RetrogeneDB ID: retro_mmul_704

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214731354:16291..16917(+)
• Located in intron of: ENSMMUG00000003765

Retrocopy information

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

Parental gene information

• Parental gene symbol: DHFR
• Ensembl ID: ENSMMUG00000018283
• Aliases: None
• Description: None

Sequence

>retro_mmul_704
TTCCGGCCAATTTTGGCCGCGCGTTCTGGTGTAGCGAGCGGGCTCGGAGGTGCTCACCGCTGCTGTCATGGTTCGTTTGC
TAAACTGCATCGTCGCTGTGTCCCAGAACACGGGCATTAGCAAGAACGGGGACCTGCCCTGGCCGCTGCTCAGGAATGAA
TTTAGGTATTTCCAGAGAATGACACAAACTCTTCAGGAGAAGGTAAACAGAATCTGGTGTTACATGTAGGAAGATCTGGT
TCTCCATTCCGGAGAAGAATCGACCTTTAAAGGATAGAATTAATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCACAA
GGAGCTCATTCTCTTGCCAGATGTCTGGATGATATCTTAAAACTTACTGAACAACCAGAATTAGCAAATAAAGTAGAGAT
GATTTGGATAGTTGGTGGTAGTTGTGTTTATAAGGAAGCCATGAATCACCCAGGCCATCTTAAACTATTTGTGACAAGGA
TCACGCGGGACTTTGAAAGTGACACAGTTTTTCCAGAAATTGATTTGGAAAAATATAAACTTCTGCCAGAATACCCAGGT
GTTCTCTCTGATGTCCAGGAGGAGAAAGACATTAAGTTCAAATTTGAAGTATATGAGAAGAATGAT

Alignment

ORF - retro_mmul_704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.43 %
• Parental protein coverage: 79.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FAPILTARSVLTSGLGGA-PAAVMVSSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMT-TTSSVEG
          F.PIL.ARS...SGLGGA..AAVMV..LNCIVAVSQN.GI.KNGDLPWP.LRNEFRYFQRMT.T.SS.EG
Retrocopy FRPILAARSGVASGLGGA>TAAVMVRLLNCIVAVSQNTGISKNGDLPWPLLRNEFRYFQRMT<TNSSGEG

Parental  KQNLV-IMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLARSLDDALKLTEQPELANKVDMIWI
          KQNLV.....K.WFSIPEKNRPLK.RINLVLSRELKEPPQGAH.LAR.LDD.LKLTEQPELANKV.MIWI
Retrocopy KQNLV<VTCRKIWFSIPEKNRPLKDRINLVLSRELKEPPQGAHSLARCLDDILKLTEQPELANKVEMIWI

Parental  VGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFLPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEK
          VGGS.VYKEAMNHPGHLKLFVTRI..DFESDT..PEIDLEKYKLLPEYPGVLSDVQEEK.IK.KFEVYEK
Retrocopy VGGSCVYKEAMNHPGHLKLFVTRITRDFESDTVFPEIDLEKYKLLPEYPGVLSDVQEEKDIKFKFEVYEK

Parental  ND
          ND
Retrocopy ND

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	0.67 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	1.19 RPM
SRP007412_cerebellum	0.00 RPM	0.13 RPM
SRP007412_heart	0.00 RPM	0.35 RPM
SRP007412_kidney	0.00 RPM	0.82 RPM
SRP007412_liver	0.00 RPM	3.21 RPM
SRP007412_testis	0.04 RPM	0.15 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_704 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_704 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_704 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015750	2 retrocopies	retro_amel_218, retro_amel_842,
Bos taurus	ENSBTAG00000007681	1 retrocopy	retro_btau_351,
Callithrix jacchus	ENSCJAG00000019556	4 retrocopies	retro_cjac_2017, retro_cjac_2298, retro_cjac_2446, retro_cjac_531,
Equus caballus	ENSECAG00000026827	1 retrocopy	retro_ecab_513,
Felis catus	ENSFCAG00000026745	3 retrocopies	retro_fcat_579, retro_fcat_705, retro_fcat_841,
Homo sapiens	ENSG00000228716	4 retrocopies	retro_hsap_1927, retro_hsap_2119, retro_hsap_3602, retro_hsap_6,
Gorilla gorilla	ENSGGOG00000022366	2 retrocopies	retro_ggor_1959, retro_ggor_2429,
Myotis lucifugus	ENSMLUG00000012200	2 retrocopies	retro_mluc_1109, retro_mluc_2577,
Macaca mulatta	ENSMMUG00000018283	13 retrocopies	retro_mmul_1496, retro_mmul_425, retro_mmul_692, retro_mmul_693, retro_mmul_695, retro_mmul_700, retro_mmul_701, retro_mmul_704 , retro_mmul_738, retro_mmul_760, retro_mmul_768, retro_mmul_82, retro_mmul_994,
Monodelphis domestica	ENSMODG00000024860	3 retrocopies	retro_mdom_1685, retro_mdom_604, retro_mdom_703,
Mustela putorius furo	ENSMPUG00000008704	1 retrocopy	retro_mputfur_1107,
Mus musculus	ENSMUSG00000021707	1 retrocopy	retro_mmus_3326,
Nomascus leucogenys	ENSNLEG00000012989	3 retrocopies	retro_nleu_1193, retro_nleu_2314, retro_nleu_2631,
Oryctolagus cuniculus	ENSOCUG00000005127	3 retrocopies	retro_ocun_1351, retro_ocun_1640, retro_ocun_650,
Otolemur garnettii	ENSOGAG00000025320	1 retrocopy	retro_ogar_222,
Pongo abelii	ENSPPYG00000015600	2 retrocopies	retro_pabe_2959, retro_pabe_41,
Pan troglodytes	ENSPTRG00000017042	3 retrocopies	retro_ptro_109, retro_ptro_1551, retro_ptro_2988,
Rattus norvegicus	ENSRNOG00000013521	1 retrocopy	retro_rnor_2030,
Sus scrofa	ENSSSCG00000014125	2 retrocopies	retro_sscr_104, retro_sscr_1131,