RetrogeneDB ID: retro_mmul_2501

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:64890414..64891666(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB
• Ensembl ID: ENSMMUG00000023684
• Aliases: TUBB, TUBB2A, TUBB2B, TUBB5
• Description: Tubulin beta chain [Source:UniProtKB/Swiss-Prot;Acc:P69895]

Sequence

>retro_mmul_2501
GCCAAGTTCTGGGAGGTGATCAGTGATGAACATGACGTCGACCCCACCGGCACCTACCATGGGGACAGCAACCTGCAGCT
GGACCATATCTCTGTGTACTACAATGAAACCACAGGTGGCAAATATGTTCCTCGTGCCATCCTGGTGGATCTAGAACCTG
GGACCATGGATTCTGTTCACTCAGGTTCTTTTGGCCAGATCTTTAGACCAGACAACTTTGTACTTGGTCAGTCTGGGGCA
GGTAACAACTGGGCCAAAGGCCACTGCACAGAGGGAGCGGAGCTGGTTGATTCTGTTCTGGATGTGGTTTGGAAGGAGGA
AGAGAGCTGTGTCTGCCTGCAGGGCTTCCAGCTGACCCGCTCACTGGGCGGGGGCACATGCTCTGGAATGGGCACTCTCC
TTATCAGCAAGATCTGAGAAGAGAACCCTGATCACATCATGAACACCTTCAGTGTGGTGCCTTCACCCAAAGTGTCTGAC
ACCGTGGTTGAGCCCTACAATGCCACCTCTTCGTCCATCAGTTGGTAGAGAACACTGATGAGACCAATTGCATTGACAAC
GAGGCCCTCTATGATATCTGCTTCCACACTCTGAAGCTGACCACACCAACCTACGGGGATCTGAACCACCTCCTCTCAGC
CACCATGAACGGTGTCACCACCTGACTCCACTTCCCTGGCCAGCTCAATGCTGACCTCGGCAAGTTGGCAGTCAACATGG
TCCCCTTCCCACGCCTCCATTTCTTTGTGCCTGGCTTTGCCCCTCTCACCAGCCATGGAAGCCAGCAGTATTGAGCTCTC
ACAGTGCTGGAACTCACCCAGGTGTTCCATGCCAAGAACATGATGGCTGCATGTGACCCCCGCCACAGCCGATACCTCAC
CGTGGCTGCTGTCTTCCGTGGTCGGATGTCCATGAAGGAGGTCGATGAGCAGATACTTAACGTGCAGAACAAGAACAGCA
GATACTTTGTGGAATGGATCCCCAACAACGTCAAGACAGCTGTCTGTGACATCCCACCACGTGGCCTCAAGATGGCAGTC
ACCTTCATCGGCAACAGCACTGCCATCCAGGAGCTCTTCAAGCGCATCTCGGAGCAGTTAACTGCCATGTTCCGCCAGAA
AGCCTTCCTCCACTGGTACACAGGCGAAGGCATGGACAAGATGGAGTTCACGAGGCTGAGAGCAACATGAACTACCTCGT
CTCTGAGCATCGGGAGTACCAGGATGCCACCGTAGAAGAGGAGGAGCATTTC

Alignment

ORF - retro_mmul_2501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.31 %
• Parental protein coverage: 94.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEPGTMDSVRSGPFGQIFRP
          AKFWEVISDEH..DPTGTYHGDS.LQLD.ISVYYNE.TGGKYVPRAILVDLEPGTMDSV.SG.FGQIFRP
Retrocopy AKFWEVISDEHDVDPTGTYHGDSNLQLDHISVYYNETTGGKYVPRAILVDLEPGTMDSVHSGSFGQIFRP

Parental  DNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIRE
          DNFV.GQSGAGNNWAKGH.TEGAELVDSVLDVV.KE.ESC.CLQGFQLT.SLGGGT.SGMGTLLISKI.E
Retrocopy DNFVLGQSGAGNNWAKGHCTEGAELVDSVLDVVWKEEESCVCLQGFQLTRSLGGGTCSGMGTLLISKI*E

Parental  EYPDRIMNTFSVVPSPKVSDTVVEPYNAT-LSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLN
          E.PD.IMNTFSVVPSPKVSDTVVEPYNAT.L.VHQLVENTDET.CIDNEALYDICF.TLKLTTPTYGDLN
Retrocopy ENPDHIMNTFSVVPSPKVSDTVVEPYNAT<LFVHQLVENTDETNCIDNEALYDICFHTLKLTTPTYGDLN

Parental  HLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQVFDA
          HL.SATM.GVTT.L.FPGQLNADL.KLAVNMVPFPRLHFF.PGFAPLTS.GSQQY.ALTV.ELT.QVF.A
Retrocopy HLLSATMNGVTT*LHFPGQLNADLGKLAVNMVPFPRLHFFVPGFAPLTSHGSQQY*ALTVLELT-QVFHA

Parental  KNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMAVT
          KNMMAACDPRH.RYLTVAAVFRGRMSMKEVDEQ.LNVQNKNS.YFVEWIPNNVKTAVCDIPPRGLKMAVT
Retrocopy KNMMAACDPRHSRYLTVAAVFRGRMSMKEVDEQILNVQNKNSRYFVEWIPNNVKTAVCDIPPRGLKMAVT

Parental  FIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFT-EAESNMNDLVSEYQQYQDATAEEEED
          FIGNSTAIQELFKRISEQ.TAMFR.KAFLHWYTGEGMD.MEFT.EAESNMN.LVSE...YQDAT.EEEE.
Retrocopy FIGNSTAIQELFKRISEQLTAMFRQKAFLHWYTGEGMDKMEFT<EAESNMNYLVSEHREYQDATVEEEEH

Parental  F
          F
Retrocopy F

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	303.43 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	518.82 RPM
SRP007412_cerebellum	0.26 RPM	315.71 RPM
SRP007412_heart	0.18 RPM	162.11 RPM
SRP007412_kidney	0.00 RPM	150.00 RPM
SRP007412_liver	0.12 RPM	235.48 RPM
SRP007412_testis	0.00 RPM	67.32 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2501 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2501 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2501 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006969	2 retrocopies	retro_btau_471, retro_btau_55,
Canis familiaris	ENSCAFG00000000443	1 retrocopy	retro_cfam_1860,
Echinops telfairi	ENSETEG00000013572	1 retrocopy	retro_etel_641,
Gorilla gorilla	ENSGGOG00000022655	4 retrocopies	retro_ggor_2388, retro_ggor_244, retro_ggor_2519, retro_ggor_2651,
Macropus eugenii	ENSMEUG00000015992	1 retrocopy	retro_meug_978,
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,
Mustela putorius furo	ENSMPUG00000011690	3 retrocopies	retro_mputfur_1123, retro_mputfur_607, retro_mputfur_807,
Nomascus leucogenys	ENSNLEG00000005348	1 retrocopy	retro_nleu_498,
Otolemur garnettii	ENSOGAG00000032213	1 retrocopy	retro_ogar_2391,
Ochotona princeps	ENSOPRG00000014770	4 retrocopies	retro_opri_1106, retro_opri_237, retro_opri_46, retro_opri_656,
Pongo abelii	ENSPPYG00000016419	4 retrocopies	retro_pabe_2920, retro_pabe_3210, retro_pabe_3698, retro_pabe_467,
Pan troglodytes	ENSPTRG00000017939	3 retrocopies	retro_ptro_151, retro_ptro_2527, retro_ptro_2677,