RetrogeneDB ID: retro_pabe_1296

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:52986663..52987493(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADH
• Ensembl ID: ENSPPYG00000014986
• Aliases: None
• Description: hydroxyacyl-CoA dehydrogenase [Source:HGNC Symbol;Acc:4799]

Sequence

>retro_pabe_1296
ATGATGGTCATCAGCATCACACAGGTTGCTGCAGTGACCGGCCACACAGTAGTGTTGCTAGACCAGACAGAGGACATCTT
GGCAAAATATAAAGAGGGAATTGAGAAAAGCCTTAGGAAAGTGACAAAGAAGTTGTTTGTAGAAAACCCTAAGGCTTTTG
ATGAATTTGTGGAGAAAACCCTAAGCAGCATATCAACCAGCACAGATGCAATATCCGTAGCCCACAGCACAGACCTGGTG
GTAGAGGCCATTGTAGAAATCTAAAGGTGAAAATCAAGCTCTCCAAGAGGTTGGACAAGTTTGTTGCTGAACATACAACT
TTTGCCAGCAACACTTCCTCTTTGCAAATTACAAGCGTAGCCAATGCTACCACCAAACAAGACCGATTTGCTGGCCTCCA
TTTACTCAACCCAGTGCCCCTGATGAAATTTGTAGAGGTCTTTAAAACACCAATGACCACCCGAAAGACATTTGAATCTT
TGGTAAACTTGAGCAAAACCCTGGGAAAGCATCCTGTTTCTTGCAAGGACACTCCTGGGTTTATTGTCAGCTGTCTCAGG
ATTCAACACCTCAAGGAAGCAGTCAGGCTGCATGAATGAGGTGATGTATCCAAGGAAAACACTGACACTGCTATGAAGTT
AGGAGCCAGGTACTCCATGGGCTCACTTGAGTTTCTAGATTACGTTGGGCTGGATTCTTTGCAGTTCATCATGGATGGAT
GGCATGAAATAGATACAAAGAACCCCATATTTCAGCCCAGCCCATCCTTGAAAAAGCTGATGGCAGAGAAGAAGCTTGGC
AAGAAGTCTGGAGAAGGATTTTACAAATAC

Alignment

ORF - retro_pabe_1296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.18 %
• Parental protein coverage: 88.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENPKAGDEFVEKTLSSITTSTDA
          .M...I.QVAA.TGHTVVL.DQTEDILAK.K.GIE.SLRKV.KK.F.ENPKA.DEFVEKTLSSI.TSTDA
Retrocopy MMVISITQVAAVTGHTVVLLDQTEDILAKYKEGIEKSLRKVTKKLFVENPKAFDEFVEKTLSSISTSTDA

Parental  ASVVHSADLVVEAIVE-NLKVKNELFKRLDKFAAEHTIFASNTSSLQITSIANATTRQDRFAGLHFFNPV
          .SV.HS.DLVVEAIVE.NLKVK..L.KRLDKF.AEHT.FASNTSSLQITS.ANATT.QDRFAGLH..NPV
Retrocopy ISVAHSTDLVVEAIVE<NLKVKIKLSKRLDKFVAEHTTFASNTSSLQITSVANATTKQDRFAGLHLLNPV

Parental  PVMKLVEVIKTPMTSQKTFESLVDFSKALGKHPVSCKDTPGFIVNRLLVPYLMEAIRLYERGDASKEDID
          P.MK.VEV.KTPMT..KTFESLV..SK.LGKHPVSCKDTPGFIV..L....L.EA.RL.E.GD.SKE..D
Retrocopy PLMKFVEVFKTPMTTRKTFESLVNLSKTLGKHPVSCKDTPGFIVSCLRIQHLKEAVRLHE*GDVSKENTD

Parental  TAMKLGAGYPMGPFELLDYVGLDTTKFIVDGWHEMDAENPLHQPSPCLNKLVAENKFGKKTGEGFYKY
          TAMKLGA.Y.MG..E.LDYVGLD...FI.DGWHE.D..NP..QPSP.L.KL.AE.K.GKK.GEGFYKY
Retrocopy TAMKLGARYSMGSLEFLDYVGLDSLQFIMDGWHEIDTKNPIFQPSPSLKKLMAEKKLGKKSGEGFYKY

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	0.06 RPM	23.11 RPM
SRP007412_cerebellum	0.12 RPM	25.54 RPM
SRP007412_heart	0.00 RPM	163.64 RPM
SRP007412_kidney	0.03 RPM	159.80 RPM
SRP007412_liver	0.06 RPM	109.58 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1296 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1296 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1296 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1571
Pan troglodytes	retro_ptro_1058
Macaca mulatta	retro_mmul_2217

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002049	2 retrocopies	retro_btau_1111, retro_btau_1685,
Callithrix jacchus	ENSCJAG00000015938	1 retrocopy	retro_cjac_772,
Echinops telfairi	ENSETEG00000013807	1 retrocopy	retro_etel_1694,
Felis catus	ENSFCAG00000022260	1 retrocopy	retro_fcat_1225,
Homo sapiens	ENSG00000138796	1 retrocopy	retro_hsap_1571,
Gorilla gorilla	ENSGGOG00000004423	1 retrocopy	retro_ggor_1196,
Macaca mulatta	ENSMMUG00000023254	1 retrocopy	retro_mmul_2217,
Nomascus leucogenys	ENSNLEG00000012951	1 retrocopy	retro_nleu_1738,
Pongo abelii	ENSPPYG00000012583	2 retrocopies	retro_pabe_2576, retro_pabe_817,
Pongo abelii	ENSPPYG00000014986	1 retrocopy	retro_pabe_1296 ,
Pan troglodytes	ENSPTRG00000016351	1 retrocopy	retro_ptro_1058,