RetrogeneDB ID: retro_mmul_1487

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:179128733..179129274(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPS2
• Ensembl ID: ENSMMUG00000006207
• Aliases: None
• Description: None

Sequence

>retro_mmul_1487
TCACCAGAGGAGACGGAAGGAACAAATTCTGACGCTGCAGGAGAAGCTGTGGGCCCGGCAGAAAGAGAAGGACCAGCTTT
TTCTGCAGCTCTAGAAAGTTTCCATGAGGAAGAAAAACCGAGGCGAAAGGAGCAGAGCGACCTGACCTCTCACATCCGCT
GTGGGCCGGCAGAGCCCGATTATTCAGGCGGGGACTCGCCGCCTCCTCCGCGTGCGGGCAGCAGGCAGCGCTGGAGGGCA
CGATCGCCCGGGCATTGTCATAGCAGCTGACCCAGCCAAGCAGATTTTCAGACCCCACGTACTTGCGACCCGGAAGTCCG
TGGGCTCAGCGGCGGCTTTTGCAGGGACCCCAGAGCAGGCAGCCTGGGCGGTGCCGCTGGGACTGCTCAGCCCCCCCCAC
CTCAGTACGGACCCACATAGCTAGCCTATGGCCCTAGTCAGCAGCTCAGAGCAGTTCAGTGCTCCCTGAGGTGCATAAAT
GTCCCAGCCACAGCCTTATGATCTGCTGGGCCACTTTCAGCACACCCAAACAGGGTTCCTC

Alignment

ORF - retro_mmul_1487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.4 %
• Parental protein coverage: 56.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SLEET-KEQILKLEEKLLALQEEKHQLFLQLKKVLHEEEKRRRKEQSDLT-TLTSAAYQQSLTVHTGTHL
          S.EET.KEQIL.L.EKL.A.Q.EK.QLFLQL.KV.....K..R.E.S..T..LTSA...QS.....GT..
Retrocopy SPEET>KEQILTLQEKLWARQKEKDQLFLQL*KV--SMRKKNRGERSRAT*PLTSAVGRQSPIIQAGTRR

Parental  L---SMQGSPGGHNRPGTLMAADRAKQMFGPQVLTTRHYV-GSAAAFAGTPEHGQFQGSPGGAYGTAQPP
          L......GS.GGH.RPG...AAD.AKQ.F.P.VL.TR..V.G....F...P......GS.GGA.GTAQ..
Retrocopy LLRVRAAGSAGGHDRPGIVIAADPAKQIFRPHVLATRKSV<GLSGGFCRDPR----AGSLGGAAGTAQXX

Parental  -PHYGPTQPAYSPSQQLRA-PSAFPTVQY-LSQPQPQPYAVHGHFQPTQTGFL
          .P.YGPT..AY.PSQQLRA..S..P.V....SQP..QPY...GHFQ.TQTGFL
Retrocopy XPQYGPT*LAYGPSQQLRA<SSVLPEVHK<MSQP--QPYDLLGHFQHTQTGFL

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	80.12 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	133.51 RPM
SRP007412_cerebellum	0.00 RPM	92.79 RPM
SRP007412_heart	0.00 RPM	60.24 RPM
SRP007412_kidney	0.00 RPM	75.59 RPM
SRP007412_liver	0.00 RPM	64.60 RPM
SRP007412_testis	0.00 RPM	190.92 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1487 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1487 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1487 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2738
Pan troglodytes	retro_ptro_1852
Gorilla gorilla	retro_ggor_1907

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000006207	1 retrocopy	retro_mmul_1487 ,