RetrogeneDB ID: retro_mmul_889

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:94328284..94328767(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000011407
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.17961
• Ensembl ID: ENSMMUG00000003073
• Aliases: None
• Description: None

Sequence

>retro_mmul_889
GTGGCGGCAGCAGCTGAAATTGATGAAGAACCAGTCAGTAAAGCAAAACAGAGTTGGAGTGAAAAGAAGACACAGAAGGC
TATGTCCAAACCTGTCTTCAACAGGTTACGGGGGTTACTAGAGTCACTATCCGGAAATCTAAGAATATCCTCTTTGTCAT
CACAAAACCAGATGTCTATAAGAGCCCTGCTTCAGATACCTATATAGTTTTGGGGGAAGCCAAGATCGAAGATTTATCTC
AGCCAGCACAAGCAGCAGCTGCTGAGAAATTCAAAGTTCAAGCTGAAGTTGTCTCAAACATTCAAGAAAACACACAGACT
CCAACAGTACAAAAGGAGAGTGAAGAATACAAAGTTGATGAAACAGGTGTAGAAGTGAAGGACATAAATTGGTCAAGTCT
CAAGGGAATGTGTGGAGAGCAAAGGCAGTCAGAGCCCTAAAGAACACAGTAATAATATTGTAAATGCTATTATGGAATTA
ACA

Alignment

ORF - retro_mmul_889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.45 %
• Parental protein coverage: 84.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LAAAAEIDEEPVSKAKQSRSEKKARKAMSK-LGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYI
          .AAAAEIDEEPVSKAKQS.SEKK..KAMSK...L.QVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYI
Retrocopy VAAAAEIDEEPVSKAKQSWSEKKTQKAMSK<TCLQQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYI

Parental  VFGEAKIEDLSQQAQLAAAEKFKVQGEAVSNIQENTQTPTVQEESEEEEVDETGVEVKDI-ELVMSQANV
          V.GEAKIEDLSQ.AQ.AAAEKFKVQ.E.VSNIQENTQTPTVQ.ESEE..VDETGVEVKDI..LV.SQ.NV
Retrocopy VLGEAKIEDLSQPAQAAAAEKFKVQAEVVSNIQENTQTPTVQKESEEYKVDETGVEVKDI<KLVKSQGNV

Parental  SRAKAVRALKN-NSNDIVNAIMELT
          .RAKAVRALKN..SN.IVNAIMELT
Retrocopy WRAKAVRALKN<HSNNIVNAIMELT

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	132.22 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	89.72 RPM
SRP007412_cerebellum	0.00 RPM	157.30 RPM
SRP007412_heart	0.06 RPM	188.14 RPM
SRP007412_kidney	0.23 RPM	220.18 RPM
SRP007412_liver	0.00 RPM	130.11 RPM
SRP007412_testis	0.04 RPM	175.05 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_889 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_889 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_889 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 76 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004175	3 retrocopies	retro_amel_1725, retro_amel_1821, retro_amel_643,
Canis familiaris	ENSCAFG00000000141	8 retrocopies	retro_cfam_1502, retro_cfam_1561, retro_cfam_1884, retro_cfam_1913, retro_cfam_2096, retro_cfam_2169, retro_cfam_710, retro_cfam_974,
Callithrix jacchus	ENSCJAG00000010701	8 retrocopies	retro_cjac_1063, retro_cjac_1452, retro_cjac_1875, retro_cjac_2202, retro_cjac_2453, retro_cjac_2696, retro_cjac_2975, retro_cjac_3232,
Dipodomys ordii	ENSDORG00000014522	2 retrocopies	retro_dord_228, retro_dord_699,
Equus caballus	ENSECAG00000015242	1 retrocopy	retro_ecab_785,
Homo sapiens	ENSG00000196531	6 retrocopies	retro_hsap_3006, retro_hsap_3027, retro_hsap_3968, retro_hsap_3992, retro_hsap_737, retro_hsap_77,
Loxodonta africana	ENSLAFG00000004598	6 retrocopies	retro_lafr_1107, retro_lafr_113, retro_lafr_1251, retro_lafr_166, retro_lafr_491, retro_lafr_958,
Macropus eugenii	ENSMEUG00000008412	3 retrocopies	retro_meug_1630, retro_meug_2063, retro_meug_2147,
Microcebus murinus	ENSMICG00000016465	5 retrocopies	retro_mmur_1122, retro_mmur_450, retro_mmur_585, retro_mmur_684, retro_mmur_807,
Myotis lucifugus	ENSMLUG00000001169	16 retrocopies	retro_mluc_1147, retro_mluc_1653, retro_mluc_1668, retro_mluc_1756, retro_mluc_1767, retro_mluc_1851, retro_mluc_1881, retro_mluc_1941, retro_mluc_2587, retro_mluc_2600, retro_mluc_414, retro_mluc_492, retro_mluc_526, retro_mluc_641, retro_mluc_725, retro_mluc_861,
Macaca mulatta	ENSMMUG00000003073	4 retrocopies	retro_mmul_1233, retro_mmul_1933, retro_mmul_2066, retro_mmul_889 ,
Mus musculus	ENSMUSG00000061315	1 retrocopy	retro_mmus_968,
Ochotona princeps	ENSOPRG00000001781	3 retrocopies	retro_opri_264, retro_opri_758, retro_opri_961,
Procavia capensis	ENSPCAG00000007067	5 retrocopies	retro_pcap_150, retro_pcap_224, retro_pcap_282, retro_pcap_305, retro_pcap_324,
Sarcophilus harrisii	ENSSHAG00000002175	1 retrocopy	retro_shar_213,
Tursiops truncatus	ENSTTRG00000002150	2 retrocopies	retro_ttru_1157, retro_ttru_760,
Vicugna pacos	ENSVPAG00000004028	2 retrocopies	retro_vpac_485, retro_vpac_611,