RetrogeneDB ID: retro_ptro_2403

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:154593008..154594321(+)
• 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_2403
TTGAGGGAGATCGTGCACCTGCAGGCTGGTGAGTTTGGCAACTAGTTCTACGGGGTGATCAGTGATGAGCATGCCATCGA
GCCTACTGGCACTTAGCATGGGGATAGCAACCTGCAGCTGGAGTGCATCAGTGTGTACTGCAATGAGACCACCGGTGGCA
AGTATGTGCCCCACGCTGAGCTCATGGATCTGGAGCCCAGCACCGGGGACTCTGGTGTGCTCAGGCTCCTTCGTGCAGAT
CTTACGGCTGGACAACTTCATCTTCCATCAGAGTGGTGCCGGAAACAACTGGGCCAATGGGCACCACGCAGAAGGTGCGG
AGCTGGTGGATTCGGTACTGGACATTGTGAGGAGGGAGGCTGAGAGCTGTGACTGCCTGCAGGATTTCCAGCTGACCCAC
TCCCTAGGAGCAGGGACTGGGCCTAAGAGGGGTACCCCTCTCATCAGCAAGATCCCAGAGAAGTATCCAGACAGGATCTG
GAACAAGTTCAGTATGCCCTTACGCAAGGTGTCAGACATGGGGGTGGAGCCCTAAAACATCACCTTCTCAGTCCACCAAC
TGGTAGAAAACACAGATATGACCTATTTCATTGATAATGAAACTCTCCATAACGTCTGCTTCAGAACCCTAAAGCTGACC
ACACCCACCTATGGTGACTTGAACCACTTGGTGTCTGCCGCCATAAGTGGGGTCACTACCTGACTAGGCTTCCCCAACCA
GCTCAATGCTGACCTGCAGAAGCTGGCTATGTACATGGTCCCATTCCCTACCTGCACTTCTTTATGCCTGTCTTCACCCT
GCTGACCATCCACAGCAGCCAGCATTACCAGGCCCTCATAGTGCCTGAGCTCACCCAGCAGATGGTTGATGCCAAGAACA
TGATGGTTCCCTGAGACCCCTGCCATGGCCACTACCTAAAGGTGGCCACAGTGTTCACGGACTACATGTCCATGAAGGAG
TTGGATGAGCAAATGCTTAATGTCCGAAACAAGAACAGCAGCTACTTTGTTGAGTGAATCCCCAACTATGTGAAAACAGC
TGTCTGTGACATCCCACTCTTGGGGCTATAAATGTCTGCCACCTTCATCAGCAACAGTGTGGCCATCCAGGAGCTGTTCA
AGCACATCTCTGAGTGGTCATGTTTCGGTGCAAAGCCTTTCTGCACTGGCACATGGGCAAGAGCATGGACTAGATGGAGT
TCACCAAGGCTGACAGCAACATGAACAACCTGGTGTCCCGGTACCAGTAATACCAGGACACCTCAGCCAAGGAGGAGAGA
AAGGTTGAGAAGGAGGCCAAGAAGAAGGTGGCC

Alignment

ORF - retro_ptro_2403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 9
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MREIVHLQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLEP
          .REIVHLQAG......G..F..VISDEH.I.PTGT.HGDS.LQLE.I.VY.NE.TGGKYVP.A.L.DLEP
Retrocopy LREIVHLQAG----EFGN*FYGVISDEHAIEPTGT*HGDSNLQLECISVYCNETTGGKYVPHAELMDLEP

Parental  GTMDS-VRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSL
          .T.DS.V.SG.F.QI.R.DNF.F.QSGAGNNWA.GH..EGAELVDSVLD.VR.EAESCDCLQ.FQLTHSL
Retrocopy STGDS>VCSGSFVQILRLDNFIFHQSGAGNNWANGHHAEGAELVDSVLDIVRREAESCDCLQDFQLTHSL

Parental  GGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYD
          G.GTG...GT.LISKI.E.YPDRI.N.FS..P..KVSD..VEP.N.T.SVHQLVENTD.TY.IDNE.L..
Retrocopy GAGTGPKRGTPLISKIPEKYPDRIWNKFSM-PLRKVSDMGVEP*NITFSVHQLVENTDMTYFIDNETLHN

Parental  ICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPR-LHFFMPGFAPLTSRGS
          .CFRTLKLTTPTYGDLNHLVSA..SGVTT.L.FP.QLNADL.KLA..MVPFP..LHFFMP.F..LT...S
Retrocopy VCFRTLKLTTPTYGDLNHLVSAAISGVTT*LGFPNQLNADLQKLAMYMVPFPT<LHFFMPVFTLLTIHSS

Parental  QQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNN
          Q.Y.AL.VPELTQQM.DAKNMM...DP.HG.YL.VA.VF...MSMKE.DEQMLNV.NKNSSYFVE.IPN.
Retrocopy QHYQALIVPELTQQMVDAKNMMVP*DPCHGHYLKVATVFTDYMSMKELDEQMLNVRNKNSSYFVE*IPNY

Parental  VKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAF-LHWYTGEGMDEMEFTEAESNMND
          VKTAVCDIP..GL.MSATFI.NS.AIQELFK.ISE.....F..K.F.LHW..G..MD.MEFT.A.SNMN.
Retrocopy VKTAVCDIPLLGL*MSATFISNSVAIQELFKHISE--WSCFGAKPF<LHWHMGKSMD*MEFTKADSNMNN

Parental  LVSEYQQYQDATAEEEGEFEEEAEEEVA
          LVS.YQ.YQD..A.EE...E.EA...VA
Retrocopy LVSRYQ*YQDTSAKEERKVEKEAKKKVA

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	0.00 RPM	194.76 RPM
SRP007412_cerebellum	0.00 RPM	51.94 RPM
SRP007412_heart	0.00 RPM	81.03 RPM
SRP007412_kidney	0.00 RPM	104.97 RPM
SRP007412_liver	0.00 RPM	106.98 RPM
SRP007412_testis	0.00 RPM	561.17 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2403 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2403 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2403 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3537
Gorilla gorilla	retro_ggor_2388
Pongo abelii	retro_pabe_2920
Macaca mulatta	retro_mmul_1849

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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,