RetrogeneDB ID: retro_cjac_313

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:147143822..147144461(-)
• Located in intron of: ENSCJAG00000018380

Retrocopy information

• Ensembl ID: ENSCJAG00000022570
• 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_313
ACGAGCAGCAAAGTCTCTGGCGACACCCTGTACGAGGCGGTGCGGGAAGTCCTGCACGGGAACCAGCGCGAGCGCCGCAA
GTTCCTGGAGACGGTGGCGTTGCAGATCAGTTTGAAGAACTATGACCCCCAGAAGGACAAGCGTTTCTCGGGCACCGTCA
GGCTTAAGTCCACTCCTCGCCCCGAGTTCTCCGTGTGTGTCCTGGGGGACCAGCAGCACTGTGACCAGGCCAAGGCCGTG
GATATCCCCCACATGGACATCGAGGCGCTGAAAAAACTCAACGTCAAGAAGCTGGCCAAGAAGTATGATGCATTTTTGGC
CTCAGAGTCTCTGATCAAGCAGATTCCACGAATCCTCGGCCCAGGCCTAAAAAAGGCAGGAAAGTTCCCCTCCCTGCTCA
CACACAATGAAAACATGGTGGCCAGAGTGGATGAGGTGAAGTCCACGATCCAGTTCCAAATGAAGAAGGTGTTATGTCTG
GCTGTGGCTGTTGGTCACGTGAAGATGACAGACGATGAGCTTGTGTATAACATTCACCTGGCTGTCAATTTCTTGGTGTC
ATTGCTCAAGAAAAACTGGCAGAATGTCCGGGCCTTATATATCAAGAGCACCATGGGCAAGCCCCAGTGCCTATATTAA

Alignment

ORF - retro_cjac_313 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.59 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGDQ
          SSKVS.DTLYEAVREVLHGNQR.RRKFLETV.LQISLKNYDPQKDKRFSGTVRLKSTPRP.FSVCVLGDQ
Retrocopy SSKVSGDTLYEAVREVLHGNQRERRKFLETVALQISLKNYDPQKDKRFSGTVRLKSTPRPEFSVCVLGDQ

Parental  QHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLTHN
          QHCD.AKAVDIPHMDIEALKKLN..KKL.KK....YDAFLASESLIKQIPRILGPGL.KAGKFPSLLTHN
Retrocopy QHCDQAKAVDIPHMDIEALKKLNV-KKLAKK----YDAFLASESLIKQIPRILGPGLKKAGKFPSLLTHN

Parental  ENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMG
          ENMVA.VDEVKSTI.FQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMG
Retrocopy ENMVARVDEVKSTIQFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMG

Parental  KPQRLY
          KPQ.LY
Retrocopy KPQCLY

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	0.20 RPM	85.44 RPM
SRP051959_heart	0.07 RPM	84.86 RPM
SRP051959_kidney	0.22 RPM	92.56 RPM
SRP051959_liver	0.22 RPM	115.71 RPM
SRP051959_lung	0.18 RPM	106.37 RPM
SRP051959_lymph_node	0.41 RPM	159.31 RPM
SRP051959_skeletal_muscle	0.11 RPM	149.20 RPM
SRP051959_spleen	0.13 RPM	135.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_313 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_313 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_313 has 0 orthologous retrocopies within eutheria group .

---

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 ,