RetrogeneDB ID: retro_cjac_439

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:82805420..82805790(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000014812
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NAA20
• Ensembl ID: ENSCJAG00000005377
• Aliases: None
• Description: N(alpha)-acetyltransferase 20, NatB catalytic subunit [Source:HGNC Symbol;Acc:15908]

Sequence

>retro_cjac_439
TATTTTATAGGTAAAGCAGAAGGCTCAGTAGCTAGGGAAGAATGGCATGGGCACGTCCCAGCTCTGTCTGTTGCCCCAGA
ATTTCGACGCCTTGGTTTGGCTCCTAAACTTAGGGAGTTATTAGAGGAGATTTCAGAGAGAAAGGGTGGTTTTTTTTGTT
GATCTCTTTGTAAGAGTATCTAACCAAGTTGCAGTCAACATGTACAAGCAGTTGGGCTACAGTGTATACAGCACAGTCAT
AGAGTACTATTCAGCCAGCAATGGAGAGCCTGATGAGGACGCTTATGATATGAGGAAAGCACTTTCCAGGGACACGGAGA
AGGAATCCATCATACCATTACCTCATCCTGTGAGGCCTGAAGACATTGAA

Alignment

ORF - retro_cjac_439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.74 %
• Parental protein coverage: 74.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YIMGKAEGSVAREEWHGHVTALSVAPEFRRLGLAAKLMELLEEISERKGGFF-VDLFVRVSNQVAVNMYK
          Y..GKAEGSVAREEWHGHV.ALSVAPEFRRLGLA.KL.ELLEEISERKGGFF.VDLFVRVSNQVAVNMYK
Retrocopy YFIGKAEGSVAREEWHGHVPALSVAPEFRRLGLAPKLRELLEEISERKGGFF>VDLFVRVSNQVAVNMYK

Parental  QLGYSVYRTVIEYYSASNGEPDEDAYDMRKALSRDIEKKSIIPLPHPVRPEDIE
          QLGYSVY.TVIEYYSASNGEPDEDAYDMRKALSRD.EK.SIIPLPHPVRPEDIE
Retrocopy QLGYSVYSTVIEYYSASNGEPDEDAYDMRKALSRDTEKESIIPLPHPVRPEDIE

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	0.02 RPM	15.11 RPM
SRP051959_heart	0.02 RPM	25.70 RPM
SRP051959_kidney	0.04 RPM	25.96 RPM
SRP051959_liver	0.02 RPM	24.84 RPM
SRP051959_lung	0.00 RPM	20.50 RPM
SRP051959_lymph_node	0.00 RPM	19.31 RPM
SRP051959_skeletal_muscle	0.04 RPM	38.52 RPM
SRP051959_spleen	0.02 RPM	18.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_439 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_439 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_439 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001144	1 retrocopy	retro_btau_899,
Canis familiaris	ENSCAFG00000032025	1 retrocopy	retro_cfam_768,
Callithrix jacchus	ENSCJAG00000005377	4 retrocopies	retro_cjac_1099, retro_cjac_1629, retro_cjac_2984, retro_cjac_439 ,
Gorilla gorilla	ENSGGOG00000004247	1 retrocopy	retro_ggor_374,
Microcebus murinus	ENSMICG00000006044	1 retrocopy	retro_mmur_540,
Macaca mulatta	ENSMMUG00000007708	1 retrocopy	retro_mmul_479,
Mustela putorius furo	ENSMPUG00000001228	2 retrocopies	retro_mputfur_1495, retro_mputfur_321,
Mus musculus	ENSMUSG00000002728	3 retrocopies	retro_mmus_1228, retro_mmus_3146, retro_mmus_3257,
Nomascus leucogenys	ENSNLEG00000009855	1 retrocopy	retro_nleu_2267,
Oryctolagus cuniculus	ENSOCUG00000015481	1 retrocopy	retro_ocun_1331,
Otolemur garnettii	ENSOGAG00000011542	1 retrocopy	retro_ogar_2007,
Pongo abelii	ENSPPYG00000010746	1 retrocopy	retro_pabe_342,
Pan troglodytes	ENSPTRG00000013299	1 retrocopy	retro_ptro_284,
Ictidomys tridecemlineatus	ENSSTOG00000014733	1 retrocopy	retro_itri_1656,
Tupaia belangeri	ENSTBEG00000000969	1 retrocopy	retro_tbel_567,