RetrogeneDB ID: retro_cjac_530

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:65242925..65243279(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COTL1
• Ensembl ID: ENSCJAG00000004056
• Aliases: None
• Description: coactosin-like 1 (Dictyostelium) [Source:HGNC Symbol;Acc:18304]

Sequence

>retro_cjac_530
GTGCGCGACAGCAGCTCGGCAGTTATCTGGGTGACTTTTGAATATGACGGCTCCACCATTGTCCCCGGCGAGCAGGGAGC
GTAGTACCAGCACTTCATCCAGCAGTGCACAGATGCCGACCAGTTGCTTGCCTTCGTGCGCTTCACCACCTGGCATGCCA
TGAGCAAGAGGTCCAAGTTCGCCCTCATCACATGGCTCAGTGAGAGTATCAGCGGGCTGCAGTGCGCCAGAATTGGGATG
GACAAGACCCTGGTGAAGGAGGTCGTATAGAATTTTCCTAAGAAGTTTGTGATCAGTGATCGGAAGGAGCTGGAGGAAGA
TTTATTTCATCAAGAGAGAGCTGAAGAAGGTGGG

Alignment

ORF - retro_cjac_530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.42 %
• Parental protein coverage: 83.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRDDGSAVIWVTFKYDGSTIVPGEQGAEYQHFIQQCTDDVRLFAFVRFTTGDAMSKRSKFALITWIGEDV
          VRD..SAVIWVTF.YDGSTIVPGEQGA.YQHFIQQCTD...L.AFVRFTT..AMSKRSKFALITW..E..
Retrocopy VRDSSSAVIWVTFEYDGSTIVPGEQGA*YQHFIQQCTDADQLLAFVRFTTWHAMSKRSKFALITWLSESI

Parental  SGLQRAKTGTDKTLVKEVVQNFAKEFVISDRKELEEDFIKSELKKAGG
          SGLQ.A..G.DKTLVKEVV.NF.K.FVISDRKELEED....E....GG
Retrocopy SGLQCARIGMDKTLVKEVV*NFPKKFVISDRKELEEDLFHQERAEEGG

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	16.62 RPM
SRP051959_heart	0.04 RPM	4.79 RPM
SRP051959_kidney	0.00 RPM	27.87 RPM
SRP051959_liver	0.09 RPM	8.40 RPM
SRP051959_lung	0.05 RPM	18.02 RPM
SRP051959_lymph_node	0.02 RPM	32.88 RPM
SRP051959_skeletal_muscle	0.02 RPM	1.29 RPM
SRP051959_spleen	0.00 RPM	28.34 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_530 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_530 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_530 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004056	4 retrocopies	retro_cjac_1182, retro_cjac_2171, retro_cjac_2172, retro_cjac_530 ,
Macaca mulatta	ENSMMUG00000007039	1 retrocopy	retro_mmul_1249,