RetrogeneDB ID: retro_cjac_2519

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:60357606..60357869(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000019472
• Aliases: None
• Description: None

Sequence

>retro_cjac_2519
TTGTCTTACCTGCTGTACCCTCCCTGCATGGAGGGTGCTGTCTATTCGATCGGGAACATCAAGTGTAAGAGCTAGTACTC
CTGATTAATATCAGCTTTGTCAACAGGGTCTATGCCTTTGGCTTCCTCTTCATGCTGCTCCAGCTCTTCCTGAACTACAA
GCTGAAGTCACTGCCCGGGAAGGCCTTCACCTACAACGCTTTCAACACCTTCATTGACTATGTCTTTGCCTTCATCATCA
CCATGCCCACGTGGTGTTTCTGG

Alignment

ORF - retro_cjac_2519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 70.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSYLLYPLCIGGAAYSLLNTKYKSWYSWLIN-SFVNGVYAFGFLFMLPQLFVNCKLKSVAHLPWKAFTYK
          LSYLLYP.C..GA.YS..N.K.KS.YS.LI..SFVN.VYAFGFLFML.QLF.N.KLKS...LP.KAFTY.
Retrocopy LSYLLYPPCMEGAVYSIGNIKCKS*YS*LIS<SFVNRVYAFGFLFMLLQLFLNYKLKS---LPGKAFTYN

Parental  AFNTFIEDVFAF-ITMPTSHWLACFW
          AFNTFI..VFAF.ITMPT..W..CFW
Retrocopy AFNTFIDYVFAFIITMPT--W--CFW

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	0.00 RPM	4.04 RPM
SRP051959_heart	0.00 RPM	2.16 RPM
SRP051959_kidney	0.00 RPM	6.61 RPM
SRP051959_liver	0.00 RPM	5.74 RPM
SRP051959_lung	0.00 RPM	4.54 RPM
SRP051959_lymph_node	0.00 RPM	5.07 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.05 RPM
SRP051959_spleen	0.00 RPM	6.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2519 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2519 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2519 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019472	1 retrocopy	retro_cjac_2519 ,
Equus caballus	ENSECAG00000013231	1 retrocopy	retro_ecab_371,
Sus scrofa	ENSSSCG00000028490	1 retrocopy	retro_sscr_215,