RetrogeneDB ID: retro_ptro_1058

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:53504594..53505190(-)
• Located in intron of: ENSPTRG00000007104

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADH
• Ensembl ID: ENSPTRG00000016351
• Aliases: HADH, HADHSC
• Description: Hydroxyacyl-CoA dehydrogenase [Source:UniProtKB/TrEMBL;Acc:K7AUA4]

Sequence

>retro_ptro_1058
ATGATGGTCATCAGCATCACACAGGTTGCTGCAGTGACCGGCCACACAGTAGTGTTGCTAGACCAGACAGAGGACATCTT
GGCAAAATATAAAGAGGGAATTGAGAAAAGCCTTAGGAAAGTGACAAAGAAGTTGTTTGTAGAAAACCCTAAGGCTTTTG
ATGAATTTGTGGAGAAAACCCTAAGCAGCATATCAACCAGCACAGATGCAATATCCATAGTCCACCGCACAGACCTAGTG
GTAGAGGCCATTGTAGAAAATCTAAAGGTGAAAATCAAGCTCTCCAAGAGGTTGGACAAGTTTGTTGCTGAACATACAAC
TTTGCCAGCAGCACTTCCTCTTTGCAAATTACAAGCATAGCCAATGCTACCACCAAACAAGACCGATTTGCTGGCCTCCA
TTTACTCAACCCAGTGCCCCTGATGAAATTTGTAGAGGTCTTTAAAACACCAATGACCACCCGAAAGACATTTGAATCTT
TGGCAAACTTGAGCAAAACCCTGGGAAAGCATCCTGTTCCTTGCAAGGACACTCCTGGGTTTATTGTCAGCTGTCTCAGG
ATTCAACACCTCATGGAAGCAGTCAGGCTGCATGAA

Alignment

ORF - retro_ptro_1058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.5 %
• Parental protein coverage: 60.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

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

Parental  ASVVHSTDLVVEAIVENLKVKNELFKRLDKFAAEHTI-FASNTSSLQITSIANATTRQDRFAGLHFFNPV
          .S.VH.TDLVVEAIVENLKVK..L.KRLDKF.AEHT..FAS.TSSLQITSIANATT.QDRFAGLH..NPV
Retrocopy ISIVHRTDLVVEAIVENLKVKIKLSKRLDKFVAEHTT<FASSTSSLQITSIANATTKQDRFAGLHLLNPV

Parental  PVMKLVEVIKTPMTSQKTFESLVDFSKALGKHPVSCKDTPGFIVNRLLVPYLMEAIRLYE
          P.MK.VEV.KTPMT..KTFESL...SK.LGKHPV.CKDTPGFIV..L....LMEA.RL.E
Retrocopy PLMKFVEVFKTPMTTRKTFESLANLSKTLGKHPVPCKDTPGFIVSCLRIQHLMEAVRLHE

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	0.05 RPM	17.12 RPM
SRP007412_cerebellum	0.14 RPM	22.19 RPM
SRP007412_heart	0.09 RPM	172.63 RPM
SRP007412_kidney	0.13 RPM	218.81 RPM
SRP007412_liver	0.00 RPM	97.52 RPM
SRP007412_testis	0.00 RPM	40.89 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1058 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1058 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1058 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1571
Pongo abelii	retro_pabe_1296
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	ENSPPYG00000014986	1 retrocopy	retro_pabe_1296,
Pan troglodytes	ENSPTRG00000011732	2 retrocopies	retro_ptro_2109, retro_ptro_664,
Pan troglodytes	ENSPTRG00000016351	1 retrocopy	retro_ptro_1058 ,