RetrogeneDB ID: retro_mmul_545

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:162652081..162653106(-)
• Located in intron of: ENSMMUG00000013596

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABHD4
• Ensembl ID: ENSMMUG00000009441
• Aliases: None
• Description: abhydrolase domain-containing protein 4 [Source:RefSeq peptide;Acc:NP_001247685]

Sequence

>retro_mmul_545
ATGGCCGATGATCTGGAGCAGCATCCTCAAGGCTGGCTGAGTAATTGGCTGCCCACGTGGCGCCCCACTTCCATGTCTCA
GCTGAAGAATGTGGAAGCCAGGATCCTCCAGTGTCTCCAGAATAAGTTCCTGGCCAGATATGTATCCCTCCCAAACCAGA
ATAAGATCTGGACAGTGACTATGAGCCCCGAGCAAAAGGACCACACCCCGCTGGTGATGGTGCACGGTTTTGGGGGCAGC
GTGGGCCTCTGGGTCCTCAACATGGACTCACTGAGTGCCCGCTGCACACTGCACACCTTCCATCTGCTTGACTTCGGGCG
ATGCTCAAGGCCAGCATTCCCGAGGGACCTGGAGGGGGCTGAGGATGAGTTTGTGACATCGATAGAGACGTGGCAGGAGA
CCATAGGGATCCCCAGCATGACCCTCCTGGGGCACAGTTTGGGAGGATTCCTGGCCACTTCTTACTCAATCAAGTACCCT
GATAGAGTTAAACACCTCATCCTGGTGGACTCATGGGGCTTTCCCCTCTGACCAACTAACCCCAGTGAGATCCGTGCACC
CCCAACCTGGGTCAAAGCTGTGGCATCTGTCCTAGGACGTTCCAATCCATTGGCTGTTCTTCGAGTAGCTGGGCCCTGGG
GGCCTGGCCTGGTGCAGCGATTCTCGCCGGATTCAAACGCAAGTTTGTAGACTTCTTTGAAGATGATACCATATCAGAGT
ATATCTATCACTGCAATGCACAGAATCCCAGTGGTGAGACGGTATTCAAAGCCATGATGGAGTCCTTTGGCTGGGCCCAG
CACCCTATGCTGGAGCGAATTCACTTGATTTGAAAAGGTGTGCCCATCACCATGATCTATGGGTCCAACACCTGGATAGA
TACCAGTACGGGAAAAAAGGTGAAGATGCAGGGGCCGGATTCCTATGTCGGAGACATGGAGATTGAGGGTGCATCTCACC
ACGTCTATGCTGACCAGCCACACATCTTCAATGCTGTAGTGGAGAAGATCTGCGACTCAGTTGAT

Alignment

ORF - retro_mmul_545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADDLEQQPQGWLSSWLPTWRPTSMSQLKNVEARILQCLQNKFLARYVSLPNQNKIWTVTVSPEQKDRTP
          MADDLEQ.PQGWLS.WLPTWRPTSMSQLKNVEARILQCLQNKFLARYVSLPNQNKIWTVT.SPEQKD.TP
Retrocopy MADDLEQHPQGWLSNWLPTWRPTSMSQLKNVEARILQCLQNKFLARYVSLPNQNKIWTVTMSPEQKDHTP

Parental  LVMVHGFGGGVGLWILNMDSLSARRTLHTFDLLGFGRSSRPAFPRDPEGAEDEFVTSIETWRETMGIPSM
          LVMVHGFGG.VGLW.LNMDSLSAR.TLHTF.LL.FGR.SRPAFPRD.EGAEDEFVTSIETW.ET.GIPSM
Retrocopy LVMVHGFGGSVGLWVLNMDSLSARCTLHTFHLLDFGRCSRPAFPRDLEGAEDEFVTSIETWQETIGIPSM

Parental  ILLGHSLGGFLATSYSIKYPDRVKHLILVDPWGFPLRPTNPSEIRAPPTWVKAVASVLGRSNPLAVLRVA
          .LLGHSLGGFLATSYSIKYPDRVKHLILVD.WGFPL.PTNPSEIRAPPTWVKAVASVLGRSNPLAVLRVA
Retrocopy TLLGHSLGGFLATSYSIKYPDRVKHLILVDSWGFPL*PTNPSEIRAPPTWVKAVASVLGRSNPLAVLRVA

Parental  GPWGPGLVQRFRPD-FKRKFADFFEDDTISEYIYHCNAQNPSGETAFKAMMESFGWARRPMLERIHLIRK
          GPWGPGLVQRF.PD.FKRKF.DFFEDDTISEYIYHCNAQNPSGET.FKAMMESFGWA..PMLERIHLI.K
Retrocopy GPWGPGLVQRFSPD<FKRKFVDFFEDDTISEYIYHCNAQNPSGETVFKAMMESFGWAQHPMLERIHLI*K

Parental  DVPITMIYGSNTWIDTSTGKKVKMQRPDSYVRDMEIEGASHHVYADQPHIFNAVVEEICDSVD
          .VPITMIYGSNTWIDTSTGKKVKMQ.PDSYV.DMEIEGASHHVYADQPHIFNAVVE.ICDSVD
Retrocopy GVPITMIYGSNTWIDTSTGKKVKMQGPDSYVGDMEIEGASHHVYADQPHIFNAVVEKICDSVD

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	0.22 RPM	4.59 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	9.68 RPM
SRP007412_cerebellum	0.19 RPM	5.04 RPM
SRP007412_heart	0.24 RPM	11.36 RPM
SRP007412_kidney	0.70 RPM	22.42 RPM
SRP007412_liver	0.44 RPM	12.98 RPM
SRP007412_testis	7.35 RPM	31.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_545 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_545 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_545 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000009441	1 retrocopy	retro_mmul_545 ,
Ictidomys tridecemlineatus	ENSSTOG00000023335	1 retrocopy	retro_itri_1727,