RetrogeneDB ID: retro_mmul_1860

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:142310329..142311129(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4286
• Ensembl ID: ENSMMUG00000021614
• Aliases: None
• Description: protein LSM14 homolog A [Source:RefSeq peptide;Acc:NP_001244883]

Sequence

>retro_mmul_1860
CGTCCAATACCACCTCGAGATGAAGTATTGGAATATATTGTGTTCTATGGGAGTGACATTAAAGACCTCACTGTTTGTGA
GCCACCAAAACCACAGGGTTCTGTGCCTGAAGACCCAGCTATCCTTCAGTCCTCACTAGGCTCATCAACTTCTTCATTCC
AGTGAGTGGGTTCTCACGGGCCTTTCGCCAGGATGCCCATATACAGTCGGTTCAGTCCAAGCTCCTTAGTTGGGTAGGAG
TTTCCTGCTGTTGGTGTTGCTGGAAGCTGTTTGGCATCGTTTGGAACAGAAACATCAAACAGTGGTATCTTACCCCAAAG
TAGTGTGTTGGCTCTGCCTTAACACAGGATACAAGATCTCTAAAAGCACAGTTGTCTCAAGTTCCCTCAAGCCCTCAGTT
AGACATTTTGAGGAAAGCTCAACCGTGGAACAAGCACTTGAAGACTGTTTCCGACCATTTACCTGCTCCAGCACCTGTTG
GGAGAAGGAGCCCTGTATCAACTAGGCCTTTGCCATCTACCAACCAAAAAGCAATAGAGAATCAAGAGCACTGGTGAGCT
GAAGTACACAATGTTCCAAGACCAGAAAACGAGCAACTCAGAAATGATAGCAAGAGACAAGTAGCTCCAGGTGCTCCTTC
AGCTCCAAGGAGAGGGCGTGCGGTTCAGGGAAGTACCAGGGGAAGATTTGGTATTTTACGAGATGGACCAATGAAATTTG
AGAAAGGTTTTGACTTTGAAAGTGCCAATGCACAATTCAACAAGGGAGAGATTGACAGAGATTTTCATAATAAACTTAAA

Alignment

ORF - retro_mmul_1860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.48 %
• Parental protein coverage: 57.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RPIPPRDEVFEYIIFRGSDIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSTSSFQSMGSYGPFGRMPTYSQ
          RPIPPRDEV.EYI.F.GSDIKDLTVCEPPKPQ.S.P.DPAI.QSSLGSSTSSFQ..GS.GPF.RMP.YS.
Retrocopy RPIPPRDEVLEYIVFYGSDIKDLTVCEPPKPQGSVPEDPAILQSSLGSSTSSFQ*VGSHGPFARMPIYSR

Parental  FSPSSLVGQQFGAVGVAGNSLTSFGTETSNSGTLPQSSA-VGSAFTQDSRSLKTQLSQGRSSPQLDPLRK
          FSPSSLVG..F.AVGVAG..L.SFGTETSNSG.LPQSS..VGSA.TQD.RSLK.QLSQ..SSPQLD.LRK
Retrocopy FSPSSLVG*EFPAVGVAGSCLASFGTETSNSGILPQSSV<VGSALTQDTRSLKAQLSQVPSSPQLDILRK

Parental  SPTMEQAVQTASAHLPAPAPVGRRSPVSTRPLPSTSQKAIENQEHRRAEVHKVSRPENEQLRNDNKRQVA
          .........T.S.HLPAPAPVGRRSPVSTRPLPST.QKAIENQEH..AEVH.V.RPENEQLRND.KRQVA
Retrocopy AQPWNKHLKTVSDHLPAPAPVGRRSPVSTRPLPSTNQKAIENQEHW*AEVHNVPRPENEQLRNDSKRQVA

Parental  PGAPSAPRRGRGGHRGGRGRFGIRRDGPMKFEKDFDFESANAQFNKEEIDREFHNKLK
          PGAPSAPRRGR......RGRFGI.RDGPMKFEK.FDFESANAQFNK.EIDR.FHNKLK
Retrocopy PGAPSAPRRGRAVQGSTRGRFGILRDGPMKFEKGFDFESANAQFNKGEIDRDFHNKLK

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	41.79 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	33.08 RPM
SRP007412_cerebellum	0.00 RPM	68.32 RPM
SRP007412_heart	0.00 RPM	48.52 RPM
SRP007412_kidney	0.00 RPM	61.50 RPM
SRP007412_liver	0.00 RPM	29.57 RPM
SRP007412_testis	0.04 RPM	106.33 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1860 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1860 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1860 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2378
Pan troglodytes	retro_ptro_2389
Pongo abelii	retro_pabe_2906

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006555	1 retrocopy	retro_chof_1375,
Callithrix jacchus	ENSCJAG00000010360	5 retrocopies	retro_cjac_1582, retro_cjac_2625, retro_cjac_3201, retro_cjac_3327, retro_cjac_840,
Gorilla gorilla	ENSGGOG00000001762	1 retrocopy	retro_ggor_2378,
Microcebus murinus	ENSMICG00000011598	1 retrocopy	retro_mmur_1605,
Myotis lucifugus	ENSMLUG00000003368	1 retrocopy	retro_mluc_1793,
Macaca mulatta	ENSMMUG00000021614	2 retrocopies	retro_mmul_1386, retro_mmul_1860 ,
Nomascus leucogenys	ENSNLEG00000011713	4 retrocopies	retro_nleu_1299, retro_nleu_2544, retro_nleu_2580, retro_nleu_485,
Oryctolagus cuniculus	ENSOCUG00000011872	2 retrocopies	retro_ocun_193, retro_ocun_860,
Otolemur garnettii	ENSOGAG00000002492	2 retrocopies	retro_ogar_2586, retro_ogar_67,
Pongo abelii	ENSPPYG00000009832	2 retrocopies	retro_pabe_1693, retro_pabe_2906,
Pan troglodytes	ENSPTRG00000010813	3 retrocopies	retro_ptro_1343, retro_ptro_2389, retro_ptro_863,
Rattus norvegicus	ENSRNOG00000021133	1 retrocopy	retro_rnor_2397,
Ictidomys tridecemlineatus	ENSSTOG00000002785	1 retrocopy	retro_itri_170,