RetrogeneDB ID: retro_cjac_2933

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:115386087..115387207(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADH5
• Ensembl ID: ENSCJAG00000007198
• Aliases: None
• Description: alcohol dehydrogenase 5 (class III), chi polypeptide [Source:HGNC Symbol;Acc:253]

Sequence

>retro_cjac_2933
GAACCCATGGACATGGTGAACCAGGTTATCAAGCGCAAGGCTGCGGTTTCCTGTGAGGCTGGAAAGCCTTCTCCTTAGAG
GAGATAGAGGTGGCATCCCCAAAGGCTCATAAAGTTCAAATCAAGATAGTTGCCACTGCAGTTTGCCACACTGAGGCCTA
CACCCTTAGCGGAGCTGATCCTGAGGCGTGTTTTCCAGCAATCCTGGGACATGAAGGCGCTGGAATTGTGGAAAGTGTTG
GTAAGGGAGTTACTAAGCTGAAAGCGGGTGACACTGTCATCCCACTTTACATCCCACAGTGCGAATGTAAATTTTTTCTA
AATCCTAAAACTAACCTTTGCCAGAAAATAAGAGTCACTCAAGGGAAAAGCTTAATGCCAGATGGTACCAGCAGATTTAC
TTGCAAAGGAAAGACAATTTTACATTATAAGGGAACCAGCACATTTTCTGAATGCACAGTGGTGGCTGATATCTCTGTTG
CTAAAGTAGCACCTTTGGATAAAGTCTGCCTTCTGGTTGTGGCATTTCAACTGGTTATGGTGCTGCTGTAAACACTCCCA
AGGTGGAGCCTGGCTCTGTTCGTGCCATCTTTGGCCTGGGAGGAGTTGGATTGGCAGTTAAAATGGGCTGTAAAGTGGCT
GGTGCATCCTGAATCATTGGTGTGGACATCAATAAAGATAAATTTGCAAGGGCTCAAGAGGTTGGAGTCACTGAACCTAC
TATCCCTCAGGATTTTAGTAAACTCATCCAGGAAGTACTCATTGAGATAACTGATGGAGGAGTGGACTATTCCTTTGAAT
GTACTGGTACCGTGAAGGTCATGAGAGCAGCACCTGAGGCATGTCACAAGAGTTGGGGTGTCAGTGTGGTGGTTGGAGTA
GCTGCTTCAGATGAAGAAATTGCAACTTGTCCATTTCAGCTGGTAACAGGTCACACATGGAAAGGCACTGCCTTTGGAGG
ATGGAAGAGTGTAGAAAGTGTCTCAGGCTGGTGCCTGAATACATATTCAAAAATAAAAAAGCTGATGAATTTGTGATTCA
CAATCTGTCTTTTGATGAAAATTAACAAAGTCTTTGAACTAGTGCATTCTAGAAAGAGCATTCAAACCCTTGTAAAGATT

Alignment

ORF - retro_cjac_2933 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.98 %
• Parental protein coverage: 96.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EPADMANQVIKCKAAVAWEAGKP-LFIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGCFPVIL
          EP.DM.NQVIK.KAAV..EAGKP....EEIEVA.PKAH.V.IKI.ATAVCHT.AYTLSGADPE.CFP.IL
Retrocopy EPMDMVNQVIKRKAAVSCEAGKP<FSLEEIEVASPKAHKVQIKIVATAVCHTEAYTLSGADPEACFPAIL

Parental  GHEGAGIVESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGK
          GHEGAGIVESVG.GVTKLKAGDTVIPLYIPQC.ECKF.LNPKTNLCQKIRVTQGK.LMPDGTSRFTCKGK
Retrocopy GHEGAGIVESVGKGVTKLKAGDTVIPLYIPQC-ECKFFLNPKTNLCQKIRVTQGKSLMPDGTSRFTCKGK

Parental  TILHYMGTSTFSEYTVVADISVAKIDPLAPLDKVCLL-GCGISTGYGAAVNTAKVEPGSVCAVFGLGGVG
          TILHY.GTSTFSE.TVVADISVAK....APLDKVCLL.GCGISTGYGAAVNT.KVEPGSV.A.FGLGGVG
Retrocopy TILHYKGTSTFSECTVVADISVAKV---APLDKVCLL<GCGISTGYGAAVNTPKVEPGSVRAIFGLGGVG

Parental  LAVIMGCKVAGASRIIGVDINKDKFARAKEFGATECVNPQDFSKPIQEVLIEMTDGGVDYSFECIGNVKV
          LAV.MGCKVAGAS.IIGVDINKDKFARA.E.G.TE...PQDFSK.IQEVLIE.TDGGVDYSFEC.G.VKV
Retrocopy LAVKMGCKVAGAS*IIGVDINKDKFARAQEVGVTEPTIPQDFSKLIQEVLIEITDGGVDYSFECTGTVKV

Parental  MRAALEACHKGWGVSVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVP-KLVSEYMSKKIKVD
          MRAA.EACHK.WGVSVVVGVAAS.EEIAT.PFQLVTG.TWKGTAFGGWKSVESV...LV.EY..K..K.D
Retrocopy MRAAPEACHKSWGVSVVVGVAASDEEIATCPFQLVTGHTWKGTAFGGWKSVESVS<RLVPEYIFKNKKAD

Parental  EFVTHSLSFDE-INEAFELMHSGKSIRTVVKI
          EFV.H.LSFDE.IN..FEL.HS.KSI.T.VKI
Retrocopy EFVIHNLSFDE>INKVFELVHSRKSIQTLVKI

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	0.00 RPM	19.35 RPM
SRP051959_heart	0.00 RPM	30.92 RPM
SRP051959_kidney	0.00 RPM	52.51 RPM
SRP051959_liver	0.00 RPM	184.03 RPM
SRP051959_lung	0.00 RPM	26.91 RPM
SRP051959_lymph_node	0.00 RPM	30.09 RPM
SRP051959_skeletal_muscle	0.00 RPM	19.59 RPM
SRP051959_spleen	0.00 RPM	24.33 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2933 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2933 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2933 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_175
Pan troglodytes	retro_ptro_166
Pongo abelii	retro_pabe_453

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013007	1 retrocopy	retro_cfam_14,
Callithrix jacchus	ENSCJAG00000007198	2 retrocopies	retro_cjac_1029, retro_cjac_2933 ,
Homo sapiens	ENSG00000197894	3 retrocopies	retro_hsap_175, retro_hsap_330, retro_hsap_3607,
Gorilla gorilla	ENSGGOG00000028244	2 retrocopies	retro_ggor_2434, retro_ggor_354,
Myotis lucifugus	ENSMLUG00000002722	1 retrocopy	retro_mluc_1702,
Macaca mulatta	ENSMMUG00000003552	1 retrocopy	retro_mmul_299,
Mustela putorius furo	ENSMPUG00000009642	1 retrocopy	retro_mputfur_1625,
Nomascus leucogenys	ENSNLEG00000013946	3 retrocopies	retro_nleu_1772, retro_nleu_2636, retro_nleu_983,
Pongo abelii	ENSPPYG00000014946	3 retrocopies	retro_pabe_176, retro_pabe_359, retro_pabe_453,
Pan troglodytes	ENSPTRG00000016303	3 retrocopies	retro_ptro_166, retro_ptro_2438, retro_ptro_266,
Sus scrofa	ENSSSCG00000009185	1 retrocopy	retro_sscr_659,
Xenopus tropicalis	ENSXETG00000009304	1 retrocopy	retro_xtro_57,