RetrogeneDB ID: retro_cjac_352

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 20:2428089..2428305(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023015
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001989
• Aliases: None
• Description: None

Sequence

>retro_cjac_352
ATGGCGCCGCCGGTGCAGGTCTCTCGGCTCATCAAGCTCGGCCGCTACTCCTTCTTGTTCCTCGGCATGGCCTACGGAGC
CACGCGCTACAGTTACCTAAAACCTCGGGCAGAAGAGGAGAGGGGGATAGCGGCAGAGGAGAAGAAGAAGCAGGATGAAC
TGAAACGGATTGCCAAGGAATTGGCAGAAGCCCAAGAGGACACCATACTTAAATGA

Alignment

ORF - retro_cjac_352 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPPVQVSPLIKLGRYSFLFLGMAYGATRYSYLKPRAEEERRIAAEEKKKQDELKRIAKELAE--EDTIL
          MAPPVQVS.LIKLGRYSFLFLGMAYGATRYSYLKPRAEEER.IAAEEKKKQDELKRIAKELAE..EDTIL
Retrocopy MAPPVQVSRLIKLGRYSFLFLGMAYGATRYSYLKPRAEEERGIAAEEKKKQDELKRIAKELAEAQEDTIL

Parental  K
          K
Retrocopy K

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	0.42 RPM	6.08 RPM
SRP051959_heart	0.61 RPM	10.07 RPM
SRP051959_kidney	0.58 RPM	7.77 RPM
SRP051959_liver	0.71 RPM	9.51 RPM
SRP051959_lung	0.13 RPM	2.86 RPM
SRP051959_lymph_node	0.32 RPM	2.72 RPM
SRP051959_skeletal_muscle	0.68 RPM	12.23 RPM
SRP051959_spleen	0.19 RPM	3.45 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_352 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_352 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_352 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016722	2 retrocopies	retro_amel_1171, retro_amel_1761,
Bos taurus	ENSBTAG00000017496	2 retrocopies	retro_btau_1222, retro_btau_219,
Canis familiaris	ENSCAFG00000023527	1 retrocopy	retro_cfam_62,
Callithrix jacchus	ENSCJAG00000001989	1 retrocopy	retro_cjac_352 ,
Cavia porcellus	ENSCPOG00000008678	1 retrocopy	retro_cpor_98,
Felis catus	ENSFCAG00000029708	1 retrocopy	retro_fcat_268,
Mustela putorius furo	ENSMPUG00000011414	1 retrocopy	retro_mputfur_494,
Mus musculus	ENSMUSG00000050856	1 retrocopy	retro_mmus_3152,
Otolemur garnettii	ENSOGAG00000012271	1 retrocopy	retro_ogar_1292,
Rattus norvegicus	ENSRNOG00000000064	1 retrocopy	retro_rnor_697,
Tursiops truncatus	ENSTTRG00000002962	1 retrocopy	retro_ttru_1938,