RetrogeneDB ID: retro_mmul_2560

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:36122568..36122935(-)
• Located in intron of: ENSMMUG00000013493

Retrocopy information

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

Parental gene information

• Parental gene symbol: TDGF1
• Ensembl ID: ENSMMUG00000003088
• Aliases: None
• Description: teratocarcinoma-derived growth factor 1 [Source:HGNC Symbol;Acc:11701]

Sequence

>retro_mmul_2560
TCACAGTTTGTGCCATCCATGGGGATAAAGGACAGTAAGGAACAAAACAGAACCTGCTGTCTAAATGGGGGAACCTACAC
GCTGGGGTGCTTTCGTGTCTGCCCTTCCTCCTATGGATGGAACTGCGACCTTGTTGTGTGCAGAGAGAGCTGTGAGTCTG
TGCACCATGACACCTGGCTGCCCAAGAAGTATTTATGTGTAAATACTGGCATGGCCAACCCCACGGCTTTCCTGAGGCAT
TTCTACCTGGTTGTGATGGTCTTGTGATGGATGAGCACCTCATGGCTCTCAGGACTCTGGAATACTACCATCTACATGTA
CCACTTTTATGCTAGCTGGCATGTGCCGTTCCATACAAAGTTACTAT

Alignment

ORF - retro_mmul_2560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SQHVSPMGIQNSKELNRTCCLNGGTCMLGSFCACPPSFYGRNCEHDVRKENCGSVPHDTWLPKK-CSLCK
          SQ.V..MGI..SKE.NRTCCLNGGT..LG.F..CP.S.YG.NC...V..E.C.SV.HDTWLPKK....CK
Retrocopy SQFVPSMGIKDSKEQNRTCCLNGGTYTLGCFRVCPSS-YGWNCDLVVCRESCESVHHDTWLPKK<VFMCK

Parental  CWHGQLRCFPQAFLPGCDGLVMDEHLVASRTPE-LPPSARTAFMLAGICLSIQSYY
          .WHGQ...FP.AFLPGCDGLVMDEHL.A.RT.E...PS..T.FMLAG.C.SIQSYY
Retrocopy YWHGQPHGFPEAFLPGCDGLVMDEHLMALRTLE<ILPSTCTTFMLAGMCRSIQSYY

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	0.11 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.08 RPM
SRP007412_cerebellum	0.00 RPM	0.13 RPM
SRP007412_heart	0.00 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	1.29 RPM
SRP007412_liver	0.28 RPM	0.04 RPM
SRP007412_testis	0.00 RPM	0.08 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2560 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2560 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4804
Pan troglodytes	retro_ptro_3194
Gorilla gorilla	retro_ggor_2990
Callithrix jacchus	retro_cjac_4151

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002174	3 retrocopies	retro_cjac_1594, retro_cjac_4151, retro_cjac_938,
Felis catus	ENSFCAG00000014508	1 retrocopy	retro_fcat_714,
Homo sapiens	ENSG00000241186	7 retrocopies	retro_hsap_1999, retro_hsap_2393, retro_hsap_2709, retro_hsap_3415, retro_hsap_3956, retro_hsap_4737, retro_hsap_4804,
Gorilla gorilla	ENSGGOG00000003453	5 retrocopies	retro_ggor_1447, retro_ggor_1815, retro_ggor_2307, retro_ggor_2943, retro_ggor_2990,
Loxodonta africana	ENSLAFG00000009140	4 retrocopies	retro_lafr_1037, retro_lafr_1067, retro_lafr_757, retro_lafr_871,
Microcebus murinus	ENSMICG00000016492	1 retrocopy	retro_mmur_635,
Macaca mulatta	ENSMMUG00000003088	6 retrocopies	retro_mmul_1744, retro_mmul_2290, retro_mmul_2560 , retro_mmul_742, retro_mmul_770, retro_mmul_967,
Mustela putorius furo	ENSMPUG00000015167	1 retrocopy	retro_mputfur_961,
Mus musculus	ENSMUSG00000032494	3 retrocopies	retro_mmus_1429, retro_mmus_1544, retro_mmus_1908,
Nomascus leucogenys	ENSNLEG00000006143	6 retrocopies	retro_nleu_1649, retro_nleu_2124, retro_nleu_2179, retro_nleu_2317, retro_nleu_2519, retro_nleu_535,
Otolemur garnettii	ENSOGAG00000017039	1 retrocopy	retro_ogar_2611,
Pan troglodytes	ENSPTRG00000014854	7 retrocopies	retro_ptro_1333, retro_ptro_1749, retro_ptro_1831, retro_ptro_2319, retro_ptro_2685, retro_ptro_3153, retro_ptro_3194,
Tarsius syrichta	ENSTSYG00000013609	2 retrocopies	retro_tsyr_295, retro_tsyr_574,
Tursiops truncatus	ENSTTRG00000017299	1 retrocopy	retro_ttru_441,