RetrogeneDB ID: retro_pabe_3323

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:48621597..48622316(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C5orf33
• Ensembl ID: ENSPPYG00000015401
• Aliases: None
• Description: None

Sequence

>retro_pabe_3323
GTATGGAGACAGCAAATCAGTTTATACCTTGAATGGATTGGAATAAACCCCAGTCCTGAGGGACTTAATTAACAGCAACT
AAATTTGAATTAACAGTGTAGAGCACTTGACACAGAAGAGTTCATGGTGAAAGAACTGAGGCTTCAGGACTCTGACATTT
GCCAATGAGAGCACTACATGAAGTCTTATTGGGAAACATCCATCCAAAATGTCCTATACTGGGACTGTGGCAATGGAAAA
TTTAAGAAGTAGACCCACTCTAAAGGATTGGCTTTCCACTATCAGATTTTAGCTTATGATGATCCATGGAAAAAATAGAA
GAGTTGAGGGCTCAATTTGTGAACTGGAACAGGAGCAAAGGCTGGCCATTCAATATTAACAGGGTTGCAGGTCTGGCTTT
GGAGCATGTTTAAAATATTGCAAAATGACAAGGACATTGGAGTCTTGCATTGAACTGAGAATTGATAGAAAAAATAGCAA
ATAAATGTAACAAATCACTGCTCTACAGTCCAAAAAACCAAAAATACTTTCCTGGATTCAAGAACCAAGAGTTTTCTCCA
GTACCTATGAGCATTGTTTCTCCTGACTGATTTGTGTTTATTCTCATTGTTGGGACACCTGTATGGTGAATGGGGGGAAC
GTCTTTTGAGCCAAATGTTGGAGCCATTGCTTCAGTGATGATCAATAAAGATGATCTTGGAACTATGCTTCTAGAACAG

Alignment

ORF - retro_pabe_3323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.02 %
• Parental protein coverage: 65.44 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LWRQRIRLYLEGTGINPVPVDLHEQQLSLNQHNRALNIE-RAHDERSEASGPQLLPVRALNEVF-IGESL
          .WRQ.I.LYLE..GINP.P..L..QQL.LN...RAL..E.R.H.ER.EASG...LP.RAL.EV..IG...
Retrocopy VWRQQISLYLEWIGINPSPEGLN*QQLNLN*QCRALDTE<RVHGERTEASGL*HLPMRALHEVL<IGKH-

Parental  SSRMSYSWAVAVDNLRRSIPTLK-GLASYYEISVDDGPWEKQKSSGLNLSTGTGSKA-WSFNINRVATQA
          .S.MSY...VA..NLR.S.PTLK.GLA..Y.I...D.PW.K.KS.GLNL.TGTG.KA.W.FNINRVA..A
Retrocopy PSKMSYTGTVAMENLR-SRPTLK<GLAFHYQILAYDDPWKK*KS*GLNL*TGTGAKA<WPFNINRVAGLA

Parental  VEDVLNIAKRQGNLSLPLNRELVEKVTNEYNESLLYSP-EEPKILFSIREPIANRVFSSSRQRCFSSKVC
          .E.V.NIAK.QG..SL.LN.EL.EK..N..N.SLLYSP...PKIL..I.EP...RVFSS....CFS...C
Retrocopy LEHV*NIAK*QGHWSLALN*ELIEKIANKCNKSLLYSP<KKPKILSWIQEP---RVFSSTYEHCFS*LIC

Parental  VRSRCWDACMVVDGG-TSFEFNDGAIASMMINKEDELRTVLLEQ
          V.S.CWD.CM.V.GG.TSFE.N.GAIAS.MINK.D.L.T.LLEQ
Retrocopy VYSHCWDTCM-VNGG>TSFEPNVGAIASVMINK-DDLGTMLLEQ

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	0.17 RPM	24.60 RPM
SRP007412_cerebellum	0.12 RPM	16.54 RPM
SRP007412_heart	0.00 RPM	15.41 RPM
SRP007412_kidney	0.07 RPM	14.15 RPM
SRP007412_liver	0.00 RPM	100.04 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3323 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3323 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3323 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000016064	1 retrocopy	retro_nleu_3046,
Ochotona princeps	ENSOPRG00000009281	1 retrocopy	retro_opri_595,
Pongo abelii	ENSPPYG00000015401	1 retrocopy	retro_pabe_3323 ,
Rattus norvegicus	ENSRNOG00000016691	1 retrocopy	retro_rnor_2925,