RetrogeneDB ID: retro_ptro_2677

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:26741178..26742477(+)
• Located in intron of: None

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_2677
AGGTGTGGCAACCAGATCGGTGCCAAGTTCTGGGAGGTGATCAGTGATGAACATGGCATCGACCCCACTGGCACCTACCA
CGGGGACAGCGACCTGCAGCTGGACCGCATCTCCGTGTACTACAGTGAAGCCACTGATGGCAGATATGTTCCTCGTGCCA
TCCTGGTGGATCTAGAACCTGAGACCATGGACTCTGTTCGCTCAGGTCCTTTTGGCCAGATCTTTAGACCAGACAACTTT
GTATTTGGTCAGTCTGGGGCAGGTAACAACTGGGCCAAAGGCCACTACACAGAGGGCGCCAAGCTGGTTGATTCTGTCCT
GGATGTGGTACGGAAGGAGGCAGAGAGCTGTGACTGCCTGCAGGGCTTCCAGCTGACCCACTCACTGGGTGGGGGCACAG
GCTCTGGAATGGGCACTCTCCTTATCAGCAAGATCCGAGAAGAATACCCTGATCGCATCATGCATACCTTCAGTGTGGTG
CCTTCACCCAAAGTGTCTGACACCGTGATCGAGCCCTACAATTCTACCCTCTCCATCCATCAGTTGGTAGAGAACACTGA
TGAGACCTATTGCATTGACAACGAGGCCCTCTATGATATCTGCTTCCGCACTCTGAGGCTGACCACACCAACCTATGGGG
ATCTGAACCACCTCGTCTCAGACACCATGAGTGGTGTCACCACCTGCCTCTGCTTCCCTGGCCAGCTCAATGCTGACCTC
CGCAAGTTGGCAGTTAACATGGTCCCCTTCCCACGTCTCCATTTCTTTATGCCTGGCTTTGCCCCTCTCACCAGCCATGG
AAGCCAGCAGTACCGAGCTCTCACAGTGCCGGAACTCACCCAGCAGGTCTTTGATGCCAAGAGCATGAATGCTGCCTGTG
ACCCCCACCACGGCCGATACCTCACCGTGGCTGCTGACTTCCGTGGTCGGATGTCCATGAAGGAGGTCGATGAGCAGATG
TTTAATGTGCAGAACAAGAACAGCAGCTACTTTGTGGAATGGATCCCCAACAATATCAAGACAGCTGTCTGTGACATCCC
ACCTCGTGGCCTCAAGATGGCAGTCACCTTCATCGGCAGTAGCACGGCCATCCAGGAGATCTTCAAGCACATCTCGGAGC
AGTTCACTGCCATGTTCCGCCGGAAGGCCTTCCTCCACTGGTACACAGGCGAGGGCATGGACGAGATGGAGTTCACCGAG
GCTGAGAGCAACATGAACGACCTCGTCTCTGAGTATCAGCAGTACCAGGATGCCACCGCAGAAGAGGAGGATTTTGGTGA
GGAGGCCGAAGAGGAGGCC

Alignment

ORF - retro_ptro_2677 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.47 %
• Parental protein coverage: 97.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEPGTMDSVRSGP
          .CGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYY.EAT.G.YVPRAILVDLEP.TMDSVRSGP
Retrocopy RCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYSEATDGRYVPRAILVDLEPETMDSVRSGP

Parental  FGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTL
          FGQIFRPDNFVFGQSGAGNNWAKGHYTEGA.LVDSVLDVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTL
Retrocopy FGQIFRPDNFVFGQSGAGNNWAKGHYTEGAKLVDSVLDVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTL

Parental  LISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTP
          LISKIREEYPDRIM.TFSVVPSPKVSDTV.EPYN.TLS.HQLVENTDETYCIDNEALYDICFRTL.LTTP
Retrocopy LISKIREEYPDRIMHTFSVVPSPKVSDTVIEPYNSTLSIHQLVENTDETYCIDNEALYDICFRTLRLTTP

Parental  TYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELT
          TYGDLNHLVS.TMSGVTTCL.FPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTS.GSQQYRALTVPELT
Retrocopy TYGDLNHLVSDTMSGVTTCLCFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSHGSQQYRALTVPELT

Parental  QQVFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
          QQVFDAK.M.AACDP.HGRYLTVAA.FRGRMSMKEVDEQM.NVQNKNSSYFVEWIPNN.KTAVCDIPPRG
Retrocopy QQVFDAKSMNAACDPHHGRYLTVAADFRGRMSMKEVDEQMFNVQNKNSSYFVEWIPNNIKTAVCDIPPRG

Parental  LKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATA
          LKMAVTFIG.STAIQE.FK.ISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATA
Retrocopy LKMAVTFIGSSTAIQEIFKHISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATA

Parental  EEEEDFGEEAEEEA
          .EEEDFGEEAEEEA
Retrocopy -EEEDFGEEAEEEA

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	0.36 RPM	376.72 RPM
SRP007412_cerebellum	0.25 RPM	279.51 RPM
SRP007412_heart	0.15 RPM	196.91 RPM
SRP007412_kidney	0.34 RPM	189.18 RPM
SRP007412_liver	0.23 RPM	550.20 RPM
SRP007412_testis	0.11 RPM	49.85 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2677 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2677 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2677 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3944
Gorilla gorilla	retro_ggor_2651
Pongo abelii	retro_pabe_3250

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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,