RetrogeneDB ID: retro_mmul_157

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:63450325..63451711(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000030822
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.13490
• Ensembl ID: ENSMMUG00000020441
• Aliases: None
• Description: None

Sequence

>retro_mmul_157
ATGAACAACTTTGGTAATGAAGAATTTGACTGCCACTTCCTCGATGAAGGTTTTACTGCCAAGGGCATTCTGGACCAAAA
AATTAATGAAGTCTCTTTTTCTGATGATAAGGATGCCTTCTATGTGGCAGACCTGGGAGACATTCTAAAGAAACATCTGA
GGTGGTTAAACGCTCTCCCTCGTGTCACCCCCTTTTATGCAGTCAAATGTAATGATAGCAAAGCCATCATGAAGACCCTT
GCTGCTGTGGGGACAGGATTTGACTGTGCTAGCAAGACTGAAATACAGTTGGTGCAGAGTCTGAGGGTGCCTCCAGAGAG
GATTATCTATGCAAATCCTTGTAAACAAGTATCTCAAACTAAGTATGCTGCTAATAATGGAGTCCAGATGATGACTTTTG
ATAGTGAAGTTGAGTTGATGAAAGTTGCCAGAGCACATCCAAAAGCAAAGTTGGTTTTGCGGATTGCCACTGATGATTCC
AAAGCAGTCTGTTGTCTCAGTGTTAAATTCCGTGCCACGCTCAGAAATAGCAGGCTCCTTTTGGAAAGGGCAAAAGAGGT
GAATATCGATGTTGTTGGTGTCAGCTTCCACGCAGGAAGTGGCTGTACCGATCCTGAGACCTTCGTGCAGGCAATCTCTG
ATACCCGCTGTGTTTTTGACATGGGGGCTGAGGTTGGTTTCAGCATGTATCTGCTTGATATTGGCGGTGGCTTTCCTGGA
TCTGAGGATGTGAAGCTTAAATTTGAAGAGATCACCAGCATAATCAACCCAGCGTTGGACAGATATTTTCTGTCAGACTC
TGGAGTGAGAATCATAGCTAAGCCTGGCAGATACTATGTTGCATCAGCTTTCACACTTGCGGTTAATATCATCTCCAAGA
AAATTGTATTAAAGGAACAGACTGGCTCTGATGATGAAGATGAATCGAGTGAACAGACCTTTATGTGTTATGTGAATTAT
GGTGTCTATGGATCATTTAATTGCATACTGTATGATCACGCACATGTAAAGCCCCTTCTGCAAAAGAGACCTAAACCAGA
TAAGAAGTATTATTCATCCAGCATATGGGGACCAATATGTGATGGCCTTGATCGGATTGTTGAGCGCTGTGACCTGCCCG
AAATGCATGTGGGTGATTGGATGCTCTTTGAAAACATGGGCGCTTACACTGTTGCTGCTGCCTCTACGTTCAATGGCTTC
CAGAGGCCGGTGATCTACTATGTGATGTCAGGGCCTGCGTGGCAACTCACGCAGCAATTCCAGAACCCCGACTTCCCACC
CGAAGTAGAGGAACAGGACACCAGCACCCTGCCTGTGTCTTGTGCCTGGGAGAGTGGGATGAAACGCCACCCAGCAGCCT
GTGCTTTAGCTGGTATTAATGTGTAG

Alignment

ORF - retro_mmul_157 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.93 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNNFGNEEFDCHFLDEGFTAKDILDQKINEVSFSDDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKC
          MNNFGNEEFDCHFLDEGFTAK.ILDQKINEVSFSDDKDAFYVADLGDILKKHLRWL.ALPRVTPFYAVKC
Retrocopy MNNFGNEEFDCHFLDEGFTAKGILDQKINEVSFSDDKDAFYVADLGDILKKHLRWLNALPRVTPFYAVKC

Parental  NDSKAIVKTLAAVGTGFDCASKTEIQLVQNLGVPPERIIYANPCKQVSQIKYAANNGVQMMTFDSEVELM
          NDSKAI.KTLAAVGTGFDCASKTEIQLVQ.L.VPPERIIYANPCKQVSQ.KYAANNGVQMMTFDSEVELM
Retrocopy NDSKAIMKTLAAVGTGFDCASKTEIQLVQSLRVPPERIIYANPCKQVSQTKYAANNGVQMMTFDSEVELM

Parental  KVTRAHPKAKLVLRIATDDSKAVCRLSVKFGATLRNSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQ
          KV.RAHPKAKLVLRIATDDSKAVC.LSVKF.ATLRNSRLLLERAKE.NIDVVGVSFH.GSGCTDPETFVQ
Retrocopy KVARAHPKAKLVLRIATDDSKAVCCLSVKFRATLRNSRLLLERAKEVNIDVVGVSFHAGSGCTDPETFVQ

Parental  AISDARCVFDMGAEVGFSMYLLDIGGGFPGSEEVKLKFEEITNVINPALDKYFPADSGVRIIAEPGRYYV
          AISD.RCVFDMGAEVGFSMYLLDIGGGFPGSE.VKLKFEEIT..INPALD.YF..DSGVRIIA.PGRYYV
Retrocopy AISDTRCVFDMGAEVGFSMYLLDIGGGFPGSEDVKLKFEEITSIINPALDRYFLSDSGVRIIAKPGRYYV

Parental  ASAFTLAVNIIAKKIVLKEQTGSDDEDESSEQTFMYYVNDGVYGSFNCILYDHAHVKPLLQKRPKPDEKY
          ASAFTLAVNII.KKIVLKEQTGSDDEDESSEQTFM.YVN.GVYGSFNCILYDHAHVKPLLQKRPKPD.KY
Retrocopy ASAFTLAVNIISKKIVLKEQTGSDDEDESSEQTFMCYVNYGVYGSFNCILYDHAHVKPLLQKRPKPDKKY

Parental  YSSSIWGPTCDGLDRIVERCDLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPTIYYVMSGPAWQLMQQF
          YSSSIWGP.CDGLDRIVERCDLPEMHVGDWMLFENMGAYTVAAASTFNGFQRP.IYYVMSGPAWQL.QQF
Retrocopy YSSSIWGPICDGLDRIVERCDLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPVIYYVMSGPAWQLTQQF

Parental  QNPDFPPEVEEQDASTLPVSCAWESGMKRHPAACASAGINV
          QNPDFPPEVEEQD.STLPVSCAWESGMKRHPAACA.AGINV
Retrocopy QNPDFPPEVEEQDTSTLPVSCAWESGMKRHPAACALAGINV

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	15.58 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	15.47 RPM
SRP007412_cerebellum	0.26 RPM	26.02 RPM
SRP007412_heart	0.24 RPM	36.57 RPM
SRP007412_kidney	0.47 RPM	80.51 RPM
SRP007412_liver	0.24 RPM	36.06 RPM
SRP007412_testis	0.49 RPM	182.10 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_157 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_157 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_157 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011415	1 retrocopy	retro_amel_414,
Bos taurus	ENSBTAG00000004256	1 retrocopy	retro_btau_552,
Choloepus hoffmanni	ENSCHOG00000010898	2 retrocopies	retro_chof_1618, retro_chof_2111,
Callithrix jacchus	ENSCJAG00000006576	2 retrocopies	retro_cjac_3170, retro_cjac_3857,
Dasypus novemcinctus	ENSDNOG00000018474	31 retrocopies	retro_dnov_1032, retro_dnov_1128, retro_dnov_1129, retro_dnov_1137, retro_dnov_1212, retro_dnov_1235, retro_dnov_1418, retro_dnov_1434, retro_dnov_1493, retro_dnov_1594, retro_dnov_1595, retro_dnov_1677, retro_dnov_1778, retro_dnov_1810, retro_dnov_1813, retro_dnov_2016, retro_dnov_2027, retro_dnov_2108, retro_dnov_2147, retro_dnov_2180, retro_dnov_2212, retro_dnov_2461, retro_dnov_2551, retro_dnov_2564, retro_dnov_392, retro_dnov_740, retro_dnov_766, retro_dnov_781, retro_dnov_923, retro_dnov_943, retro_dnov_958,
Equus caballus	ENSECAG00000022690	2 retrocopies	retro_ecab_1002, retro_ecab_957,
Loxodonta africana	ENSLAFG00000005330	2 retrocopies	retro_lafr_218, retro_lafr_850,
Myotis lucifugus	ENSMLUG00000010423	1 retrocopy	retro_mluc_281,
Macaca mulatta	ENSMMUG00000020441	2 retrocopies	retro_mmul_157 , retro_mmul_1645,
Monodelphis domestica	ENSMODG00000014779	1 retrocopy	retro_mdom_262,
Mustela putorius furo	ENSMPUG00000013321	1 retrocopy	retro_mputfur_1272,
Mus musculus	ENSMUSG00000011179	12 retrocopies	retro_mmus_2588, retro_mmus_2744, retro_mmus_2745, retro_mmus_2746, retro_mmus_2747, retro_mmus_2834, retro_mmus_2922, retro_mmus_3237, retro_mmus_3677, retro_mmus_503, retro_mmus_912, retro_mmus_984,
Nomascus leucogenys	ENSNLEG00000013820	1 retrocopy	retro_nleu_1119,
Pongo abelii	ENSPPYG00000012654	1 retrocopy	retro_pabe_3090,
Ictidomys tridecemlineatus	ENSSTOG00000000386	2 retrocopies	retro_itri_1751, retro_itri_801,
Tursiops truncatus	ENSTTRG00000004611	3 retrocopies	retro_ttru_1940, retro_ttru_731, retro_ttru_843,