RetrogeneDB ID: retro_pabe_3210

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7_random:15281264..15282589(+)
• 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_3210
ATGAGGGAAATTGTGCACATCCAAGCCAGTCACTGTGGCAAACAGATCGGTGCCAAGTTCTGGGAGGGGATCAGTGATGA
ACACGGCATCGACCCAGCGGCACCTACCACAGGGACAGCGCCCTGCAGCTGGACCGCATCTCCGTGTACTACAATGAAGC
CACCGGTGGCAAATATGTTCCTCGTGCCATCCTGGTGGATCTAGAACCTGGGACCATGGACTCTGTTCACTCAGGTCCTT
TTGGCCAGATCTTTAGACCAGACAACTCTGTTTTTGATCAGTCTGGGGCAGGCAACAACTGGGTCAAAGGCCACTACACA
GAGGGGGCTGAGCTGGTTTATTTGGTCCTGGATGTGATATGGAGGAGGCGGAGAGCTGTGACTGCCTGCAGGGCTTCCAG
CTGACCCACTCACTTGACTGGGACACAGACTCTGGAATCTGCACTTTCCTTATCAGCAAGATCCAAAAAGAGTACCCTGA
TTGCTTCATGAATACCTTCAGTGTGGTACCTTCACACAAGATATCTGACACCATGGTTGAGCCCTACAGTGCCACCCTCT
CCATCCATCATTTGGTAGAGAACACTGATGAGACCTATTGCATTGACAATGAGGCCCTCTAGGATATCTGCTTCTGCACT
CTGAAGCTAACCACACAACCTACTGGGATCTGAACTACCTTGTCTTAGCCACCATGAGTGGTGTCACCACCTGCCTCCAC
TTCCCTGGCCAGCTCAGTGCTGACCTCTGCCAAGTTGGCAGTCAACACGGTTCCCTTCCCTTCCCATATCTCCACTTCTT
TATGCCTGGCTTTGCTCCTTTCACCAGCCATGGAAGCCAGTAGTATCAAGCTCTCACAGTGCCCGAACTCACCCAGCAGG
TCTTCAATACCAAAAACCTGATGGCTGCTTGTGACAGCTGATACCTCTCCACGGCTGCTGTCTCCAGTGGTCAGATGTCC
ATGAAGGAGGTCGATGAGCAGATGCTCAACCTGCAGAACAAGAACAGCAGCTACTTTGTGAAATGGATCCCCAAGAACAT
CAAGACAGCTGTCTGTGACATCCACCTCATGGCCTCAAGATGGCTGTCACCTTCATCGGAAACAGCACTGGCATCCAGTA
GCTCTTCAAGTGCATCTTGGAGCAGTTCACTGCCATGTTCTACCAGAAGGCCTTCCTCCACTGATACACAGGCGAGGGCA
TGGACGAGATGGAGTTCACTGAGGCTGACAGCAACATGAACAATCTCGTCACTGAGGATCAGCAGTACCAGGATGCTACC
ACAGAAGAGGAAGAGGATTTCAGTAAGGAGGCTGAAGAGGAGGCC

Alignment

ORF - retro_pabe_3210 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDP-TGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLE
          MREIVHIQA..CG.QIGAKFWE.ISDEHGIDP..GTYH.DS.LQLDRISVYYNEATGGKYVPRAILVDLE
Retrocopy MREIVHIQASHCGKQIGAKFWEGISDEHGIDP<SGTYHRDSALQLDRISVYYNEATGGKYVPRAILVDLE

Parental  PGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV-RKEAESCDCLQGFQLTHS
          PGTMDSV.SGPFGQIFRPDN.VF.QSGAGNNW.KGHYTEGAELV..VLDV....EAESCDCLQGFQLTHS
Retrocopy PGTMDSVHSGPFGQIFRPDNSVFDQSGAGNNWVKGHYTEGAELVYLVLDVI<MEEAESCDCLQGFQLTHS

Parental  LGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALY
          L...T.SG..T.LISKI..EYPD..MNTFSVVPS.K.SDT.VEPY.ATLS.H.LVENTDETYCIDNEAL.
Retrocopy LDWDTDSGICTFLISKIQKEYPDCFMNTFSVVPSHKISDTMVEPYSATLSIHHLVENTDETYCIDNEAL*

Parental  DICFRTLKLTTP-TYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVN--MVPFPRLHFFMPGFAPLTS
          DICF.TLKLTT..TY.DLN.LV.ATMSGVTTCL.FPGQL.ADL..........PFP.LHFFMPGFAP.TS
Retrocopy DICFCTLKLTTQ<TYWDLNYLVLATMSGVTTCLHFPGQLSADLCQVGSQHGSLPFPYLHFFMPGFAPFTS

Parental  RGSQQYRALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWI
          .GSQ.Y.ALTVPELTQQVF..KN.MAACD......L..AAV..G.MSMKEVDEQMLN.QNKNSSYFV.WI
Retrocopy HGSQ*YQALTVPELTQQVFNTKNLMAACDS*Y---LSTAAVSSGQMSMKEVDEQMLNLQNKNSSYFVKWI

Parental  PNNVKTAVCDI-PPRGLKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESN
          P.N.KTAVCDI.PP.GLKMAVTFIGNST.IQ.LFK.I.EQFTAMF..KAFLH.YTGEGMDEMEFTEA.SN
Retrocopy PKNIKTAVCDI<PPHGLKMAVTFIGNSTGIQ*LFKCILEQFTAMFYQKAFLH*YTGEGMDEMEFTEADSN

Parental  MNDLVSEYQQYQDATAEEEEDFGEEAEEEA
          MN.LV.E.QQYQDAT.EEEEDF..EAEEEA
Retrocopy MNNLVTEDQQYQDATTEEEEDFSKEAEEEA

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_3210 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3210 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3210 has 0 orthologous retrocopies within eutheria group .

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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,