RetrogeneDB ID: retro_cjac_772

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:33531631..33532414(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADH
• Ensembl ID: ENSCJAG00000015938
• Aliases: None
• Description: hydroxyacyl-CoA dehydrogenase [Source:HGNC Symbol;Acc:4799]

Sequence

>retro_cjac_772
ATAATGGTCATCAGCATCACACAGATTGCTGCAGTGACCAGCCACACAGTAGTGTTGCTAGACCAGACAGAGGACATCTT
GGCAGAATATAAAAAGGGAATTGAGAAGAGCCTTGGGAAAGTGGCAAAGAAGTTGTTTGCAGAAAACACTAAGGCTGATG
ATGAATTTGTGGAGAAAACCCTAAGCAACATATCAACCAGCACAGATGCAGCATCCATAGTTCACAGTACAGACCTGGTG
GTAGAAGCCATTGTAGAGAATCTAAAGACAATTGTAGAGAATCAAGCTCTCAAGAGGCTGCACAGGTTTGCGGCTGAACA
TACAGTTTTTGCCAGTAATACTTCCTCCTTGCAGATTGCAAGCATAGCCAATACTGCCACCAAACAAGACTGATTTGCTG
GCCTCCATTTACTCAATCCAGTGCCCCTGATGAAACTTGCAGAGGTCCTTAAAACATCAGTGGTCACTCAAAAGACATTT
CAATCTTTGGTAAACTTGAGCAAAACCCTGAGAAAACATCCTGTTTCTTGCAAGGACACTCCTGGGTTTATTATCAGCTG
TCTCAGGATTCAACACCTCATGGAAGCAGTCAGGTTGCATATATAAGGTGATGCATCCAAGGAAAACATTGATACCGCTA
TGAAGGTAGGATCCAGGAACCCCATGGACTCACTTGAGCTTCTAGATTACGTTGGGCTGGATACTGTGAAGTTCATTATG
GATGGATTGCATCAATAGATTTCAGACCAGCCCATCCTTGAAAAAGCTGATGGCAAAGAGAAG

Alignment

ORF - retro_cjac_772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.52 %
• Parental protein coverage: 82.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LMGSGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAEDPKAGDEFVVKTLSSITTSTDA
          .M...I.Q.AA.T.HTVVL.DQTEDILA..KKGIE.SL.KVAKK.FAE..KA.DEFV.KTLS.I.TSTDA
Retrocopy IMVISITQIAAVTSHTVVLLDQTEDILAEYKKGIEKSLGKVAKKLFAENTKADDEFVEKTLSNISTSTDA

Parental  ASVVHSTDLVVEAIAENLQ--LKNELFKRLDKFAAEHTIFASNTSSLQITSIANATTRQDRFAGLHFFNP
          AS.VHSTDLVVEAI.ENL.....N...KRL..FAAEHT.FASNTSSLQI.SIAN..T.QD.FAGLH..NP
Retrocopy ASIVHSTDLVVEAIVENLKTIVENQALKRLHRFAAEHTVFASNTSSLQIASIANTATKQD*FAGLHLLNP

Parental  VPMMKLVEVIKTPMTSQKTFESLVDFTKTLGKHPVSCKDTPGFVVNRLLVPYLMEAIRLYERGDASKEDI
          VP.MKL.EV.KT....QKTF.SLV...KTL.KHPVSCKDTPGF....L....LMEA.RL...GDASKE.I
Retrocopy VPLMKLAEVLKTSVVTQKTFQSLVNLSKTLRKHPVSCKDTPGFIISCLRIQHLMEAVRLHI*GDASKENI

Parental  DTAMKLGAGYPMGPFELLDYVGLDTTKFIVDGWHEIDAKNPLFQPSPSLNK
          DTAMK.G...PM...ELLDYVGLDT.KFI.DG.H......P.........K
Retrocopy DTAMKVGSRNPMDSLELLDYVGLDTVKFIMDGLHQ*ISDQPILEKADGKEK

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
SRP051959_colon	1.06 RPM	10.52 RPM
SRP051959_heart	0.82 RPM	24.08 RPM
SRP051959_kidney	1.29 RPM	22.94 RPM
SRP051959_liver	0.67 RPM	25.47 RPM
SRP051959_lung	1.82 RPM	9.84 RPM
SRP051959_lymph_node	2.31 RPM	9.98 RPM
SRP051959_skeletal_muscle	0.79 RPM	14.33 RPM
SRP051959_spleen	1.41 RPM	11.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_772 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_772 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_772 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 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	ENSPTRG00000016351	1 retrocopy	retro_ptro_1058,