RetrogeneDB ID: retro_ptro_2158

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:71823108..71824437(+)
• Located in intron of: ENSPTRG00000016843

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1B
• Ensembl ID: ENSPTRG00000012950
• Aliases: TUBA1B, K-ALPHA-1
• Description: Pan troglodytes tubulin, alpha 1b (TUBA1B), mRNA. [Source:RefSeq mRNA;Acc:NM_001034095]

Sequence

>retro_ptro_2158
ATGAGTGAGTGCATCTCCATCTCATTGGCCAGGCTGGTGTCCAGGTTGGCAATGCCTGCTGGGAGCCCTACTGCCTGGAA
CATGGCATCCAGCCCAATGGCCAGATGCCAAGTGACAAGACAACTCGGGGAGGAGATGACTCCTTCAACAGCTTCTTCAG
TGAGACGGGCTCCGGCAAGCATGTGCCCAGGGCAGTGTTTCTAGACTTGAAACCCATGATAATTGATGATGAAGTTTGCA
CTGGCACCTACCACCAGCTCTTCCACCCTGAGCAGCTCATCACAGGCAAGAAGATGCTGCCAGTAAATATGCCTGAAGGC
ACTACACCATTGGCCAGGAGATCACTGACCTTGTTTTGGACCAAATTTGTAAACTGGCTGACCAGTGCAAGGATCGCCAA
GGCTTCTTGTTTTTCCACAGCTTTGGTGAAGGAATTGGTTCTGGGTTCACCTCCCTGCTCGTGGAACAACTCCCGGTTGA
TTATGGCAAGAAGTCCAAGCTGCAGTTCTCCATTTACTCACCACCCCAGGTTTCCACAGCTGCAGTTGAGACCTACAACT
CCATCCTCACCTCCCGCACCACCCTGGAGCACTCTGATTTTGTCTTCATGGTAGACAATGAGGCCACTTATGATATCTGG
CATAGAACCTTGATACTGAACGCCCAACCTATACTAAACTGAATAGGTTGATAGGTCAAATTGTGTCCTCCATCACTGCT
TCCCTGAGATTTGATGGAGCCCTGAATGTTGATCTGACAGAATTCCAGACAAAGCTGGTGCCCTATCCCCCCATCCACTT
CCCTCTGGACACATATGCCCCGTCATCTCTGCTGAGAAAACCTACCATGAAACAGCTTTCTGTAGCAGAGACTGCCAGTG
CTTGCTTTGAGCCTGCCAACCAGATGATGAAATGTGAGCCTTGCCATGGTAAATACATGGCTTGCTGCCTGTTTTACCGT
GGTGACATGGTTCTCAAAGACGTCAATGCTGCCATTGCCACCATCAATCAAGACCAAGTGTATCATCCAATTTGTGGTTT
GGTGCCCCCCTGGCTTCAAGGTTGGCATTAACTGCCAGACCTCCCACTGTTGTGACTGGTGGAGACCTGGTCAAGATACA
GAGAGCTGTGTGCATGCTGAGCAATACCACAGCCATTGCTGAGGCCTGGGCTCGCCTGGACCACAAGTTTGACTTGAATG
TATGACAAGAGTGCTTTCGTTCACTGGTACGTGGATGAGAGAAGGGAGGAAGGAGAGTTTTCTGAGGCCGGTGAGGACAT
GACTGCCCTTGAGAAGGATTATAAGGAGGTTGGTGTGGATTCAAGAGAG

Alignment

ORF - retro_ptro_2158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.16 %
• Parental protein coverage: 97.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MRECISIH-VGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVD
          M.ECISI...GQAGVQ.GNACWE.YCLEHGIQP.GQMPSDKT..GGDDSFN.FFSETG.GKHVPRAVF.D
Retrocopy MSECISIS<IGQAGVQVGNACWEPYCLEHGIQPNGQMPSDKTTRGGDDSFNSFFSETGSGKHVPRAVFLD

Parental  LEPTVID-EVRTGTYRQLFHPEQLITGK-EDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLV
          L.P..ID.EV.TGTY.QLFHPEQLITGK.EDAA..YA..HYTIG.EI.DLVLD.I.KLADQC...QGFL.
Retrocopy LKPMIIDDEVCTGTYHQLFHPEQLITGK<EDAASKYA*RHYTIGQEITDLVLDQICKLADQCKDRQGFLF

Parental  FHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNE
          FHSFG.G.GSGFTSLL.E.L.VDYGKKSKL.FSIY..PQVSTA.VE.YNSILT..TTLEHSD..FMVDNE
Retrocopy FHSFGEGIGSGFTSLLVEQLPVDYGKKSKLQFSIYSPPQVSTAAVETYNSILTSRTTLEHSDFVFMVDNE

Parental  AIYDICRR-NLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYA-PV
          A.YDI..R.NLD.ERPTYT.LNRLI.QIVSSITASLRFDGALNVDLTEFQT.LVPYP.IHFPL.TYA.PV
Retrocopy ATYDIWHR<NLDTERPTYTKLNRLIGQIVSSITASLRFDGALNVDLTEFQTKLVPYPPIHFPLDTYA<PV

Parental  ISAEKAYHE-QLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATI-KTKRSIQF
          ISAEK.YHE.QLSVAE...ACFEPANQM.KC.P.HGKYMACCL.YRGD.V.KDVNAAIATI.....S...
Retrocopy ISAEKTYHE>QLSVAETASACFEPANQMMKCEPCHGKYMACCLFYRGDMVLKDVNAAIATI<QSRPSVSS

Parental  VDW--CPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDL-MYAKRAFVHWYVG
          ..W...P..........PPTVV.GGDL.K.QRAVCMLSNTTAIAEAWARLDHKFDL.MY.K.AFVHWYV.
Retrocopy NLWFGAPLASRLALTARPPTVVTGGDLVKIQRAVCMLSNTTAIAEAWARLDHKFDL>MYDKSAFVHWYVD

Parental  EGMEEGEFSEAREDMAALEKDYEEVGVDSVE
          E..EEGEFSEA.EDM.ALEKDY.EVGVDS.E
Retrocopy ERREEGEFSEAGEDMTALEKDYKEVGVDSRE

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	0.30 RPM	812.43 RPM
SRP007412_cerebellum	0.11 RPM	150.10 RPM
SRP007412_heart	0.00 RPM	77.85 RPM
SRP007412_kidney	0.03 RPM	120.85 RPM
SRP007412_liver	0.00 RPM	158.76 RPM
SRP007412_testis	0.32 RPM	80.09 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2158 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2158 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2158 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3313

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012244	1 retrocopy	retro_btau_402,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Callithrix jacchus	ENSCJAG00000020874	2 retrocopies	retro_cjac_1603, retro_cjac_1861,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Homo sapiens	ENSG00000123416	1 retrocopy	retro_hsap_808,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Macropus eugenii	ENSMEUG00000011167	4 retrocopies	retro_meug_1121, retro_meug_157, retro_meug_1616, retro_meug_1964,
Monodelphis domestica	ENSMODG00000015206	2 retrocopies	retro_mdom_1632, retro_mdom_348,
Mus musculus	ENSMUSG00000023004	6 retrocopies	retro_mmus_1562, retro_mmus_1607, retro_mmus_1742, retro_mmus_1987, retro_mmus_3297, retro_mmus_3327,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pan troglodytes	ENSPTRG00000012950	1 retrocopy	retro_ptro_2158 ,
Sus scrofa	ENSSSCG00000000190	2 retrocopies	retro_sscr_380, retro_sscr_702,