RetrogeneDB ID: retro_mmul_1692

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:82336778..82338130(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBG2
• Ensembl ID: ENSMMUG00000016797
• Aliases: None
• Description: tubulin gamma-1 chain [Source:RefSeq peptide;Acc:NP_001247940]

Sequence

>retro_mmul_1692
ATGCCGAGGGAAATCATCACCCTACAGTTGGGCCAGTGCGGCAGTCAGATTGGGTTCAAGTTCTGGAAACAGCTGTGCAC
TGAGCATTTTATCAGCCCCGAGGGTACTGTAGAGGAGTTCGCTATCAAGGGCACTGACCACAAGGACATCTTTTTCTAAC
AGGCAGAAGATGAGCACTATATCCCCTGGGCCGTGCTGCTGGACCTGGAGCCCCGGGTGATCCACTCCATCCTCAACTCC
CCCTATCCCAAGCTCTACAACCCAGAGAACATCTACCTGTTGGAGCATGGAGGAGGAGCTGGCAACAACTGAGCCAGCAG
ATTCTCCCAGAGAGAGAAGCTCCATGAGGACATTTTTAACATCATAGACTGAGAGGCAGATGGTAGTGACAATCTAGATG
GCTGTGTGCTGTGTCAGTCCACTGCTGGGGGGACAGGCTCTGACTTCGGCTCCTACCTCTTAGAATGGCTGAATGATAGG
TATCCTAAGAAGCTGGTGCAGACATACTCAGTGTTTCTCAACCAGGACGAGATAAGCGACGTGGTGATCCAGCTTTATAA
TTCACTTCTCACACTCAAGAGGCTGATGCAGAATGCAGACTGTGTGGTGGTGCTGCACAACACAGCCCTGAACCAGATTG
CCATAGACCCTCTGAATATCCAGAACCCATCCTTCTCTCAGACCAACCAGCTGGTGTCCACCATCATGTCAGCCAGCACC
TTCACCCTGCACTACCCGGCTACATGAACAATGACCTCATCAGCCTCATCGCCTCACTCATTCCCACACCATGGCTCCAC
TTTCTCATGACCGGCTACACCCTGCTAACTATGGACCAGTCGGTGGCCAGTGTGAGGAAGATCACGGTCCTGGATGTCAT
GACGTAGCTGCTGCAGCCCAAGAATGTGATGGTGTCCACAGGCCGAGACCGCCACACCAACCACTCCTACATCACCATCC
TCAACACGATCCAGGGAGACGTGAACCCCACCCAGGTCCACAAGAACCTGCAGAGGATCCGGAAACGGAAGTTGGCCAAC
TTTATCCTGTGGGGCCCCACCAGCATCCAGGTGGCCCTGTCGAGGAAGTCTCCTTACCTGCCCTTGGCCCACCGGGTCAG
TGGGCTCATGATGGCCAACCATACCAGCATCTCCTCACTCTTCGAGAGAACCTGTCACCAATATGACAAGCTGCGGAAGA
GGGAGGCCTTCCTGGAGCCGTTTCGCAAGGAGGACATGTTCAAGGACAACTTTGATGAGATGGACACATCCAGGGAGATT
GTGCAGCAGCTCATGGATGAGTACCACATGGCCACACGGCCAGATTACATCTCCTGGGGCACCCAGGAGCAG

Alignment

ORF - retro_mmul_1692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.84 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPREIITLQLGQCGNQIGFEFWKQLCAEHGISPEGIVEEFATEGTDRKDVFFYQADDEHYIPRAVLLDLE
          MPREIITLQLGQCG.QIGF.FWKQLC.EH.ISPEG.VEEFA..GTD.KD.FF.QA.DEHYIP.AVLLDLE
Retrocopy MPREIITLQLGQCGSQIGFKFWKQLCTEHFISPEGTVEEFAIKGTDHKDIFF*QAEDEHYIPWAVLLDLE

Parental  PRVIHSILNSPYAKLYNPENIYLSEHGGGAGNNWASGFSQGEKIHEDIFDIIDREADGSDSLEGFVLCHS
          PRVIHSILNSPY.KLYNPENIYL.EHGGGAGNN.AS.FSQ.EK.HEDIF.IID.EADGSD.L.G.VLC.S
Retrocopy PRVIHSILNSPYPKLYNPENIYLLEHGGGAGNN*ASRFSQREKLHEDIFNIID*EADGSDNLDGCVLCQS

Parental  IAGGTGSGLGSYLLERLNDRYPKKLVQTYSVFPNQDEMSDVVVQPYNSLLTLKRLTQNADCVVVLDNTAL
          .AGGTGS..GSYLLE.LNDRYPKKLVQTYSVF.NQDE.SDVV.Q.YNSLLTLKRL.QNADCVVVL.NTAL
Retrocopy TAGGTGSDFGSYLLEWLNDRYPKKLVQTYSVFLNQDEISDVVIQLYNSLLTLKRLMQNADCVVVLHNTAL

Parental  NRIATDRLHIQNPSFSQINQLVSTIMSASTTTLRY-PGYMNNDLIGLIASLIPTPRLHFLMTGYTPLTTD
          N.IA.D.L.IQNPSFSQ.NQLVSTIMSAST.TL.Y.PGYMNNDLI.LIASLIPTP.LHFLMTGYT.LT.D
Retrocopy NQIAIDPLNIQNPSFSQTNQLVSTIMSASTFTLHY<PGYMNNDLISLIASLIPTPWLHFLMTGYTLLTMD

Parental  QSVASVRKTTVLDVMRRLLQPKNVMVSTGRDRQTNHCYIAILNIIQGEVDPTQVHKSLQRIRERKLANFI
          QSVASVRK.TVLDVM..LLQPKNVMVSTGRDR.TNH.YI.ILN.IQG.V.PTQVHK.LQRIR.RKLANFI
Retrocopy QSVASVRKITVLDVMT*LLQPKNVMVSTGRDRHTNHSYITILNTIQGDVNPTQVHKNLQRIRKRKLANFI

Parental  PWGPASIQVALSRKSPYLPSAHRVSGLMMANHTSISSLFERTCRQYDKLRKREAFLEQFRKEDMFKDNFD
          .WGP.SIQVALSRKSPYLP.AHRVSGLMMANHTSISSLFERTC.QYDKLRKREAFLE.FRKEDMFKDNFD
Retrocopy LWGPTSIQVALSRKSPYLPLAHRVSGLMMANHTSISSLFERTCHQYDKLRKREAFLEPFRKEDMFKDNFD

Parental  EMDTSREIVQQLIDEYHAATRPDYISWGTQEQ
          EMDTSREIVQQL.DEYH.ATRPDYISWGTQEQ
Retrocopy EMDTSREIVQQLMDEYHMATRPDYISWGTQEQ

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	1.12 RPM	63.31 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	122.41 RPM
SRP007412_cerebellum	0.71 RPM	48.43 RPM
SRP007412_heart	0.29 RPM	18.73 RPM
SRP007412_kidney	0.70 RPM	19.01 RPM
SRP007412_liver	0.51 RPM	9.58 RPM
SRP007412_testis	0.34 RPM	115.87 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1692 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1692 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1692 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3725
Gorilla gorilla	retro_ggor_2515
Pongo abelii	retro_pabe_3132

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004907	1 retrocopy	retro_cjac_4142,
Homo sapiens	ENSG00000131462	1 retrocopy	retro_hsap_3725,
Macaca mulatta	ENSMMUG00000016797	1 retrocopy	retro_mmul_1692 ,
Nomascus leucogenys	ENSNLEG00000011686	1 retrocopy	retro_nleu_71,
Pan troglodytes	ENSPTRG00000009211	1 retrocopy	retro_ptro_2520,
Rattus norvegicus	ENSRNOG00000020213	2 retrocopies	retro_rnor_2070, retro_rnor_2072,
Tupaia belangeri	ENSTBEG00000015835	3 retrocopies	retro_tbel_188, retro_tbel_3516, retro_tbel_955,