RetrogeneDB ID: retro_cjac_2020

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:6359122..6359425(+)
• Located in intron of: ENSCJAG00000008790

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX5
• Ensembl ID: ENSCJAG00000018847
• Aliases: None
• Description: chromobox homolog 5 [Source:HGNC Symbol;Acc:1555]

Sequence

>retro_cjac_2020
AGAAAATCCAATTTCTCAAACAGTGCTGACAGTATCAAGTCCAAAAAAGGTAACAGAGCAATGGTATTTATTGCTCCGGG
CTTTGAGATAAGACTGGAACCAGAAAAGATTACTGGGAGTGACAGATTCCCGTGGTGATTTATGGTTTTAATGAACTGGA
AAGACACAGATGAAGCAGACCTGGTTCTTGCAAAAGAAGCTAATGTGAAATGTCTACAAACTATGACAGCATTTTGTGAA
GAGAGACTGATGTTGCATGCATACTTTGAGGATGTAGAAAACAAGAAAAGAAAAAACAGCAAA

Alignment

ORF - retro_cjac_2020 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.93 %
• Parental protein coverage: 52.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKSNFSNSADDIKSKKKREQSNDIARGFERGLEPEKI-IGATDSCGDLMF-LMKWKDTDEADLVLAKEAN
          RKSNFSNSAD.IKSKK.......IA.GFE..LEPEKI..G.TDS.GDL.F.LM.WKDTDEADLVLAKEAN
Retrocopy RKSNFSNSADSIKSKKGNRAMVFIAPGFEIRLEPEKI>LGVTDSRGDLWF<LMNWKDTDEADLVLAKEAN

Parental  VKCPQIVIAFYEERLTWHAYPEDAENKEKETAK
          VKC.Q...AF.EERL..HAY.ED.ENK.....K
Retrocopy VKCLQTMTAFCEERLMLHAYFEDVENKKRKNSK

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	0.91 RPM	15.42 RPM
SRP051959_heart	0.54 RPM	21.29 RPM
SRP051959_kidney	1.13 RPM	27.56 RPM
SRP051959_liver	0.80 RPM	7.43 RPM
SRP051959_lung	0.70 RPM	22.95 RPM
SRP051959_lymph_node	1.00 RPM	21.87 RPM
SRP051959_skeletal_muscle	0.39 RPM	9.13 RPM
SRP051959_spleen	0.90 RPM	24.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2020 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2020 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2020 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007532	2 retrocopies	retro_cjac_191, retro_cjac_51,
Callithrix jacchus	ENSCJAG00000007952	8 retrocopies	retro_cjac_1100, retro_cjac_1414, retro_cjac_1612, retro_cjac_2405, retro_cjac_2623, retro_cjac_2728, retro_cjac_3322, retro_cjac_869,
Callithrix jacchus	ENSCJAG00000018847	1 retrocopy	retro_cjac_2020 ,
Echinops telfairi	ENSETEG00000001220	1 retrocopy	retro_etel_678,
Homo sapiens	ENSG00000094916	1 retrocopy	retro_hsap_2811,
Gorilla gorilla	ENSGGOG00000000041	1 retrocopy	retro_ggor_1955,
Nomascus leucogenys	ENSNLEG00000017671	1 retrocopy	retro_nleu_428,
Pongo abelii	ENSPPYG00000004599	1 retrocopy	retro_pabe_2307,
Pan troglodytes	ENSPTRG00000005034	1 retrocopy	retro_ptro_1905,
Tursiops truncatus	ENSTTRG00000004524	1 retrocopy	retro_ttru_1859,