RetrogeneDB ID: retro_mmul_2325

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:26402240..26402946(-)
• Located in intron of: ENSMMUG00000008028

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMP12
• Ensembl ID: ENSMMUG00000004250
• Aliases: None
• Description: None

Sequence

>retro_mmul_2325
GGCCATTCCTTGGGTCTTGGCCACTCCAAAGATCCAAAAGCTATTTTTTCTCTCTCTACAGTTATGTTGATCCAACCAGA
TTTTGCCTCTCTACTGATGACATCTATGACATTCAGTTTCTCTGTGGAAGCCCATAAAAGCATCAACCCCTGTCACACCC
TTACACTCTAAAACCTGCTACCTGTGACTCCAAGTTAAGCTTTGATGCTGTCACTACAATTGAAGGAAAAATCTTTTTCT
TTAAAGACAGGTTTTTTTGGTGGAAGCTTCCTGAACTATCAAAGAGCAGTGTTAGTTTAATTTCTTCCTTACGGCTGATC
TTGTCATCTGGCATTCAAGCTGCTTATAAAATTGGATCCAGGAGTCAAATTCTTCTTTTTAAAGATGAAAGTACTCATTA
ATCAGTCGTTTAAAACCAGATGATCACAAGAGGATATATTCTCTGAGCTTCCCTGTCTCTGTGAAAAGACGTGATGGTGC
CATTTTTAATTCACTTAACTACAAGACCTACTTCTTTGTGCATAAACAATATTGGAGGTGAGATGAGAAAAGGCCATTCA
TGAACCCTGATTATCCTGTACTAGTTACCAAGAAATTTCTGGGAATTAGACCCCAAATTGATGCAGTCTTCTACTCTAAA
GAATACTACTGTGTCTTCTAAGGTTGTAATCAAGTTGAATATGACATACTAACCAATTGTGTCACC

Alignment

ORF - retro_mmul_2325 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.34 %
• Parental protein coverage: 50.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GHSLGLGHSSDPKAIM-FPTYKYVDINTFHLSADDIRGIQSLYGGPKEHQPMPQPDDLEPALCDPNLSFD
          GHSLGLGHS.DPKAI..F..Y.YVD...F.LS.DDI..IQ.L.G.P..HQP...P..L.PA.CD..LSFD
Retrocopy GHSLGLGHSKDPKAIF<FSLYSYVDPTRFCLSTDDIYDIQFLCGSP*KHQPLSHPYTLKPATCDSKLSFD

Parental  AVTTVGDKIFFFKDRFFLLKLSERPGTSVDLISSLWPTLPSGIEAAYEIKARNQVFLFKDD-KYWLISNL
          AVTT...KIFFFKDRFF..KL.E....SV.LISSL...L.SGI.AAY.I..R.Q..LFKD..KY.LIS.L
Retrocopy AVTTIEGKIFFFKDRFFWWKLPELSKSSVSLISSLRLILSSGIQAAYKIGSRSQILLFKDE<KYSLISRL

Parental  RPQSDYPKSIHSFGFPDFVKKIDAAVFNPHFYRTYFFVDNQYWRYDERRQMMDPGYPKLITKNFRGIGPK
          .P..D..K.I.S..FP..VK..D.A.FN...Y.TYFFV..QYWR.DE.R..M.P.YP.L.TK.F.GI.P.
Retrocopy KP--DDHKRIYSLSFPVSVKRRDGAIFNSLNYKTYFFVHKQYWR*DEKRPFMNPDYPVLVTKKFLGIRPQ

Parental  IDAVFYSKNKYYYFFQGSNQFEYDFLLQRIT
          IDAVFYSK..YY..F.G.NQ.EYD.L....T
Retrocopy IDAVFYSK-EYYCVF*GCNQVEYDILTNCVT

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	0.00 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.04 RPM	0.11 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2325 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2325 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2325 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008413	6 retrocopies	retro_chof_1424, retro_chof_1611, retro_chof_2207, retro_chof_325, retro_chof_595, retro_chof_645,
Equus caballus	ENSECAG00000019445	1 retrocopy	retro_ecab_153,
Loxodonta africana	ENSLAFG00000010062	1 retrocopy	retro_lafr_147,
Macaca mulatta	ENSMMUG00000004250	1 retrocopy	retro_mmul_2325 ,
Otolemur garnettii	ENSOGAG00000010221	1 retrocopy	retro_ogar_965,