFRRLPTRPRKGSPEFSV
          FHFR.LPTRPRKG.PEFSV
Retrocopy FHFRWLPTRPRKGGPEFSV

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	6.79 RPM
SRP051959_heart	0.02 RPM	8.52 RPM
SRP051959_kidney	0.07 RPM	22.87 RPM
SRP051959_liver	0.13 RPM	5.42 RPM
SRP051959_lung	0.05 RPM	13.00 RPM
SRP051959_lymph_node	0.05 RPM	9.82 RPM
SRP051959_skeletal_muscle	0.04 RPM	12.54 RPM
SRP051959_spleen	0.06 RPM	13.11 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1437 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1437 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1437 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004119	1 retrocopy	retro_cjac_1437 ,
Callithrix jacchus	ENSCJAG00000011824	1 retrocopy	retro_cjac_934,
Echinops telfairi	ENSETEG00000016077	1 retrocopy	retro_etel_1105,
Microcebus murinus	ENSMICG00000011194	1 retrocopy	retro_mmur_1362,
Macaca mulatta	ENSMMUG00000020674	1 retrocopy	retro_mmul_1448,
Sus scrofa	ENSSSCG00000002667	1 retrocopy	retro_sscr_267,
Tursiops truncatus	ENSTTRG00000016028	1 retrocopy	retro_ttru_363,