RetrogeneDB ID: retro_cjac_1941

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:93970417..93970924(-)
• Located in intron of: ENSCJAG00000016536

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAA50
• Ensembl ID: ENSCJAG00000020261
• Aliases: None
• Description: N(alpha)-acetyltransferase 50, NatE catalytic subunit [Source:HGNC Symbol;Acc:29533]

Sequence

>retro_cjac_1941
ATGAAAGGTAGCCGGATCGAGCTGGGAGATGTGACACCACACAATATTAAATAGTTGAAAAGATTGAATCGGGCCGTCTT
TCCAGTCAGCTACAATGACAAGTTCTACAAGGATGTGCTGGAGGTTGGCGAGCTAGCAAAACTTGCCTGTTTCAATGATA
TTGCTGTAGGTCTGGTATGCTGTAGGTTGGATCATTTACAGAACCAGAAGAGACTTTACATCATGACACTAGGATGTCTG
GCACCTTACTGAAGGCTAGGAATAGGAACTAAAATGTTAAATCATGTCTTAAACATCTGTGAAAAAGATGGTACTTTTGA
CAACGTCTATCTGCATGCCCAGATCAGCAATGAGTTGGCAATTGAGTTCTACAGGAAGTTTGGCTTTGAGATTATCGAGA
CAAAAAAGAACTACTATAAGAGGATAGAGCCCACAGATGCTCATGTGCTGCAGAAAAACCTCAAAGTTCCTTCTGGTCAG
AATGCAGATGTACAAAAGACATACAAC

Alignment

ORF - retro_cjac_1941 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKGSRIELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKDVLEVGELAKLAYFNDIAVGAVCCRVDHSQNQK
          MKGSRIELGDVTPHNIK.LKRLN...FPVSYNDKFYKDVLEVGELAKLA.FNDIAVG.VCCR.DH.QNQK
Retrocopy MKGSRIELGDVTPHNIK*LKRLNRAVFPVSYNDKFYKDVLEVGELAKLACFNDIAVGLVCCRLDHLQNQK

Parental  RLYIMTLGCLAPYRRLGIGTKMLNHVLNICEKDGTFDNIYLHVQISNESAIDFYRRFGFEIIETKKNYYK
          RLYIMTLGCLAPY.RLGIGTKMLNHVLNICEKDGTFDN.YLH.QISNE.AI.FYR.FGFEIIETKKNYYK
Retrocopy RLYIMTLGCLAPY*RLGIGTKMLNHVLNICEKDGTFDNVYLHAQISNELAIEFYRKFGFEIIETKKNYYK

Parental  RIEPADAHVLQKNLRVPSAQNADVQKTDN
          RIEP.DAHVLQKNL.VPS.QNADVQKT.N
Retrocopy RIEPTDAHVLQKNLKVPSGQNADVQKTYN

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	0.62 RPM	38.16 RPM
SRP051959_heart	0.44 RPM	42.11 RPM
SRP051959_kidney	0.91 RPM	38.14 RPM
SRP051959_liver	0.32 RPM	34.90 RPM
SRP051959_lung	0.96 RPM	34.75 RPM
SRP051959_lymph_node	0.75 RPM	38.90 RPM
SRP051959_skeletal_muscle	0.09 RPM	82.66 RPM
SRP051959_spleen	0.80 RPM	36.43 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1941 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1941 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1941 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020261	2 retrocopies	retro_cjac_1941 , retro_cjac_2823,
Otolemur garnettii	ENSOGAG00000011197	1 retrocopy	retro_ogar_157,
Procavia capensis	ENSPCAG00000009780	2 retrocopies	retro_pcap_205, retro_pcap_459,
Ictidomys tridecemlineatus	ENSSTOG00000009438	1 retrocopy	retro_itri_1703,