RetrogeneDB ID: retro_pabe_2920

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:156164296..156165430(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB
• Ensembl ID: ENSPPYG00000016419
• Aliases: TUBB2A, TUBB, TUBB5
• Description: Tubulin beta chain [Source:UniProtKB/Swiss-Prot;Acc:Q5R943]

Sequence

>retro_pabe_2920
TTGAGGGAGAGCGTGCACCTGCAGGCTGGTGAGTTTGGCAACTAGTTCTATGGGGTGATCAGTGATGAGCATGCCATCAA
GCCTACTGGCTCTTAGCATGGGGATAGCAACCTGCAGCTGGAGTGCATCAGTGTGTACTACAATGAGACCACCGGTGGCA
AGTATGTGCCCCATGCTGAGCTCATGGATCTAGAGCCCAGCACTGTGGACTCTCGTGTATTCAGGCTCCATCGTGCAGAT
CTTACAGCTGGACAACTTCATCTTCCATCAGAGTGGTGCCGGAAACAACTGGGCCAATGGGCACTACACAGAAGGTGCGG
AGCTGGTGGATTCGGTACTGGACATTGTGAGGAGGGAGGCTGAGAACTGTGACTGCCTGCAGGATTTCCAGCTGACCCAC
TCCCTGGGAGCAGGGACTGGGCCTAAGAGGGGTACCCCTATCATCAGCAAGATCCCAGAGAAGTATCCAGACAGAATCTT
GAACATGTTCAGTGTGCCCTTGTGCAAGGTGTCAGACATGGGGGTGGAGTCCTAAAACATCACCTTCTCAGTCTACCAAC
TGGTAGAAAACACAGATATGACCTATTGCATTGATAATGAAACTCTCCATAACGTCTGCTTCAGAACCCTAAAGCTGACC
ACACCCACCTATGGTGACTTGAACCACCTGGTGTCTGCCACCATAAATGGGGTCGCTACCTGCCTAGGCTTCCCCAGCCA
CCTCAATGCTGACCTGCAGAAGCTGGCTATGTACATGGTCCCATTCCCTACCTGCACTTCTTTATGCCTGTCTTCACCTT
GCTGACCATCCAGAGCAGCCAGCACTACCAGGCCCTGATAGTGCCTGAGCTCACCCAGCAGGTGTTTGAGGCCAAGAACA
TGATGGTTCCCTGAGACCCCTGCCATGGCCACTACCTAAATGTGGCCACGGTGTTCACAGACTACATGTCCATGAAGAAG
TTGGATGAGCAAACGCTTAACATCCAAAACAAGAACAGCAGCTACTTTGTTGAGCGAATCCCCAACCATGTGAAAACAGC
TGTCTGTGACATCCCACTCTTGGGGCTATAAATGTTTGCCACCTTCATCAGCAACAGAGTGGCCATCCAGGAGCTGTTCA
AGCATATCTCTGAG

Alignment

ORF - retro_pabe_2920 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.91 %
• Parental protein coverage: 86.26 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEP
          .RE.VH.QAG......G..F..VISDEH.I.PTG..HGDS.LQL..ISVYYNE.TGGKYVP.A.L.DLEP
Retrocopy LRESVHLQAG----EFGN*FYGVISDEHAIKPTGS*HGDSNLQLECISVYYNETTGGKYVPHAELMDLEP

Parental  GTMDS-VRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSL
          .T.DS.V.SG...QI...DNF.F.QSGAGNNWA.GHYTEGAELVDSVLD.VR.EAE.CDCLQ.FQLTHSL
Retrocopy STVDS>VYSGSIVQILQLDNFIFHQSGAGNNWANGHYTEGAELVDSVLDIVRREAENCDCLQDFQLTHSL

Parental  GGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYD
          G.GTG...GT..ISKI.E.YPDRI.N.FSV.P..KVSD..VE..N.T.SV.QLVENTD.TYCIDNE.L..
Retrocopy GAGTGPKRGTPIISKIPEKYPDRILNMFSV-PLCKVSDMGVES*NITFSVYQLVENTDMTYCIDNETLHN

Parental  ICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPR-LHFFMPGFAPLTSRGS
          .CFRTLKLTTPTYGDLNHLVSAT..GV.TCL.FP..LNADL.KLA..MVPFP..LHFFMP.F..LT...S
Retrocopy VCFRTLKLTTPTYGDLNHLVSATINGVATCLGFPSHLNADLQKLAMYMVPFPT<LHFFMPVFTLLTIQSS

Parental  QQYRALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNN
          Q.Y.AL.VPELTQQVF.AKNMM...DP.HG.YL.VA.VF...MSMK..DEQ.LN.QNKNSSYFVE.IPN.
Retrocopy QHYQALIVPELTQQVFEAKNMMVP*DPCHGHYLNVATVFTDYMSMKKLDEQTLNIQNKNSSYFVERIPNH

Parental  VKTAVCDIPPRGLKMAVTFIGNSTAIQELFKRISE
          VKTAVCDIP..GL.M..TFI.N..AIQELFK.ISE
Retrocopy VKTAVCDIPLLGL*MFATFISNRVAIQELFKHISE

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	297.35 RPM
SRP007412_cerebellum	0.00 RPM	155.53 RPM
SRP007412_heart	0.00 RPM	108.46 RPM
SRP007412_kidney	0.00 RPM	127.75 RPM
SRP007412_liver	0.00 RPM	135.81 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2920 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2920 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2920 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3537
Pan troglodytes	retro_ptro_2403
Gorilla gorilla	retro_ggor_2388
Macaca mulatta	retro_mmul_1849

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 16 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,
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,
Pongo abelii	ENSPPYG00000011180	1 retrocopy	retro_pabe_3250,
Pongo abelii	ENSPPYG00000016419	4 retrocopies	retro_pabe_2920 , retro_pabe_3210, retro_pabe_3698, retro_pabe_467,