RetrogeneDB ID: retro_mmul_1448

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:98113608..98114298(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC7
• Ensembl ID: ENSMMUG00000020674
• Aliases: None
• Description: zinc finger, DHHC-type containing 7 [Source:HGNC Symbol;Acc:18459]

Sequence

>retro_mmul_1448
TACTCTGTGGTCAATGGGGTCATCTTTAACTACTTGGCCGCGTTTGCCCTGTTGTCCCACCTGAGAACCATGCTCACCGA
CCCCGGGGCAGTACCCAGAGGAAATGCTACAAAAGAATACATGGAGAGTTTGCAGCTGAAGCCCAGGGAAGTGATCTACA
AGTGCCCCCAAGTGCTGCTGTATCAAACCAGAGCTCACCCACCATAGCAGTATTTGCAAAAGACATATTAGGAAAATGGA
TCATCACTGCCTGTGGGTGAACAATTGTGTAGGAGAAAAGAATCAAAGATGTTTTGAGCTCTTCACTATGTATATAGCTC
TGTCTTCAGTCCATGCCCTGATTCTCTGTGGATTTCAGTTTATCACCTGCATCTGAGGCAGTGGACTGAATGCAGTGATT
TTTCACCTCCATTCACTGTAATCCTGTTGACCTTCCTGTGCCTGGAGGGTCTTCTGTTTTTCACTTTCACTGCAGTTATA
TTTGGCACCCAAATCCACTCCATATGCAATGATGAGAGGGAGATCCAGTGATTGAAAAGCGAGAAGCCCACATGGGAGTG
GAGGCTGCCCAGGAAGGGATGAAATCAGTCCTTAGGGACCCTGTTACTCCCCTGGATGAATCCCTTTGTCAGCTTCTGTT
TTAGGCGACTGCCCAGGAGACCCAGAAAAGGCGGTCTGGAGTTCTCAGTG

Alignment

ORF - retro_mmul_1448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.54 %
• Parental protein coverage: 74.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YSVVNGVIFNCLAVLALSSHLRTMLTDPGAVPKGNATKEYMESLQLKPGEVIYKCP-KCCCIKPERAHHC
          YSVVNGVIFN.LA..AL.SHLRTMLTDPGAVP.GNATKEYMESLQLKP.EVIYKCP.KCCCIKPE..HH.
Retrocopy YSVVNGVIFNYLAAFALLSHLRTMLTDPGAVPRGNATKEYMESLQLKPREVIYKCP>KCCCIKPELTHHS

Parental  SICKRCIRKMDHHCPWVNNCVGEKNQRFFVLFTMYIALSSVHALILCGFQFISCVRG-QWT--GKFPGCV
          SICKR.IRKMDHHC.WVNNCVGEKNQR.F.LFTMYIALSSVHALILCGFQFI.C..G.QWT....F....
Retrocopy SICKRHIRKMDHHCLWVNNCVGEKNQRCFELFTMYIALSSVHALILCGFQFITCI*G<QWTECSDFSPPF

Parental  SFLAVHAICSEGLLFFTFTAVMFGTQIHSICNDETEIERLKSEKPTWERRLRWEGMKSVFGGPPSLLWMN
          ........C.EGLLFFTFTAV.FGTQIHSICNDE.EI..LKSEKPTWE.RL...G.....G....L.WMN
Retrocopy TVILLTFLCLEGLLFFTFTAVIFGTQIHSICNDEREIQ*LKSEKPTWEWRLPRKG*NQSLG-TLLLPWMN

Parental  PFVGFRFRRLPTRPRKGGPEFSV
          PFV.F.FRRLP.RPRKGG.EFSV
Retrocopy PFVSFCFRRLPRRPRKGGLEFSV

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
SRP007412_brain	1.90 RPM	24.88 RPM
SRP007412_brain_prefrontal_cortex	1.11 RPM	32.05 RPM
SRP007412_cerebellum	1.74 RPM	25.77 RPM
SRP007412_heart	0.06 RPM	27.15 RPM
SRP007412_kidney	2.23 RPM	27.70 RPM
SRP007412_liver	0.71 RPM	14.73 RPM
SRP007412_testis	0.00 RPM	16.06 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1448 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1448 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1448 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,
Echinops telfairi	ENSETEG00000016077	1 retrocopy	retro_etel_1105,
Microcebus murinus	ENSMICG00000011194	1 retrocopy	retro_mmur_1362,
Macaca mulatta	ENSMMUG00000007373	1 retrocopy	retro_mmul_1288,
Macaca mulatta	ENSMMUG00000020674	1 retrocopy	retro_mmul_1448 ,
Sus scrofa	ENSSSCG00000002667	1 retrocopy	retro_sscr_267,
Tursiops truncatus	ENSTTRG00000016028	1 retrocopy	retro_ttru_363,