RetrogeneDB ID: retro_mmul_1836

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:68856840..68857477(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HORMAD2
• Ensembl ID: ENSMMUG00000004713
• Aliases: None
• Description: HORMA domain containing 2 [Source:HGNC Symbol;Acc:28383]

Sequence

>retro_mmul_1836
GTATTTCCCAATAAGATATCACCTGAACACCAGTGTTTGGTGTTAGTGAAGAGGCTCCTAGCAGTTTCAGTATCCTGTAT
CACATATTTGAGAGGAATATTTCCAGAATGTTCTTATAGAACCAGATATCTAGATGATCTTTTGGTCAAAATACTGAGAG
AAGATAAAAATTGCCCAGGATCTACACAGTTACTGAAATAGATGCTAGGACATTATGATGCTTTACAGAAAAAATACCTA
AGGATGGCTGTTCTAGCTATATACACAAACCCAGAAGATCCTCAGACAATTTCAGAATGTTACCATTTCAAATTCAAATA
TGCCAACAATGGACCACTCATGGACTTACTTCGTAAGTAAAAACCAAAGCAACAAATCTAGCATGTCATGTACTGATACC
AAGAAAGCAAGCATTCTCCTTATTCGCAAGATTGATATCCTAATGCAAAATCTGGGGCCTTTACCTAATGATGTTTGTTT
GACCATGAAACCTTTTTATTATGATGAACTTACACCCCTAGATTACCAGCCTCTCGGTTTTAAGGATGGTGATTGTGAAG
GAGTTATATTTGAAGGGAAGCCTAGGTATTTAAATGTGTGTGAAGTCTCAACACCTTTTCACACCTTCAAAGTAAAA

Alignment

ORF - retro_mmul_1836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.39 %
• Parental protein coverage: 69.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VFPSQITNEHESLKMVKKLFATSISCITYLRGLFPESSYGERHLDDLSLKILREDKKCPGSLHIIRWIQG
          VFP..I..EH..L..VK.L.A.S.SCITYLRG.FPE.SY..R.LDDL..KILREDK.CPGS........G
Retrocopy VFPNKISPEHQCLVLVKRLLAVSVSCITYLRGIFPECSYRTRYLDDLLVKILREDKNCPGSTQLLK*MLG

Parental  CFDALEKRYLRMAVLTLYTNPMGSEKVTE-MYQFKFKYTKEGATMDFDS-HSSSTSFESGTNNEDIKKAG
          ..DAL.K.YLRMAVL..YTNP.......E.M..F.........T....S..S...S..S.....D.KKA.
Retrocopy HYDALQKKYLRMAVLAIYTNPEDPQTISE<MLPFQIQICQQWTTHGLTS<VSKNQSNKSSMSCTDTKKAS

Parental  VLLIRKLYILMQDLEPLPNNVVLTMKLHYYNAVTPHDYQPLGFKEEVNSHFLLFDKEPINVQVGFVSTGF
          .LLIRK..ILMQ.L.PLPN.V.LTMK..YY...TP.DYQPLGFK.........F...P....V..VST.F
Retrocopy ILLIRKIDILMQNLGPLPNDVCLTMKPFYYDELTPLDYQPLGFKDG-DCEGVIFEGKPRYLNVCEVSTPF

Parental  HSMKVK
          H..KVK
Retrocopy HTFKVK

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	0.00 RPM	0.78 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.79 RPM
SRP007412_cerebellum	0.00 RPM	0.52 RPM
SRP007412_heart	0.00 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	1.76 RPM
SRP007412_liver	0.00 RPM	1.23 RPM
SRP007412_testis	0.00 RPM	63.82 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1836 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1836 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1836 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3612

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000000213	1 retrocopy	retro_etel_240,
Macaca mulatta	ENSMMUG00000004713	1 retrocopy	retro_mmul_1836 ,
Otolemur garnettii	ENSOGAG00000015658	3 retrocopies	retro_ogar_2155, retro_ogar_3422, retro_ogar_3438,