RetrogeneDB ID: retro_mmul_1718

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:123454128..123454801(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSN
• Ensembl ID: ENSMMUG00000021119
• Aliases: None
• Description: translin [Source:RefSeq peptide;Acc:NP_001253608]

Sequence

>retro_mmul_1718
ATGTCTGTGACTGAGATCTTCGTAGAGCTGCAGGACTTTTGTCTGCCTAGCAGGACATCAGACAGGAAATCCAAAAATTT
GTAGAGTTTACAACAAACAGCTTAAGAGATTGTTAACTCTACCACAACATGTCCATCAGGGTGCTGGGTTTCAGGAGTTT
CCAAGAGGGGTTTGAAAGCTTAGGAATCTTTTGGTACGGTAAAAACACACCCAACACCTCTGAAGAGCAAGTTGCCTGCT
GAACAGTGTGCTATGAGATTCATGAACACTGGAGGTTTGTGTTGCAGCATACGATTGTCTTCCCAGAATTTGTTGTGTGT
TTGGAAACAGAAACTCCAGAAGCGATTACAGAAATTTGTGTCATTGAGCCAGATAAGGAGAAAGGATTTCATCTGGATGT
AGAAGATCCTCTCTCAGAAGTTCGATTCTTGCTAGTGAGCCACTGAGGTTGTCCCTCAATGGCATGACTGCTGGAGACAA
CTCCCAGCCCCTCCATGTCGCCACCTTTAACAATGAGTGGCATCCCAATTTCCACCTTCTCAGCCTAAAACACTTGTCTC
TAAGGAAGTCTTATGATGGCTTGTTGTAGGATGTGAAGAAAACAGAGGGGATAGTCTATATTATCTCCATCCAAGGCTTC
AATAAGGAGATAGAAGCTGCCTGTGCTGAAAAA

Alignment

ORF - retro_mmul_1718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSVSEIFVELQGFLAAEQDIREEIRKVVQSLEQTAREI-LTLLQGVHQGAGFQDIP-KRCLKAREHFGTV
          MSV.EIFVELQ.F............K...SL.QTA.EI.LTL.Q.VHQGAGFQ..P.KR.LKA.E.FGTV
Retrocopy MSVTEIFVELQDFCLPSRT-SDRKSKNL*SLQQTA*EI>LTLPQHVHQGAGFQEFP<KRGLKA*ESFGTV

Parental  KTHLTSLKTKFPAEQ-YYRF-HEHWRFVLQRLVFLAAFVVYLETETLVTREAVTEILGIEPDREKGFHLD
          KTH.T.LK.K.PAEQ...RF.HEHWRFVLQ.......FVV.LETET....EA.TEI..IEPD.EKGFHLD
Retrocopy KTHPTPLKSKLPAEQCAMRF<HEHWRFVLQHTIVFPEFVVCLETET---PEAITEICVIEPDKEKGFHLD

Parental  VEDYLSGV-LILASELSRLSVNSVTAGDYSRPLHISTFINELDSGFRLLNLKNDSLRKRYDGLKYDVKKV
          VED.LS.V..ILASE..RLS.N..TAGD.S.PLH..TF.NE....F.LL.LK..SLRK.YDGL..DVKK.
Retrocopy VEDPLSEV<SILASEPLRLSLNGMTAGDNSQPLHVATFNNEWHPNFHLLSLKHLSLRKSYDGLL*DVKKT

Parental  EEVVYDLSIRGFNKETAAACVEK
          E..VY..SI.GFNKE..AAC.EK
Retrocopy EGIVYIISIQGFNKEIEAACAEK

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	14.68 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	14.36 RPM
SRP007412_cerebellum	0.00 RPM	16.34 RPM
SRP007412_heart	0.00 RPM	10.01 RPM
SRP007412_kidney	0.00 RPM	16.08 RPM
SRP007412_liver	0.00 RPM	7.36 RPM
SRP007412_testis	0.00 RPM	31.59 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1718 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1718 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1718 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006059	1 retrocopy	retro_btau_1598,
Dasypus novemcinctus	ENSDNOG00000025740	2 retrocopies	retro_dnov_1581, retro_dnov_907,
Felis catus	ENSFCAG00000027149	1 retrocopy	retro_fcat_1577,
Homo sapiens	ENSG00000211460	1 retrocopy	retro_hsap_3760,
Gorilla gorilla	ENSGGOG00000002216	2 retrocopies	retro_ggor_2528, retro_ggor_2610,
Myotis lucifugus	ENSMLUG00000012656	1 retrocopy	retro_mluc_1420,
Macaca mulatta	ENSMMUG00000021119	1 retrocopy	retro_mmul_1718 ,
Monodelphis domestica	ENSMODG00000000147	1 retrocopy	retro_mdom_1896,
Nomascus leucogenys	ENSNLEG00000001202	1 retrocopy	retro_nleu_170,
Ornithorhynchus anatinus	ENSOANG00000003457	1 retrocopy	retro_oana_120,
Oryctolagus cuniculus	ENSOCUG00000023529	1 retrocopy	retro_ocun_271,
Otolemur garnettii	ENSOGAG00000030436	3 retrocopies	retro_ogar_1221, retro_ogar_2875, retro_ogar_3426,
Pan troglodytes	ENSPTRG00000012420	1 retrocopy	retro_ptro_2551,
Tarsius syrichta	ENSTSYG00000004395	1 retrocopy	retro_tsyr_1593,