RetrogeneDB ID: retro_cjac_659

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:6625280..6625774(+)
• Located in intron of: ENSCJAG00000005023

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000007182
• Aliases: None
• Description: None

Sequence

>retro_cjac_659
TGTGTGCCCTGCAGCGACGAGGTGGAGCTACCCGCAGATGGGAAGCCCTGGATGCCCCAGCCCTCCAAAATCCAGAGGCT
CTAAGAACCGTTGGCTGCCCACGGTACCCTGGAGCTGCAAGCAGAGATCCTGCCCCGCCGGCCGCCCACCCGAGGCCCAG
AGCTAAGAGGAGAGATCTGATGAGGAGCTGGAGGCCAAAGAAGAGGAAGAGGAAAAACCACACATGCCCACGGAATTTGA
TTTTGATGATGAGCCATGACACCGAAGGACTCCCTGACTGACCGGAGACGCACCCCAGGAAGCTCAGCCCGGAGCCAGAA
ATGGGAGGCCCACCTGGACAAGGTGCTCTCGAACATGAAGCGACAGAAGAAGCTGGAGGCACAGATCCTTCGTACTGGGA
GGGACCTCTTCAGCCTGGTCCCTCCAGGGACCCCAGCCCCACCAGCCCCCAACTCCAGTCCTCAGGGAGCAGTCTCTTCC
CTCGGCGGAAATAC

Alignment

ORF - retro_cjac_659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.46 %
• Parental protein coverage: 65.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CVPCSDEEVELPPDGQPWMPQPSEIQRLYELLAAHGTLELQAEILPRRPPT-PEAQSEEERSDEEPEAKE
          CVPCSDE.VELP.DG.PWMPQPS.IQRL.E.LAAHGTLELQAEILP.R.P..PEAQS.EERSDEE.EAKE
Retrocopy CVPCSDE-VELPADGKPWMPQPSKIQRL*EPLAAHGTLELQAEILP-RRPP>PEAQS*EERSDEELEAKE

Parental  EEEEKPHMPTEFDFDDEP-VTPKDSLIDRRRTPGSSARSQKREARLDKVLSDMKRHKKLEEQILRTGRDL
          EEEEKPHMPTEFDFDDEP..TPKDSL.DRRRTPGSSARSQK.EA.LDKVLS.MKR.KKLE.QILRTGRDL
Retrocopy EEEEKPHMPTEFDFDDEP<MTPKDSLTDRRRTPGSSARSQKWEAHLDKVLSNMKRQKKLEAQILRTGRDL

Parental  FSL-DSEDPSP-TSPPLRSSGSSLFPRQRKY
          FSL.....P.P.TSP.L.SSGSSLFPR.RKY
Retrocopy FSL>SLQGPQP>TSPQLQSSGSSLFPR-RKY

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	0.11 RPM	3.64 RPM
SRP051959_heart	0.02 RPM	4.16 RPM
SRP051959_kidney	0.07 RPM	4.70 RPM
SRP051959_liver	0.06 RPM	3.29 RPM
SRP051959_lung	0.05 RPM	6.31 RPM
SRP051959_lymph_node	0.09 RPM	8.88 RPM
SRP051959_skeletal_muscle	0.09 RPM	3.54 RPM
SRP051959_spleen	0.04 RPM	5.80 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_659 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_659 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_659 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007182	1 retrocopy	retro_cjac_659 ,
Tarsius syrichta	ENSTSYG00000008812	1 retrocopy	retro_tsyr_1714,