RetrogeneDB ID: retro_ptro_3166

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:124077428..124078759(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB2C
• Ensembl ID: ENSPTRG00000023373
• Aliases: TUBB2C, TUBB2
• Description: Pan troglodytes tubulin, beta 2C (TUBB2C), mRNA. [Source:RefSeq mRNA;Acc:NM_001246378]

Sequence

>retro_ptro_3166
ATGCGGGAGATCATGCACCTGCAGGCCGGCCAGTGTGGCAGCCAGATCAGGGCCAAGTTTTGGGAGGTTATCAGTGACGA
ACATGGGCATCGACCCCACAGGCACATACTATAGGGACAGTGACCTGCAACCAGAGAGGATCAACGTGTACTACAACAAG
GCCAGAGGAGGAAATTATGTCCCCAGAGCGGTGCTGGTGGACCTGGAGCCCAGCACCATGGACTCTATCCTTTCCGGCCC
CTTTGGTCAGATCTTTCGGCCGGACAACTTCGTGTTTGGCCAGTCCAGAGCCGGCAACAACTGGGTGAAGGGGCACTACA
TGGAGGGCACAGAGCTGGTAGACACTGTCCTGGACGTGGTCCAGAGGGAGGCCTAGAACTGCGACTGCCTTCAAGGCTTC
CAGCTGACGCACTTGCTCGGGGGTGGCACGGGGTCCGGGATGGGCACGCTGCTCATCAGTAAGATCCGTGAGGAGTTCCC
AGACTGCATCATGAACACCTTCAGCATGGTGCCCTCGCCCAAAGTGTCAGATACGGTGTGGAGCCCTACAATGCCATGCT
GTCTGTGCACCAGCTGGTGGAGAATACGAATGAGACCTACTGCATCAACAATGGGGCACTCTATGACATCTGCTTCCGCA
CCCTTAAGCTGACCACCCCCACCTACGGGGACCTCAACCACCTGGTGTCAGCCACCATGAGCAGAGTCACCACCTGCCTG
TGCTTCCTGGGCCAGCTGAACACCAACCTGCACAAGCTGGCCGTCAACATGGTCCCCTTTCCTTGCCCGCACTTCTTCAT
GCCTGGCTTCGCACCCCTGACCAGCCGGGGCAGCCAGCAGTACCAGGCCCTGAGGGTGCCTGAGCTCACGCAGCAGATGT
TCGATGCCAAGAACATGATGGCCATGTGCAACCCGCGACATGGCCGCTACCTGACCATGGCCACCGTGTTCCGGGCCGCA
TGTCCATGAAGGAGGTGGACAGGCAGATGCTGAGCGTGCAGAGCAAGAACAGCAGCTACTTCGTGGAGTGGATCCCCAAC
AACATGAAGACGGCCGTGTGCGACATCTCGCCCCAGGGCCTGAAGATAGCTGCAACTTTCATCAGCAACAACACAGCCTT
CCAGGAGCTGTTCAAGCGCATCTCTGCACAGTTCACGGCCATGTTGTGGTGCAAGGCGTTCCTGCACTGGTACACAGGCG
AGGGCATGGACGAGATGGAGTTCACCGAGGCTGACAGCAACATGAATGACCTGGTATCTGAGTACCAGCAGTACCAGGAT
GCCACAGCCGAGGAGGGCGAGTTCAAGCAGGAGGCCAAGGAGGAGGTGGCC

Alignment

ORF - retro_ptro_3166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MREIVHLQAGQCGNQIGAKFWEVISDEHG-IDPTGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLE
          MREI.HLQAGQCG.QI.AKFWEVISDEHG.IDPTGTY..DSDLQ.ERINVYYN.A.GG.YVPRAVLVDLE
Retrocopy MREIMHLQAGQCGSQIRAKFWEVISDEHG>IDPTGTYYRDSDLQPERINVYYNKARGGNYVPRAVLVDLE

Parental  PGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSL
          P.TMDS..SGPFGQIFRPDNFVFGQS.AGNNW.KGHY.EG.ELVD.VLDVV..EA..CDCLQGFQLTH.L
Retrocopy PSTMDSILSGPFGQIFRPDNFVFGQSRAGNNWVKGHYMEGTELVDTVLDVVQREA*NCDCLQGFQLTHLL

Parental  GGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTV-VEPYNATLSVHQLVENTDETYCIDNEALY
          GGGTGSGMGTLLISKIREE.PD.IMNTFS.VPSPKVSDTV.VEPYNA.LSVHQLVENT.ETYCI.N.ALY
Retrocopy GGGTGSGMGTLLISKIREEFPDCIMNTFSMVPSPKVSDTV<VEPYNAMLSVHQLVENTNETYCINNGALY

Parental  DICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGS
          DICFRTLKLTTPTYGDLNHLVSATMS.VTTCL.F.GQLN..L.KLAVNMVPFP..HFFMPGFAPLTSRGS
Retrocopy DICFRTLKLTTPTYGDLNHLVSATMSRVTTCLCFLGQLNTNLHKLAVNMVPFPCPHFFMPGFAPLTSRGS

Parental  QQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFR-GRMSMKEVDEQMLNVQNKNSSYFVEWIPN
          QQY.AL.VPELTQQMFDAKNMMA.C.PRHGRYLT.A.VFR.GRMSMKEVD.QML.VQ.KNSSYFVEWIPN
Retrocopy QQYQALRVPELTQQMFDAKNMMAMCNPRHGRYLTMATVFR<GRMSMKEVDRQMLSVQSKNSSYFVEWIPN

Parental  NVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMND
          N.KTAVCDI.P.GLK..ATFI.N.TA.QELFKRIS.QFTAM...KAFLHWYTGEGMDEMEFTEA.SNMND
Retrocopy NMKTAVCDISPQGLKIAATFISNNTAFQELFKRISAQFTAMLWCKAFLHWYTGEGMDEMEFTEADSNMND

Parental  LVSEYQQYQDATAEEEGEFEEEAEEEVA
          LVSEYQQYQDATA.EEGEF..EA.EEVA
Retrocopy LVSEYQQYQDATA-EEGEFKQEAKEEVA

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	0.18 RPM	194.76 RPM
SRP007412_cerebellum	7.78 RPM	51.94 RPM
SRP007412_heart	0.00 RPM	81.03 RPM
SRP007412_kidney	0.05 RPM	104.97 RPM
SRP007412_liver	0.00 RPM	106.98 RPM
SRP007412_testis	0.11 RPM	561.17 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3166 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3166 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3166 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4751
Pongo abelii	retro_pabe_3698
Macaca mulatta	retro_mmul_2533

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 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,
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	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 ,
Rattus norvegicus	ENSRNOG00000010170	2 retrocopies	retro_rnor_742, retro_rnor_867,