RetrogeneDB ID: retro_cjac_133

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:31597749..31598070(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021731
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000005285
• Aliases: None
• Description: None

Sequence

>retro_cjac_133
ATGTCCACTAACAATATGTCGGACCCACGGAGGCCAAACAAAGTACTGAGGTACAAGCCCCCACCGAGCGAGTGTAACCC
GGCCTTGGATGACCCGACGCCAGACTACATGGACCTGCTGGGCATGATCTTCAGCATGTGCGGCCTCATGCTTAAGCTGA
AGTGGTGTGCTTGGGTCGCTGTCTACTGCTCCTTCATCAGCTGTGCCAACTCTCGGAGCTCAGAGGACACGAAGCAAATG
ATGAGTAGCTTCATGCTCTCCATCTCTGCCGTGGTGATGTCCTATCTGCAGAACTCTCAGCCCATGACGCCCCCGTGGTG
A

Alignment

ORF - retro_cjac_133 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTNNMSDPRRPNKVLRYKPPPSECNPALDDPTPDYMNLLGMIFSMCGLMLKLKWCAWVAVYCSFISFAN
          MSTNNMSDPRRPNKVLRYKPPPSECNPALDDPTPDYM.LLGMIFSMCGLMLKLKWCAWVAVYCSFIS.AN
Retrocopy MSTNNMSDPRRPNKVLRYKPPPSECNPALDDPTPDYMDLLGMIFSMCGLMLKLKWCAWVAVYCSFISCAN

Parental  SRSSEDTKQMMSSFMLSISAVVMSYLQNPQPMTPPW
          SRSSEDTKQMMSSFMLSISAVVMSYLQN.QPMTPPW
Retrocopy SRSSEDTKQMMSSFMLSISAVVMSYLQNSQPMTPPW

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	0.00 RPM	7.81 RPM
SRP051959_heart	0.04 RPM	7.95 RPM
SRP051959_kidney	0.04 RPM	11.49 RPM
SRP051959_liver	0.02 RPM	10.98 RPM
SRP051959_lung	0.05 RPM	7.58 RPM
SRP051959_lymph_node	0.00 RPM	6.48 RPM
SRP051959_skeletal_muscle	0.02 RPM	10.39 RPM
SRP051959_spleen	0.02 RPM	7.39 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_133 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_133 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_133 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028908	2 retrocopies	retro_cfam_1489, retro_cfam_1951,
Callithrix jacchus	ENSCJAG00000005285	1 retrocopy	retro_cjac_133 ,
Echinops telfairi	ENSETEG00000019481	1 retrocopy	retro_etel_1133,
Felis catus	ENSFCAG00000000463	1 retrocopy	retro_fcat_1902,
Macropus eugenii	ENSMEUG00000014450	3 retrocopies	retro_meug_1695, retro_meug_1733, retro_meug_2081,
Mus musculus	ENSMUSG00000059355	2 retrocopies	retro_mmus_1327, retro_mmus_2061,
Pteropus vampyrus	ENSPVAG00000013403	1 retrocopy	retro_pvam_1464,
Sus scrofa	ENSSSCG00000013721	1 retrocopy	retro_sscr_488,
Tupaia belangeri	ENSTBEG00000001250	1 retrocopy	retro_tbel_2034,