RetrogeneDB ID: retro_cjac_1029

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:39298069..39298918(-)
• 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_1029
CCCTTGCGCCGACCAGAACCCGCAGACATGGCGAATCAGGTTATCAAGTGCAAGGCTGCAGTTGCCTGGGAGGCTGGAAA
GCCTCTCTCCATAGAGGAGATAGAGGTGGCACCTCCAAAGGCTCATGAAGTTCGAATCAAGATCATTGCCACTGCAGTTT
GCCACACTGATGCCTATACTCTGAGTGGAGCTGATCCTGAGGGTTGTTTTCCAGTGATCTTGGAACATGAAGGTGCTGGA
ATTGTGGAAAGTGTTGGCGAGGGAGTTACTAAGCTGAAGGCGGGTGACACTGTCATCCCACTTTACATCCCACAGTGTGG
AGAATGCAAATTTTGTCTAAATCCTAAAACTAACCTTTGCCAGAAGATAAGAGTCACTCAAGGGAAAGGATTAATGCCAG
ATGGTACCAGCAGATTTACTTGCAAAGGAAAGACAATTTTACATTACATGGGAACCAGCACATTTTCTGAATACACAGTT
GTGGCTGATATCTCTGTTGCTAAAATAGATCCTTTAGCACCTTTGGATAAATTCTGCCTTCTAGGTTGTGGCATTTCAAC
TGGTTACGGTGCTGCTGTGAACACTGCTAAGGTTGAGCCTGGCTCTGTTTGTGCCATCTTTGGCCTGGGAGGAGTTGGAT
TGGCAGTTATCATGGGCTGTAAAGTGGCTGGTGCATCCCAGATCATTGGTGTGGACATCAATAAAGACAAATTTGCAGGG
GCCAAAGAGTTTGGAGCCACTGAATGTGTTAACCCTCAGGATTTTAGTAAACCTATCCAGGAAGTGCTCATTGAGATGAC
TGATGGAGGAGTGGACTATTCCTTTGAATGTATTGGTAATGTGAAGGTC

Alignment

ORF - retro_cjac_1029 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.88 %
• Parental protein coverage: 72.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLRRPEPADMANQVIKCKAAVAWEAGKPLFIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGCF
          PLRRPEPADMANQVIKCKAAVAWEAGKPL.IEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGCF
Retrocopy PLRRPEPADMANQVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGCF

Parental  PVILGHEGAGIVESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFT
          PVIL.HEGAGIVESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFT
Retrocopy PVILEHEGAGIVESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFT

Parental  CKGKTILHYMGTSTFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKVEPGSVCAVFGLG
          CKGKTILHYMGTSTFSEYTVVADISVAKIDPLAPLDK.CLLGCGISTGYGAAVNTAKVEPGSVCA.FGLG
Retrocopy CKGKTILHYMGTSTFSEYTVVADISVAKIDPLAPLDKFCLLGCGISTGYGAAVNTAKVEPGSVCAIFGLG

Parental  GVGLAVIMGCKVAGASRIIGVDINKDKFARAKEFGATECVNPQDFSKPIQEVLIEMTDGGVDYSFECIGN
          GVGLAVIMGCKVAGAS.IIGVDINKDKFA.AKEFGATECVNPQDFSKPIQEVLIEMTDGGVDYSFECIGN
Retrocopy GVGLAVIMGCKVAGASQIIGVDINKDKFAGAKEFGATECVNPQDFSKPIQEVLIEMTDGGVDYSFECIGN

Parental  VKV
          VKV
Retrocopy VKV

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	0.04 RPM	19.35 RPM
SRP051959_heart	0.04 RPM	30.92 RPM
SRP051959_kidney	0.13 RPM	52.51 RPM
SRP051959_liver	0.35 RPM	184.03 RPM
SRP051959_lung	0.11 RPM	26.91 RPM
SRP051959_lymph_node	0.07 RPM	30.09 RPM
SRP051959_skeletal_muscle	0.04 RPM	19.59 RPM
SRP051959_spleen	0.04 RPM	24.33 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1029 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1029 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1029 has 0 orthologous retrocopies within eutheria group .

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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,