RetrogeneDB ID: retro_ggor_244

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:54682650..54683537(+)
• Located in intron of: ENSGGOG00000024745

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_244
ATGAGGGAAATCGTGCACATCCAGGCCTGTCAGTGTCGCAACCGGATGGGTGCCAAGTGCTGGGATGTGATCAGTGATGA
ACGTGAAATCGACCCCACCAGCACCTAACATGGGGACAGCGACCTGCAGCTGGACTGTGTCTCCATGTACTACAGTGAAG
CCATAGATGGCAAATATGTTCCTTGTGCTAACCTGGTGGATCTAGAACCTGGGACCATGGACTCTGCTAGCTCAGGCCCT
TTTGGCCAGGTGCTTAAACCAGACAACTTTGTTTTTGGTCAATCTGGGGCAGGCAACAACTGGGCCAAAGGCCACTACAT
AGAGGGGGCCAAGCTGGTTGATTCAGTTGTAGATGTGGTGCAGGAGGAGTAAGAGAGCTGTGACTGCCTGCAGGGCTTCC
AGCTGACCCACTCAATGGGCTCTGGAATGGGTACTCTCTTTATCAGCAAGATCCGAGAAGAGTGCCCTGATTGCATCATG
AACACCTTCAGTGTGGTGCCTCCACCCACAGTGTCTGACACCGTGGTCGAGCCCTACAACATCACCCTCTCCGTCCATCA
GTCGGTAGAGAACACTGATGAGACCTACTGCATTGACAACGAGGCCCTCTATGACATCTGCTTCCGCACTTTGAAGCTGA
CCACACCAAACTATGGGGACTTGAACCACCTTGTCTCAGCCACCATAAGCAGTGTTACCACCTGTCTCCGCTTCCCTGGC
CAGCTCAATGCTGACCTCCACAAGTTGGCAGTCAAACTGGTGCCCTTACCACATCTCCACTACTTCATGGCTGGCTTTGC
CCTCTCACCAGCTGTGGAAGCCAGCAGCATCGAGCTTTCACAGTGCCCAAACTCATCCGGCAGGATTTCAATGCCAAGAA
CATAATG

Alignment

ORF - retro_ggor_244 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.4 %
• Parental protein coverage: 67.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEP
          MREIVHIQA.QC.N..GAK.W.VISDE..IDPT.T.HGDSDLQLD..S.YY.EA..GKYVP.A.LVDLEP
Retrocopy MREIVHIQACQCRNRMGAKCWDVISDEREIDPTST*HGDSDLQLDCVSMYYSEAIDGKYVPCANLVDLEP

Parental  GTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLG
          GTMDS..SGPFGQ...PDNFVFGQSGAGNNWAKGHY.EGA.LVDSV.DVV..E.ESCDCLQGFQLTHS.G
Retrocopy GTMDSASSGPFGQVLKPDNFVFGQSGAGNNWAKGHYIEGAKLVDSVVDVVQEE*ESCDCLQGFQLTHSMG

Parental  GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDI
          .G....MGTL.ISKIREE.PD.IMNTFSVVP.P.VSDTVVEPYN.TLSVHQ.VENTDETYCIDNEALYDI
Retrocopy SG----MGTLFISKIREECPDCIMNTFSVVPPPTVSDTVVEPYNITLSVHQSVENTDETYCIDNEALYDI

Parental  CFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFA-PLTSRGSQ
          CFRTLKLTTP.YGDLNHLVSAT.S.VTTCLRFPGQLNADL.KLAV..VP.P.LH.FM.GFA.PLTS.GSQ
Retrocopy CFRTLKLTTPNYGDLNHLVSATISSVTTCLRFPGQLNADLHKLAVKLVPLPHLHYFMAGFA<PLTSCGSQ

Parental  QYRALTVPELTQQVFDAKNMM
          Q.RA.TVP.L..Q.F.AKN.M
Retrocopy QHRAFTVPKLIRQDFNAKNIM

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	0.82 RPM	302.16 RPM
SRP007412_cerebellum	0.98 RPM	211.45 RPM
SRP007412_heart	0.16 RPM	106.69 RPM
SRP007412_kidney	0.37 RPM	102.02 RPM
SRP007412_liver	3.80 RPM	176.52 RPM
SRP007412_testis	0.41 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_244 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_244 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_155
Pan troglodytes	retro_ptro_151
Pongo abelii	retro_pabe_467
Macaca mulatta	retro_mmul_375

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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,