RetrogeneDB ID: retro_cjac_58

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:60702970..60703756(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022161
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000010369
• Aliases: None
• Description: None

Sequence

>retro_cjac_58
ATGTCTCGAAGATATGACTCCAGGACCACTATATTTTCTCCAGAAGGTCGCTTATACCAAGTTGAATATGCCATGGAAGC
GATTGGACATGCAGGCACCTGTTTGGGAATTTTAGCAAATGATGGTGTTTTGCTTGCAGCAGAGAGACGCAACATCCACA
AGCTTCTTGATGAAGTCTTTTTTTCTGAAAAAATTTATAAACTCAATGAGGACATGGCTTGCAGTGTGGCAGGCATAACT
TCTGATGCTAATGTTCTGACTAATGAACTAAGGCTCATTGCTCAAAGGTATTTATTACAGTATCAGGAGCCAATACCTTG
TGAGCAGTTGGTTACAGCACTATGTGACATCAAACAAGCTTATACACAATTTGGAGGAAAACGTCCCTTTGGTGTTTCAT
TGCTCTACATTGGCTGGGATAAGCACTATGGCTTTCAGCTCTATCAGAGTGACCCTAGTGGAAATTACGGGGGATGGAAG
GCCACATGCATTGGAAATAATAGCGCTGCGGCTGTGTCAATGTTGAAACAAGACTACAAAGAAGGAGAAATGACGTTGAA
GTCAGCACTGGCTTTAGCTATCAAAGTGCTCAATAAGACCATGGATGTTAGTAAACTGTCTGCTGAGAAAGTGGAAATTG
CAACACTAACAAGAGAGAATGGAAAGACGGTAATCAGAGTTCTCAAACAAAAAGAAGTGGAACAGTTGATCAAAAAACAT
GAGGAAGAAGAAGCTAAAGCTGAGCGTGAGAAGAAAGAAAAAGAACAGAAAGAAAAGGATAAATAG

Alignment

ORF - retro_cjac_58 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFFSEKIYKLNE
          MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFFSEKIYKLNE
Retrocopy MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFFSEKIYKLNE

Parental  DMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWD
          DMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWD
Retrocopy DMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWD

Parental  KHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMDVSKLSAEK
          KHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMDVSKLSAEK
Retrocopy KHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMDVSKLSAEK

Parental  VEIATLTRENGKTVIRVLKQKEVEQLIKKHEEEEAKAEREKKEKEQKEKDK
          VEIATLTRENGKTVIRVLKQKEVEQLIKKHEEEEAKAEREKKEKEQKEKDK
Retrocopy VEIATLTRENGKTVIRVLKQKEVEQLIKKHEEEEAKAEREKKEKEQKEKDK

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	0.69 RPM	13.07 RPM
SRP051959_heart	0.89 RPM	11.56 RPM
SRP051959_kidney	0.55 RPM	12.22 RPM
SRP051959_liver	0.61 RPM	13.06 RPM
SRP051959_lung	0.65 RPM	11.88 RPM
SRP051959_lymph_node	0.50 RPM	14.82 RPM
SRP051959_skeletal_muscle	0.61 RPM	11.31 RPM
SRP051959_spleen	0.86 RPM	16.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_58 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_58 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_58 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010369	1 retrocopy	retro_cjac_58 ,
Myotis lucifugus	ENSMLUG00000027860	1 retrocopy	retro_mluc_1404,
Mus musculus	ENSMUSG00000032301	2 retrocopies	retro_mmus_1035, retro_mmus_1707,
Pteropus vampyrus	ENSPVAG00000009182	2 retrocopies	retro_pvam_1229, retro_pvam_824,
Tupaia belangeri	ENSTBEG00000011678	5 retrocopies	retro_tbel_1746, retro_tbel_2953, retro_tbel_3324, retro_tbel_4164, retro_tbel_614,
Tarsius syrichta	ENSTSYG00000011745	1 retrocopy	retro_tsyr_21,