RetrogeneDB ID: retro_nleu_498

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397266.1:45018009..45019136(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB
• Ensembl ID: ENSNLEG00000005348
• Aliases: None
• Description: None

Sequence

>retro_nleu_498
TTGAGGGAGATCGTGCACCTGCAGGCTGGTGAGTTTGGCAACTAGTTCTACGGGGTGATCAGTGATGAGCATGCCATCGA
GCCCACTGGCACTTAGCATGGGGATAGCAACCTGCAGCTGGAGTGCATCAGTGTGTACTACAATGAGACCACTGGTGGCA
AGTATGTGCCCCACGCTGAGCTCATGGATCTGGAGCCCAGCACCGTGGACTCTCGTGTACTCAGGCTCCATCGTGCAGAT
CTTACGGCTGGACAACTTCATCTTCCATCAGAGTGGTGCCGGAAACAACTAGGCCAATGGGCACTACACAGAAGGTGCGG
AGCTGGTGGATTCGGTACTGGACATTGTGAGGAGGGAGGCTGAGAGCTGTGACTGCCTGCAGGGTTTCCAGCTGACCTGG
GAGCAGGGACTGGGCCTGAGAGGGGTACCCCTCTCATCAGCAAGATCCCAGGGAAGTATCCAGGCAGGATCGTGAACATG
TTCAGTGTGCCCTTGCGCAAGGTGTCAGACATGGGGGTGGAGCCCTAAAACATCACCTTCTCAGTCCGCCAACTGATAGA
AAACACAGATATGACCTATTGCATTGATAATGAAACTCTCCAGAACGTCTGCTTCAGAACCCTAAAGCTGACCACACCCA
CCTATGATGACTTGAACCACTTGGTGTCTGCCACCATAAGTGGGGTCACTACCTGCCTAGGCTTCCCCAGCCAGCTCAAT
GTTGACCTGCAGAAGCTGGCTATGTACGTGGTACCATTCCCTACCTGCACTTCTTTATGCCCGGCTTCACCCTGCTGACC
ATCCAGGGCAGCCAGCACTACCAGGCCCTGATAGTGCCTGAGCTGACCCAGCAGATGTTTGATGCCAAGAACATGATGGC
TCCCTGAGACTCCTGCCATGGCCACTACCTAAAGGTGACCACAGTGTTCACAGACTACATGTCCATGAAGGAGTTGGATG
AGCAAATGCTTAATATCCAAAACAAGAACAGCAGCTACTTTGTTGAGTGAATCCCCAACCATGTGAAAACAGCTGTCTGT
GACATCCCACTCTTGGGGCTATGAATGTCTGCCACCTTCATCAGCAACAGCGTGGCCATCCAGGAGCTGTTCAAGCACAT
CTCTGAG

Alignment

ORF - retro_nleu_498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.24 %
• Parental protein coverage: 86.26 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

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

Parental  GTMDS-VRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQ-GFQLTHS
          .T.DS.V.SG...QI.R.DNF.F.QSGAGNN.A.GHYTEGAELVDSVLD.VR.EAESCDCLQ.GF.....
Retrocopy STVDS>VYSGSIVQILRLDNFIFHQSGAGNN*ANGHYTEGAELVDSVLDIVRREAESCDCLQ<GFPA--D

Parental  LGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALY
          LG.GTG...GT.LISKI...YP.RI.N.FSV.P..KVSD..VEP.N.T.SV.QL.ENTD.TYCIDNE.L.
Retrocopy LGAGTGPERGTPLISKIPGKYPGRIVNMFSV-PLRKVSDMGVEP*NITFSVRQLIENTDMTYCIDNETLQ

Parental  DICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPR-LHFFMPGFAPLTSRG
          ..CFRTLKLTTPTY.DLNHLVSAT.SGVTTCL.FP.QLN.DL.KLA...VPFP..LHFFMPGF..LT..G
Retrocopy NVCFRTLKLTTPTYDDLNHLVSATISGVTTCLGFPSQLNVDLQKLAMYVVPFPT<LHFFMPGFTLLTIQG

Parental  SQQYRALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPN
          SQ.Y.AL.VPELTQQ.FDAKNMMA..D..HG.YL.V..VF...MSMKE.DEQMLN.QNKNSSYFVE.IPN
Retrocopy SQHYQALIVPELTQQMFDAKNMMAP*DSCHGHYLKVTTVFTDYMSMKELDEQMLNIQNKNSSYFVE*IPN

Parental  NVKTAVCDIPPRGLKMAVTFIGNSTAIQELFKRISE
          .VKTAVCDIP..GL.M..TFI.NS.AIQELFK.ISE
Retrocopy HVKTAVCDIPLLGL*MSATFISNSVAIQELFKHISE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_498 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006969	2 retrocopies	retro_btau_471, retro_btau_55,
Canis familiaris	ENSCAFG00000000443	1 retrocopy	retro_cfam_1860,
Echinops telfairi	ENSETEG00000013572	1 retrocopy	retro_etel_641,
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,
Mustela putorius furo	ENSMPUG00000011690	3 retrocopies	retro_mputfur_1123, retro_mputfur_607, retro_mputfur_807,
Nomascus leucogenys	ENSNLEG00000005348	1 retrocopy	retro_nleu_498 ,
Nomascus leucogenys	ENSNLEG00000015940	1 retrocopy	retro_nleu_3106,
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,
Pongo abelii	ENSPPYG00000016419	4 retrocopies	retro_pabe_2920, retro_pabe_3210, retro_pabe_3698, retro_pabe_467,
Pan troglodytes	ENSPTRG00000017939	3 retrocopies	retro_ptro_151, retro_ptro_2527, retro_ptro_2677,