RetrogeneDB ID: retro_mmul_1849

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:110152121..110152919(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18776
• Ensembl ID: ENSMMUG00000012164
• Aliases: None
• Description: tubulin beta-2C chain [Source:RefSeq peptide;Acc:NP_001181720]

Sequence

>retro_mmul_1849
AGCAACCTGCAGCTGGAGTGCATCAGTGTTTACTACAATGAGACCACCAGTGGCAAGTATGTGCCCCACGCTGAGCTCAC
GGATCTGGAGCCCAGCACCGTGGACTCTCGTGTGCTCAGGCTCCTTCAGGCAGATCTTACGGCTGGACAACTTCATCTTC
CATCACAGTGGTGCCGGAAACAACTGGGCCAATGGGCACTACACAGAAGGTGCGGAGCTGGTGGATTCGGTGCTGGACAT
TGTGAGGAGGGAGGCTGAGAGCTGTGACTGCCTGCAGGGTTTCCAGCTGACCCACTCCCTGGGAGCAGGGACTGGGCCTG
AGAGGGGTACCCTTCTCATCAGCAAGATCCCAGAGAAGTATCCAGACAGGATCTTGAACATGTTCAGTGTGGCGCCCTTG
CGCAAGGTGTCAGATATGGGGGTGGAGCCCTAAAACATCACCTTCTTAGTCCACCAACTGGTAGAAAACACAGCTATGAC
CTATTGCATTGATAATGAAACTCTCCATAACATCTGCTTCTGAACCCTAAAGCTAACCACACTCACCTATGGTGACCCGA
ACTACCTGATGTCTGCCACCATAAGTGGGGTCACTACCTGCCTAAGCTTCCCCACTCAGCTCAATGCTGACCTGCAGAAA
CCAGCTAAGTACATGGTCCCATTCCCTACCTGCACTTCTTTATGCCTGGCTTCACCCTGCTGACCATCCACGGCAGCCAG
CAGTACCAGGCCCTGACAGTGCCTGAGCTTACCCAGCAGATGTTTGATGCCAAGAACATGATGGCTCCCTGAGACCCC

Alignment

ORF - retro_mmul_1849 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.75 %
• Parental protein coverage: 59.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SDLQLERINVYYNEATGGKYVPRAVLVDLEPGTMDS-VRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTE
          S.LQLE.I.VYYNE.T.GKYVP.A.L.DLEP.T.DS.V.SG.F.QI.R.DNF.F..SGAGNNWA.GHYTE
Retrocopy SNLQLECISVYYNETTSGKYVPHAELTDLEPSTVDS>VCSGSFRQILRLDNFIFHHSGAGNNWANGHYTE

Parental  GAELVDSVLDVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDT
          GAELVDSVLD.VR.EAESCDCLQGFQLTHSLG.GTG...GTLLISKI.E.YPDRI.N.FSV.P..KVSD.
Retrocopy GAELVDSVLDIVRREAESCDCLQGFQLTHSLGAGTGPERGTLLISKIPEKYPDRILNMFSVAPLRKVSDM

Parental  VVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNA
          .VEP.N.T..VHQLVENT..TYCIDNE.L..ICF.TLKLTT.TYGD.N.L.SAT.SGVTTCL.FP.QLNA
Retrocopy GVEP*NITFLVHQLVENTAMTYCIDNETLHNICF*TLKLTTLTYGDPNYLMSATISGVTTCLSFPTQLNA

Parental  DLRKLAVNMVPFPR-LHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDP
          DL.K.A..MVPFP..LHFFMPGF..LT..GSQQY.ALTVPELTQQMFDAKNMMA..DP
Retrocopy DLQKPAKYMVPFPT<LHFFMPGFTLLTIHGSQQYQALTVPELTQQMFDAKNMMAP*DP

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	9.75 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	51.96 RPM
SRP007412_cerebellum	0.00 RPM	9.94 RPM
SRP007412_heart	0.00 RPM	12.72 RPM
SRP007412_kidney	0.00 RPM	21.36 RPM
SRP007412_liver	0.00 RPM	124.33 RPM
SRP007412_testis	0.00 RPM	224.20 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1849 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1849 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1849 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3537
Pan troglodytes	retro_ptro_2403
Gorilla gorilla	retro_ggor_2388
Pongo abelii	retro_pabe_2920

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011966	1 retrocopy	retro_cpor_497,
Microcebus murinus	ENSMICG00000010939	1 retrocopy	retro_mmur_792,
Macaca mulatta	ENSMMUG00000012164	2 retrocopies	retro_mmul_1849 , retro_mmul_2533,
Macaca mulatta	ENSMMUG00000023684	2 retrocopies	retro_mmul_2501, retro_mmul_375,
Macaca mulatta	ENSMMUG00000029059	1 retrocopy	retro_mmul_1777,
Monodelphis domestica	ENSMODG00000017213	1 retrocopy	retro_mdom_117,
Mus musculus	ENSMUSG00000036752	2 retrocopies	retro_mmus_158, retro_mmus_422,
Otolemur garnettii	ENSOGAG00000005927	2 retrocopies	retro_ogar_3410, retro_ogar_3450,
Pan troglodytes	ENSPTRG00000023373	2 retrocopies	retro_ptro_2403, retro_ptro_3166,
Rattus norvegicus	ENSRNOG00000010170	2 retrocopies	retro_rnor_742, retro_rnor_867,