RetrogeneDB ID: retro_ptro_151

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:53442792..53443676(+)
• Located in intron of: ENSPTRG00000000748

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB
• Ensembl ID: ENSPTRG00000017939
• Aliases: TUBB, TUBB2A
• Description: Pan troglodytes tubulin, beta (TUBB), mRNA. [Source:RefSeq mRNA;Acc:NM_001045509]

Sequence

>retro_ptro_151
ATGAGGGAAATCGTGCACATCCAGGCCTGTCAGTGTGGCAACCGGATGGGTGCCAAGTGCTGGGATGTGATCAGTGATGA
ACGTGAAATCGACCCCACCAGCACCTAACATGGGGACAGCGACCTGCAGCTGGACTGTGTCACCATGTACTACAGTGAAG
CCATAGATGGCAAATATGTTCCTTGTGCTAACCTGGTGGATCTAGAACCTGGGACCATGGACTCTGCTAGCTCAGGCCCT
TTTGGCCAGGTGCTTAAACCAGACAACTTTGTTTTTGGTCAATCTGGGGCAGGCAACAACTGGGCCAAAGGCCACTACAT
AGAGGGGGCCAAGCTGGTTGATTCAGTTGTAGATGTGGTGCAGGAGTAAGAGAGCTGTGACTGCCTGCAGGGCTTCCAGC
TGACCCACTCAATGGGCTCTGGAATGGGTACTCTCTTTATCAGCAAGATCCGAGAAGCGTGCCCTGATTGCATCATGAAC
ACCTTCAGTGTAGTGCCTCCACCCAAAGTGTCTGACACCGTGGTCGAGCCCTACAACATCACCCTCTCCGTCCATCAGTC
GGTAGAGAACACTGATGAGACCTACTGCATTGACAATGAGGCCCTCTATGACATCTGCTTCCGCACTTTGAAGCTGACCA
CACCAAACTATGGGGACTTGAACCACCTTGTCTCAGCCACCACAAGCAGTGTTACCACCTGTCTCCACTTCCCTGGCCAG
CTCAATGCTGACCTCCGCAAGTTGGCAGTCAAACTGGTGCCCTTACCACATCTCCACTACTTCATGGCTGGCTTTGCCCT
CTCACCAGCTGTGGAAGCTAGCAGCATCGAGCTTTCACAGTGACCAAACTCATCCGGCAGGATTTCAATGCCAAGAACAT
AATG

Alignment

ORF - retro_ptro_151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.07 %
• Parental protein coverage: 67.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEP
          MREIVHIQA.QCGN..GAK.W.VISDE..IDPT.T.HGDSDLQLD....YY.EA..GKYVP.A.LVDLEP
Retrocopy MREIVHIQACQCGNRMGAKCWDVISDEREIDPTST*HGDSDLQLDCVTMYYSEAIDGKYVPCANLVDLEP

Parental  GTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLG
          GTMDS..SGPFGQ...PDNFVFGQSGAGNNWAKGHY.EGA.LVDSV.DVV..E.ESCDCLQGFQLTHS..
Retrocopy GTMDSASSGPFGQVLKPDNFVFGQSGAGNNWAKGHYIEGAKLVDSVVDVVQ-E*ESCDCLQGFQLTHSM-

Parental  GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDI
          ...GSGMGTL.ISKIRE..PD.IMNTFSVVP.PKVSDTVVEPYN.TLSVHQ.VENTDETYCIDNEALYDI
Retrocopy ---GSGMGTLFISKIREACPDCIMNTFSVVPPPKVSDTVVEPYNITLSVHQSVENTDETYCIDNEALYDI

Parental  CFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFA-PLTSRGSQ
          CFRTLKLTTP.YGDLNHLVSAT.S.VTTCL.FPGQLNADLRKLAV..VP.P.LH.FM.GFA.PLTS.GS.
Retrocopy CFRTLKLTTPNYGDLNHLVSATTSSVTTCLHFPGQLNADLRKLAVKLVPLPHLHYFMAGFA<PLTSCGS*

Parental  QYRALTVPELTQQVFDAKNMM
          Q.RA.TV..L..Q.F.AKN.M
Retrocopy QHRAFTVTKLIRQDFNAKNIM

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_prefrontal_cortex	0.48 RPM	376.72 RPM
SRP007412_cerebellum	0.65 RPM	279.51 RPM
SRP007412_heart	0.41 RPM	196.91 RPM
SRP007412_kidney	1.10 RPM	189.18 RPM
SRP007412_liver	3.60 RPM	550.20 RPM
SRP007412_testis	0.00 RPM	49.85 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_151 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_151 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_151 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_155
Gorilla gorilla	retro_ggor_244
Pongo abelii	retro_pabe_467
Macaca mulatta	retro_mmul_375

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
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	ENSMMUG00000023684	2 retrocopies	retro_mmul_2501, retro_mmul_375,
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,
Pan troglodytes	ENSPTRG00000008496	1 retrocopy	retro_ptro_2369,
Pan troglodytes	ENSPTRG00000017939	3 retrocopies	retro_ptro_151 , retro_ptro_2527, retro_ptro_2677,
Pan troglodytes	ENSPTRG00000023373	2 retrocopies	retro_ptro_2403, retro_ptro_3166,