RetrogeneDB ID: retro_mmul_892

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:98921205..98921580(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.13905
• Ensembl ID: ENSMMUG00000002050
• Aliases: None
• Description: platelet-activating factor acetylhydrolase IB subunit beta [Source:RefSeq peptide;Acc:NP_001244668]

Sequence

>retro_mmul_892
ATGAGCCAAGCAGACTCAAACACAGCAGCTATTCCACATGCAGTGGAAGATATTCAAGGAGACGACAGATGGATATCTCA
GCACAACAGATTTGTCCTGGATGGTAAAGACAAAAAGCCTAATGTTCTGTTTGTTGGAGACCCCATGGTGTAGTTAATGC
AGCAACATGAGATATGGCGAGAGCTTTTTTCCCCATTTCACGCACTGAATTTTGGAACTGAGGAAGATACAAGACATGTT
TTATAGAAACGAAAGAGTAGAGAACTGGAGAATATTAAACCTAAGGTCATTGTTGTCTGGGTAGGAACAAACAACCATGA
AAATACAGCAGTAGAGTTAGAAAGTGGGATCAAGGCCATCATTCACTCTATCAAT

Alignment

ORF - retro_mmul_892 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 55.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSQGDSNPAAIPHAAEDIQGDDRWMSQHNRFVLDCKDKEPDVLFVGDSMVQLMQQYEIWRELFSPLHALN
          MSQ.DSN.AAIPHA.EDIQGDDRW.SQHNRFVLD.KDK.P.VLFVGD.MV.LMQQ.EIWRELFSP.HALN
Retrocopy MSQADSNTAAIPHAVEDIQGDDRWISQHNRFVLDGKDKKPNVLFVGDPMV*LMQQHEIWRELFSPFHALN

Parental  FGIGGDTTRHVLWRLKNGELENIKPKVIVVWVGTNNHENTAEEVAGGIEAIVQLIN
          FG...D.TRHVL...K..ELENIKPKVIVVWVGTNNHENTA.E...GI.AI...IN
Retrocopy FGTEED-TRHVL*KRKSRELENIKPKVIVVWVGTNNHENTAVELESGIKAIIHSIN

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	0.11 RPM	64.88 RPM
SRP007412_brain_prefrontal_cortex	0.32 RPM	50.77 RPM
SRP007412_cerebellum	0.00 RPM	59.67 RPM
SRP007412_heart	0.00 RPM	18.25 RPM
SRP007412_kidney	0.00 RPM	22.89 RPM
SRP007412_liver	0.00 RPM	8.87 RPM
SRP007412_testis	0.87 RPM	31.13 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_892 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_892 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_892 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1148
Pan troglodytes	retro_ptro_782
Gorilla gorilla	retro_ggor_893
Pongo abelii	retro_pabe_953
Callithrix jacchus	retro_cjac_3325

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008628	2 retrocopies	retro_amel_1145, retro_amel_818,
Canis familiaris	ENSCAFG00000013226	1 retrocopy	retro_cfam_1335,
Callithrix jacchus	ENSCJAG00000012698	1 retrocopy	retro_cjac_3325,
Dipodomys ordii	ENSDORG00000011274	1 retrocopy	retro_dord_560,
Felis catus	ENSFCAG00000029945	1 retrocopy	retro_fcat_270,
Homo sapiens	ENSG00000168092	2 retrocopies	retro_hsap_1148, retro_hsap_4661,
Gorilla gorilla	ENSGGOG00000028197	2 retrocopies	retro_ggor_2893, retro_ggor_893,
Macaca mulatta	ENSMMUG00000002050	2 retrocopies	retro_mmul_2481, retro_mmul_892 ,
Macaca mulatta	ENSMMUG00000012172	1 retrocopy	retro_mmul_18,
Mustela putorius furo	ENSMPUG00000004246	1 retrocopy	retro_mputfur_898,
Nomascus leucogenys	ENSNLEG00000007337	2 retrocopies	retro_nleu_1096, retro_nleu_946,
Pongo abelii	ENSPPYG00000003907	2 retrocopies	retro_pabe_3621, retro_pabe_953,
Pan troglodytes	ENSPTRG00000004318	2 retrocopies	retro_ptro_3097, retro_ptro_782,
Rattus norvegicus	ENSRNOG00000018032	1 retrocopy	retro_rnor_2585,
Sarcophilus harrisii	ENSSHAG00000011403	1 retrocopy	retro_shar_617,