RetrogeneDB ID: retro_ggor_2388

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:153923191..153924325(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB
• Ensembl ID: ENSGGOG00000022655
• Aliases: None
• Description: None

Sequence

>retro_ggor_2388
TTGAGGGAGATCGTGCACCTGCAGGCTGGTGAGTTTGGCAACTAGTTCTACGGGGTGATCAGTGATGAGCATGCCATCGA
GCCTACTGGCACTTAGCATGGGGATAGCAACCTGCAGCTGGAGTGCATCAGTGTGTACTACAATGAGACCACCGGTGGCA
AGTATGTGCCCCACGTTGAGCTCATGGATCTGGAGCCCAGCACCGGGGACTCGGGTGTGCTCAGGCTCCTTCGTGCAGAT
CTTACGGCTGGACAACTTCATCTTCCATCAGAGTGGTGCTGGAAACAACTGGGCCAATGGGCACTACGCAGAAGGTGCGG
AGCTGGTGGATTCGGTACTGGACATTGTGAGGAGGGAGGCTGAGAGCTGTGACTGCCTGCAGGATTTCCAGCTGACCCAT
TCCCTAGGAGCAGGGACTGGGCCTAAGAGGGGTACCCCTCTCATCAGCAAGATCCCAGAGAAGTATCCAGACAGGATCTT
GAACAAGTTCAGTGTGCCCTTACGCAAGGTGTCAGACATGGGGGTGGAGCCCTAAAACATCACCTTCTCAGTCCACCAAC
TGGTAGAAAACACAGATATGACCTATTGCATTGATAATGAAGCTCTCCATAACGTCTGCTTCAGAACCCTAAAGCTGACC
ACACCCACCTATGGTGACTTGAACCACTTGGTGTCTGCTGCCATAAGTGGGGTCACTACCTGCCTAGGCTTCCCCAACCA
GCTCAATGCTGACCTGCAGAAGCTGGCTATGTACATGGTCTCATTCCCTACCTGCACTTCTTTATGCCTGTCTTCACCCT
GCTGACCATCCACAGCAGCCAGCACTACCAGGCCCTCATAGTGCCTGAGCTCACCCAGCAGATGGTTGATGCCAAGAACA
TGATGGTTCCCTGAGACCCCTGCCATGGCCACTACCTAAAGGTGGCCACAGTGTTCACGGACTGCATGTCCATGAAGGAG
TTGGATGAGCAAATGCTTAATGTCCAAAACAAGAACAGCAGCTACTTTGTTGAGTGAATCCCCAACTATGTGAAAACAGG
TGTCTGTGACATCCCACTCTTGGGGCTATAAATGTCTGCCACCTTCATCAGCAACAGCGTGGCCATCCAGGAGCTGTTCA
AGCACATCTCTGAG

Alignment

ORF - retro_ggor_2388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.51 %
• Parental protein coverage: 86.26 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEP
          .REIVH.QAG......G..F..VISDEH.I.PTGT.HGDS.LQL..ISVYYNE.TGGKYVP...L.DLEP
Retrocopy LREIVHLQAG----EFGN*FYGVISDEHAIEPTGT*HGDSNLQLECISVYYNETTGGKYVPHVELMDLEP

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

Parental  GGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYD
          G.GTG...GT.LISKI.E.YPDRI.N.FSV.P..KVSD..VEP.N.T.SVHQLVENTD.TYCIDNEAL..
Retrocopy GAGTGPKRGTPLISKIPEKYPDRILNKFSV-PLRKVSDMGVEP*NITFSVHQLVENTDMTYCIDNEALHN

Parental  ICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPR-LHFFMPGFAPLTSRGS
          .CFRTLKLTTPTYGDLNHLVSA..SGVTTCL.FP.QLNADL.KLA..MV.FP..LHFFMP.F..LT...S
Retrocopy VCFRTLKLTTPTYGDLNHLVSAAISGVTTCLGFPNQLNADLQKLAMYMVSFPT<LHFFMPVFTLLTIHSS

Parental  QQYRALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNN
          Q.Y.AL.VPELTQQ..DAKNMM...DP.HG.YL.VA.VF...MSMKE.DEQMLNVQNKNSSYFVE.IPN.
Retrocopy QHYQALIVPELTQQMVDAKNMMVP*DPCHGHYLKVATVFTDCMSMKELDEQMLNVQNKNSSYFVE*IPNY

Parental  VKTAVCDIPPRGLKMAVTFIGNSTAIQELFKRISE
          VKT.VCDIP..GL.M..TFI.NS.AIQELFK.ISE
Retrocopy VKTGVCDIPLLGL*MSATFISNSVAIQELFKHISE

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	302.16 RPM
SRP007412_cerebellum	0.00 RPM	211.45 RPM
SRP007412_heart	0.00 RPM	106.69 RPM
SRP007412_kidney	0.00 RPM	102.02 RPM
SRP007412_liver	0.00 RPM	176.52 RPM
SRP007412_testis	0.00 RPM	156.23 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2388 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2388 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3537
Pan troglodytes	retro_ptro_2403
Pongo abelii	retro_pabe_2920
Macaca mulatta	retro_mmul_1849

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000002192	1 retrocopy	retro_ggor_2364,
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	ENSPTRG00000017939	3 retrocopies	retro_ptro_151, retro_ptro_2527, retro_ptro_2677,