RetrogeneDB ID: retro_mmul_2533

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:121786752..121788080(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000006642
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2533
ATGAGGGAGATCGTGCACCTGCAGGCTGGCCAGTGTGGTAACCAGATCCGGGCCAAGTTTTGGGAGGTTATCAGTGATGA
ACATGGCATCACCCCACAGGCACATACTATGGGGACAGTGACCTGCAACTGGAGAGGATCAACGTATACTACAACGAGGC
CAGAGGAGGAAATTATGTTCCCAGAGCAGTGCTGGTGGACCTGGAACCCAGCACCATGGACTCTGTCCTTTCCAGCCCCT
TCGGTCAGATCTTTCAGCCAGACAACTTCATGTTTGGCCAATCTGGAGCTGGCAACAACTGGGCAAAGGGGCACTACATG
GAGTGCATGGAGCTGGTGAACGCTGTCCTGGATGTGGTCCAGAAGGAGGCCAAGAGCTGCGACTGCCTTCAAGGCTTCCA
GCTGATCCACTCGCTGGGGGGTGGCATGGGGTCTGGGATGGGCACGCTGCTCATCAGTAAGATCCACAAGGAGTTCCCAG
ACCACATTATGAACACCTTCAGCGTGGTGCTCTCACCCAAAGTGTCAGACATGGTGGTGGAGCCCTACAATGCCACGCTG
TCCGTGCACCAGCTGGTGGAGAATATGGATGAGACCTACTGCATTGACAATGAGGCACTCTATGACATCTGCTTCTGCAC
CCTCAAGCTGACCACCCCCACCTACAAGGACCTCAACCACCTGGTGTCGGCCACCACGAGCAGAGTCACCACCTGCCTGT
GCTTCCCAGGCCAGCTGAACACCAGCCTGCACAAGCTGGCCATCAACATGGTCCCCTTTCCTTACCTGCACTTCTTCATG
CCTGGCTTCACGCCCCTGACGAGCCGGGGCAGCCAGCAGTACCGGGCCCTGACAGTGCCTGAGCTCACCCAGCAGATGTT
CGACACCAAGAACATGATGGCCATGTGCAACCCGCACCACAACTACTATCTGACTGTGGCTGCCGTGTTCTGGGGCCGCG
TGTCCATGAAGGTGGACAAGCAGATGCTGAGCGTGCAGAGCAAGAACAGCAGCTACTTCGTGGAGTGGATCCCCAACAAC
TTGAAGACAGCCGTGTGCAACATCCCGCCCCGTGGCCTGAAGATGGCTGTGACCTTCATCAGCAGTAGCATGGCCTTCCA
GGAGCTGTTCAAGCGCATCTCCAAGCAGTTCAAAGCCATGTTCTGGCCCAAGGCGCTCCTGCACTGGTACACAGGTGAGG
GCATGGATGAGATGGAGTTCACTGAGGCTGACAGCAACATGAATGACCTGGTATCTGAGTACCAGCAGTACCAGGACACC
ACAGCCGAGGAGGGCAAGTTCGAGGAGGGGGCCGAGGAGAAGGTGGCC

Alignment

ORF - retro_mmul_2533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.53 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREIVHLQAGQCGNQIGAKFWEVISDEHGIDP-TGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLE
          MREIVHLQAGQCGNQI.AKFWEVISDEHGI.P.TGTY.GDSDLQLERINVYYNEA.GG.YVPRAVLVDLE
Retrocopy MREIVHLQAGQCGNQIRAKFWEVISDEHGITP<TGTYYGDSDLQLERINVYYNEARGGNYVPRAVLVDLE

Parental  PGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSL
          P.TMDSV.S.PFGQIF.PDNF.FGQSGAGNNWAKGHY.E..ELV..VLDVV.KEA.SCDCLQGFQL.HSL
Retrocopy PSTMDSVLSSPFGQIFQPDNFMFGQSGAGNNWAKGHYMECMELVNAVLDVVQKEAKSCDCLQGFQLIHSL

Parental  GGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYD
          GGG.GSGMGTLLISKI..E.PD.IMNTFSVV.SPKVSD.VVEPYNATLSVHQLVEN.DETYCIDNEALYD
Retrocopy GGGMGSGMGTLLISKIHKEFPDHIMNTFSVVLSPKVSDMVVEPYNATLSVHQLVENMDETYCIDNEALYD

Parental  ICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQ
          ICF.TLKLTTPTY.DLNHLVSAT.S.VTTCL.FPGQLN..L.KLA.NMVPFP.LHFFMPGF.PLTSRGSQ
Retrocopy ICFCTLKLTTPTYKDLNHLVSATTSRVTTCLCFPGQLNTSLHKLAINMVPFPYLHFFMPGFTPLTSRGSQ

Parental  QYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNV
          QYRALTVPELTQQMFD.KNMMA.C.P.H..YLTVAAVF.GR.SMK.VD.QML.VQ.KNSSYFVEWIPNN.
Retrocopy QYRALTVPELTQQMFDTKNMMAMCNPHHNYYLTVAAVFWGRVSMK-VDKQMLSVQSKNSSYFVEWIPNNL

Parental  KTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLV
          KTAVC.IPPRGLKM..TFI..S.A.QELFKRIS.QF.AMF..KA.LHWYTGEGMDEMEFTEA.SNMNDLV
Retrocopy KTAVCNIPPRGLKMAVTFISSSMAFQELFKRISKQFKAMFWPKALLHWYTGEGMDEMEFTEADSNMNDLV

Parental  SEYQQYQDATAEEEGEFEEEAEEEVA
          SEYQQYQD.TA.EEG.FEE.AEE.VA
Retrocopy SEYQQYQDTTA-EEGKFEEGAEEKVA

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	20.95 RPM	9.75 RPM
SRP007412_brain_prefrontal_cortex	24.04 RPM	51.96 RPM
SRP007412_cerebellum	48.69 RPM	9.94 RPM
SRP007412_heart	0.12 RPM	12.72 RPM
SRP007412_kidney	0.12 RPM	21.36 RPM
SRP007412_liver	0.12 RPM	124.33 RPM
SRP007412_testis	1.96 RPM	224.20 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2533 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2533 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2533 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4751
Pan troglodytes	retro_ptro_3166
Pongo abelii	retro_pabe_3698

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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,