RetrogeneDB ID: retro_mmul_375

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:55879612..55880549(+)
• Located in intron of: ENSMMUG00000004952

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_375
ATGAGGGAAATCATGCACATCCAGGCCGGTCAGTGTGGCAACCAGATGGGTGCTAAGTGCTGGGATGTGATCAATGATGA
ACGTGAAATCGACCCCACCAGCACCTAACATGGGGACAGTGACCTGCAGCTGGACTGCATCTCCATGTACTACAGTGAAG
CCACAGATGGCAAATATGTTCCTTGTGCTCTCCTGGTGGATCTAGAACCTGGGACCATGGACTCTGCTAGCTCAGGCCCT
TTTGGCCAGGTGCTTAAACCAGACAACTTTGTTTTTGGTCAGTCTGGGGCAAGCAACAACTGGGCCAAAGGCCACTACAT
AGAGGGGGCCGAGCTGGTTGATTCAGTCATAGATGTGGTGCAGGAGGACGCAGAGAGCTGTGACTGCCTGCAGGGCTTCC
AGCTGACCCACTCAATGGGCTCTGGAATGTGTACTCTCCTTATCAGCAAGATCCGAGAAGAGTGCCCTGATTGCATCATG
AGCATCTTTTGTGTGGTGCCTCCACCCAAAGTATCTGACACCGTGGTCGAGCCCTACAACATCACCTCTCCATCCATCAG
TTGGTAGAGAACACTGATGAGACCTACTGCATTGACAACGAGGCCCTCTATGACATCTGCTTCCGTACTTTGAAGCTGAC
CACACCAACCTATGGGCACCTGAACCACCTTCTCTCAGCCACCATAAGCATTGTTACCACCTGTCTCCACTTCCCTGGCC
AGCTCAATGATGACATCCGCAAGTTGGCAGTCAACCTGGTGCCCTTCCCACGTCTCCACTACTTCATGGCTGGCTTTGCC
CTCTCACCAGCTGTGGAAGCCAGCAGCATCAAGCTCTCACAGTGCCCAAACTCACCTGGCAGGTCTTTGATGCCAAGAAC
ATAATGGCTGCCTGTGACCCCTGCCACAGCTTATATCTCACTGTGGCTGCTGTCTTT

Alignment

ORF - retro_mmul_375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.56 %
• Parental protein coverage: 71.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEP
          MREI.HIQAGQCGNQ.GAK.W.VI.DE..IDPT.T.HGDSDLQLD.IS.YY.EAT.GKYVP.A.LVDLEP
Retrocopy MREIMHIQAGQCGNQMGAKCWDVINDEREIDPTST*HGDSDLQLDCISMYYSEATDGKYVPCALLVDLEP

Parental  GTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLG
          GTMDS..SGPFGQ...PDNFVFGQSGA.NNWAKGHY.EGAELVDSV.DVV...AESCDCLQGFQLTHS.G
Retrocopy GTMDSASSGPFGQVLKPDNFVFGQSGASNNWAKGHYIEGAELVDSVIDVVQEDAESCDCLQGFQLTHSMG

Parental  GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNAT-LSVHQLVENTDETYCIDNEALYD
          .G....M.TLLISKIREE.PD.IM..F.VVP.PKVSDTVVEPYN.T.LS.HQLVENTDETYCIDNEALYD
Retrocopy SG----MCTLLISKIREECPDCIMSIFCVVPPPKVSDTVVEPYNIT<LSIHQLVENTDETYCIDNEALYD

Parental  ICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFA-PLTSRGS
          ICFRTLKLTTPTYG.LNHL.SAT.S.VTTCL.FPGQLN.D.RKLAVN.VPFPRLH.FM.GFA.PLTS.GS
Retrocopy ICFRTLKLTTPTYGHLNHLLSATISIVTTCLHFPGQLNDDIRKLAVNLVPFPRLHYFMAGFA<PLTSCGS

Parental  QQYRALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVF
          QQ..ALTVP.LT.QVFDAKN.MAACDP.H..YLTVAAVF
Retrocopy QQHQALTVPKLTWQVFDAKNIMAACDPCHSLYLTVAAVF

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	0.32 RPM	518.82 RPM
SRP007412_cerebellum	0.58 RPM	315.71 RPM
SRP007412_heart	0.18 RPM	162.11 RPM
SRP007412_kidney	0.12 RPM	150.00 RPM
SRP007412_liver	0.44 RPM	235.48 RPM
SRP007412_testis	0.15 RPM	67.32 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_375 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_375 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_375 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_155
Pan troglodytes	retro_ptro_151
Gorilla gorilla	retro_ggor_244
Pongo abelii	retro_pabe_467

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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,