RetrogeneDB ID: retro_cjac_10

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:95771582..95772233(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023039
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DEF6
• Ensembl ID: ENSCJAG00000015575
• Aliases: None
• Description: differentially expressed in FDCP 6 homolog (mouse) [Source:HGNC Symbol;Acc:2760]

Sequence

>retro_cjac_10
AGCAGCAAAGTCTCTCGCGACACCCTGTACGAGGCGGTGCGGGAAGTCCTGCACGGGAACCAGCGCAAGCGCCGCAAGTT
CCTGGAGACGGTGGAGTTGCAGATCAGTTTGAAGAACTATGACCCCCAGAAGGACAAGCGTTTCTCGGGCACCGTCAGGC
TTAAGTCCACTCCTCGCCCCAAGTTCTCCGTGTGTGTCCTGGGGGACCAGCAGCACTGTGACGAGGCCAAGGCTGTGGAT
ATCCCCCACATGGACATCGAGGCGCTGAAAAAACTCAACAAGAATAAAAAACTGGTCAAGAAGCTGGCCAAGAAGTATGA
TGCATTTTTGGCCTCAGAGTCTCTGATCAAGCAGATTCCAGGAATCCTCGGCCCAGGCCTAAATAAGGCAGGAAAGTTCC
CCTCCCTGCTCACACACAATGAAAACATGGTGGCCAAAGTGGATGAGGTGAAGTCCACGATCAAGTTCCAAATGAAGAAG
GTGTTATGTCTGGCTGTGGCTGTTGGTCACATGAAGATGACAGATGATGAGCTTGTGTATAACATTCACCTGGCTGTCAA
TTTCTTGGTGTCATTGCTCAAGAAAAACTGGCAGAATGTCCGGGCCTTATATATCAAGAGCACCATGGGCAAGCCCCAGC
TCCTGTATTAA

Alignment

ORF - retro_cjac_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.61 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGDQ
          SSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGDQ
Retrocopy SSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGDQ

Parental  QHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLTHN
          QHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIP.ILGPGLNKAGKFPSLLTHN
Retrocopy QHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPGILGPGLNKAGKFPSLLTHN

Parental  ENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMG
          ENMVAKVDEVKSTIKFQMKKVLCLAVAVGH.KMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMG
Retrocopy ENMVAKVDEVKSTIKFQMKKVLCLAVAVGHMKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMG

Parental  KPQRLY
          KPQ.LY
Retrocopy KPQLLY

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	0.35 RPM	85.44 RPM
SRP051959_heart	0.26 RPM	84.86 RPM
SRP051959_kidney	0.29 RPM	92.56 RPM
SRP051959_liver	0.26 RPM	115.71 RPM
SRP051959_lung	0.26 RPM	106.37 RPM
SRP051959_lymph_node	0.53 RPM	159.31 RPM
SRP051959_skeletal_muscle	0.46 RPM	149.20 RPM
SRP051959_spleen	0.17 RPM	135.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_10 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_10 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_10 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011252	1 retrocopy	retro_cjac_1605,
Callithrix jacchus	ENSCJAG00000015575	2 retrocopies	retro_cjac_10 , retro_cjac_313,