RetrogeneDB ID: retro_pabe_3698

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:122719299..122720622(+)
• 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_3698
ATGCGGGAGATCGTGCACCTGCAGGCCGGCCAGTGTGGCAGCCAGATCGGGGCCAAGTTTTGGGAGGTTATCAGTGACGA
ACATGGGCATTGACCCCACAGGCACATACTATGGGGACAGTGACCTGCAACTGGAGAGGATCAACGTGTACTACAATGAG
GCCAGAGGAGGAAATTATGTCCCCAGAGCAGTGCTGGTGGACCTGGAACCCAGCACCATGGACTCTATCCTTTCTGGCCC
CTTCGGTCAGATCTTTCGGCCGGACAACTTCGTGTTTGGCCAGTCCAGAGCCGGCAACAACTGGGTGAAGGGGCACTACA
CGGAGGGCACAGAGCTGGTAGACGCTGTCCTGGACGTGGTCCAGAAGGCCTAGAACTGCAACTGCCTTCAAGGCTTCCAG
CTGACGCACTCGCTGGGGGGTGGCACGGGGTCCGGGATGCGCACACTGCTCATCAGTAAGATCCGTGAGGAGTTCCCAGA
CCGCATCATGAACACCTTCAGCATGGTGCCCTCGCCCAAAGTGTCAGACACGGTGGTGGAGCCCTACAATGCCACGCTGT
CTGTGCACCAGCTGGTGGAGAATACGAATGAGACCTACTGCATCAACAATGAGGCACTCTACGACATCTGCTTCCGCACC
CTCAAGCTGACCACACCCACCTACGGGGACCTCAACCACCTGGTGTCAGCCACCATGAGCAGAGTCACCACCTGCCTGCG
CTTCCTGGGCTAGCTGAACACCAACCTGCGCAAGCTGGCCGTCAACATGGTCCCCTTTCCCCGCCTGCACTTCTTCATGC
CCGGCTTCGCACCCCTGACCAGCCGGGGCAGCCAGCAGTACCGGGCCCTGAGGGTGCCTGAGCTCACGCAGCAGATGTTC
GACGCCAAGAACATGATGGCCATGTGCAACCCGCGACATGGCCGCTACCTGACCATGGCCACCGTGTTCCGGGCCACATG
TCCATGAAGGAGGTGGACAAGCAGATGCTGAGCGTGCAGAGCAAGAACAGCAGCTACTTCATGGAGTGGATCCCCAGCAA
CGTGAAGACGGCCGTGTGCGACATCTCGCCCCACGGCCTGAAGATAGCCGCAACCTTCATCAGCAACAACACAGCCTTCC
AGGAGCTGCTCAAGCGCATCTCTGCGCAGTTCACGGCCATGTTCCGGTGCAAGGCGTTCCTGCACTGGTACACAGGCGAG
GGTATGGACGAGATGGAGTTCACCGAGGCTGACAGCAACATGAATGACCTGGTATCTGAGTACCAGCAGTACCAGGATGC
CACAGCCGAGGAGGGCGAGTTCAAGGAGGAGGCCGAGGAGGAG

Alignment

ORF - retro_pabe_3698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.97 %
• Parental protein coverage: 99.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHG-IDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLE
          MREIVH.QAGQCG.QIGAKFWEVISDEHG.IDPTGTY.GDSDLQL.RI.VYYNEA.GG.YVPRA.LVDLE
Retrocopy MREIVHLQAGQCGSQIGAKFWEVISDEHG>IDPTGTYYGDSDLQLERINVYYNEARGGNYVPRAVLVDLE

Parental  PGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSL
          P.TMDS..SGPFGQIFRPDNFVFGQS.AGNNW.KGHYTEG.ELVD.VLDVV.K.A..C.CLQGFQLTHSL
Retrocopy PSTMDSILSGPFGQIFRPDNFVFGQSRAGNNWVKGHYTEGTELVDAVLDVVQK-A*NCNCLQGFQLTHSL

Parental  GGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYD
          GGGTGSGM.TLLISKIREE.PDRIMNTFS.VPSPKVSDTVVEPYNATLSVHQLVENT.ETYCI.NEALYD
Retrocopy GGGTGSGMRTLLISKIREEFPDRIMNTFSMVPSPKVSDTVVEPYNATLSVHQLVENTNETYCINNEALYD

Parental  ICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQ
          ICFRTLKLTTPTYGDLNHLVSATMS.VTTCLRF.G.LN..LRKLAVNMVPFPRLHFFMPGFAPLTSRGSQ
Retrocopy ICFRTLKLTTPTYGDLNHLVSATMSRVTTCLRFLG*LNTNLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQ

Parental  QYRALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVFR-GRMSMKEVDEQMLNVQNKNSSYFVEWIPNN
          QYRAL.VPELTQQ.FDAKNMMA.C.PRHGRYLT.A.VFR.G.MSMKEVD.QML.VQ.KNSSYF.EWIP.N
Retrocopy QYRALRVPELTQQMFDAKNMMAMCNPRHGRYLTMATVFR<GHMSMKEVDKQMLSVQSKNSSYFMEWIPSN

Parental  VKTAVCDIPPRGLKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDL
          VKTAVCDI.P.GLK.A.TFI.N.TA.QEL.KRIS.QFTAMFR.KAFLHWYTGEGMDEMEFTEA.SNMNDL
Retrocopy VKTAVCDISPHGLKIAATFISNNTAFQELLKRISAQFTAMFRCKAFLHWYTGEGMDEMEFTEADSNMNDL

Parental  VSEYQQYQDATAEEEEDFGEEAEEE
          VSEYQQYQDATAEE.E.F.EEAEEE
Retrocopy VSEYQQYQDATAEEGE-FKEEAEEE

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	0.77 RPM	297.35 RPM
SRP007412_cerebellum	5.47 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_3698 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3698 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3698 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4751
Pan troglodytes	retro_ptro_3166
Macaca mulatta	retro_mmul_2533

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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,