RetrogeneDB ID: retro_mmul_1439

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:75642531..75643017(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED2
• Ensembl ID: ENSMMUG00000031491
• Aliases: None
• Description: None

Sequence

>retro_mmul_1439
GTCACCTCAGGCACCAAGATGGGCCTCATCTTAGAAGGTGGCTTCCTGGACAGCAACGTGGAGATTACAGGACCTGAGAA
GAAAGGGATTTGTAAAGGAGACCAAGAATCCAGTGGGAAATACACATTTGCTGCTCACGTGGATGGAACACATACATTTT
GTTTTAGTAACCGAGTGTCCGCCATAACTCCAAAGATAGTGATATTCACCACTGATATTGGGGACGCTCCAAAAGGAGAA
GATATGAAAACAGAAGCTCACCAGAACAAGCTAGAAGAAATGATCAGTGAACTGGCTGTGGCCATGACAGCTTTACAGCA
TGAAGAGGAATACACGAAAGTCTGGCAGAGGATACACAGAGCCATCAGCGACAACACAAACAGCCCAGTGGTCCTTCGGT
CCCTCTTTGAAGCTCTTGTTCTAATCACCATGACATTGGGACACATCTACTACCTGAAGAGATTTTTTGAAGTCCAGAGG
GTTGTT

Alignment

ORF - retro_mmul_1439 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.15 %
• Parental protein coverage: 82.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTSGTKMGLIFEVAEGGFLDIDVEITGPDNKGIYKGDRESSGKYTFAAHMDGTYKFCFSNRMSTMTPKIV
          VTSGTKMGLI....EGGFLD..VEITGP..KGI.KGD.ESSGKYTFAAH.DGT..FCFSNR.S..TPKIV
Retrocopy VTSGTKMGLIL---EGGFLDSNVEITGPEKKGICKGDQESSGKYTFAAHVDGTHTFCFSNRVSAITPKIV

Parental  MFTIDIGEAPKGQDMETEAHQNKLEEMINELAVAMTAVKHEQEYMEVRERIHRAINDNTNSRVVLWSSLK
          .FT.DIG.APKG.DM.TEAHQNKLEEMI.ELAVAMTA..HE.EY..V..RIHRAI.DNTNS.VVL.S...
Retrocopy IFTTDIGDAPKGEDMKTEAHQNKLEEMISELAVAMTALQHEEEYTKVWQRIHRAISDNTNSPVVLRSLFE

Parental  LFVLVAMTLGQIYYLKRFFEVRRVV
          ..VL..MTLG.IYYLKRFFEV.RVV
Retrocopy ALVLITMTLGHIYYLKRFFEVQRVV

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	74.74 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	54.50 RPM
SRP007412_cerebellum	0.00 RPM	66.77 RPM
SRP007412_heart	0.06 RPM	76.02 RPM
SRP007412_kidney	0.00 RPM	98.82 RPM
SRP007412_liver	0.00 RPM	86.49 RPM
SRP007412_testis	0.08 RPM	35.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1439 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1439 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1439 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2793
Gorilla gorilla	retro_ggor_1943
Pongo abelii	retro_pabe_2227
Callithrix jacchus	retro_cjac_1392

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015262	2 retrocopies	retro_amel_1923, retro_amel_337,
Bos taurus	ENSBTAG00000039630	2 retrocopies	retro_btau_52, retro_btau_819,
Choloepus hoffmanni	ENSCHOG00000012728	6 retrocopies	retro_chof_104, retro_chof_1277, retro_chof_2323, retro_chof_2601, retro_chof_2709, retro_chof_981,
Callithrix jacchus	ENSCJAG00000020466	1 retrocopy	retro_cjac_1392,
Echinops telfairi	ENSETEG00000000556	2 retrocopies	retro_etel_2109, retro_etel_2154,
Homo sapiens	ENSG00000086598	1 retrocopy	retro_hsap_2793,
Gorilla gorilla	ENSGGOG00000028536	1 retrocopy	retro_ggor_1943,
Macaca mulatta	ENSMMUG00000031491	2 retrocopies	retro_mmul_1439 , retro_mmul_613,
Mustela putorius furo	ENSMPUG00000001598	1 retrocopy	retro_mputfur_1241,
Mus musculus	ENSMUSG00000029390	2 retrocopies	retro_mmus_1361, retro_mmus_3262,
Nomascus leucogenys	ENSNLEG00000001652	2 retrocopies	retro_nleu_2454, retro_nleu_2794,
Otolemur garnettii	ENSOGAG00000009192	1 retrocopy	retro_ogar_2548,
Pongo abelii	ENSPPYG00000005090	3 retrocopies	retro_pabe_1919, retro_pabe_2227, retro_pabe_3597,