RetrogeneDB ID: retro_cjac_194

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:13686997..13687441(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022227
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000017286
• Aliases: None
• Description: None

Sequence

>retro_cjac_194
ATGTCATCTGAGCCTCCGCCTCCACCACAGCCCCCCACCCATCAGGCTTCAGCTGGGCTGCTGGACACCCCTCGGACCCG
AGAGCGCTCACCATCCCCTCTGCGGGGCAACGTGGTCCCAAGCCCACTGCCCACTCGCCGGACAAGGACCTTCTCAGCGA
CCGTGCGGGCTTCACAGGGCCCCGTCTACAAAGGAGTCTGCAAATGTTTCTGCCGATCCAAGGGCCATGGCTTCATTACC
CCAGCTGACGGCGGCCCTGACATCTTCCTGCACATCTCTGATGTGGAAGGGGAGTATGTCCCAGTGGAAGGCGACGAGGT
CACCTATAAGATGTGCTCCATCCCGCCCAAGAATGAGAAGCTGCAGGCTGTGGAGGTTGTCATCACCCACCTGGCACCGG
GCACCAAGCATGAGACTTGGTCCGGACATGTCATCAGCTCCTAG

Alignment

ORF - retro_cjac_194 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSEPPPPPQPPTHQASVGLLDTPRTRERSPSPLRGNVVPSPLPTRRTRTFSATVRASQGPVYKGVCKCF
          MSSEPPPPPQPPTHQAS.GLLDTPRTRERSPSPLRGNVVPSPLPTRRTRTFSATVRASQGPVYKGVCKCF
Retrocopy MSSEPPPPPQPPTHQASAGLLDTPRTRERSPSPLRGNVVPSPLPTRRTRTFSATVRASQGPVYKGVCKCF

Parental  CRSKGHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYKMCSIPPKNEKLQAVEVVITHLAPGTKHETW
          CRSKGHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYKMCSIPPKNEKLQAVEVVITHLAPGTKHETW
Retrocopy CRSKGHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYKMCSIPPKNEKLQAVEVVITHLAPGTKHETW

Parental  SGHVISS
          SGHVISS
Retrocopy SGHVISS

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	0.13 RPM	4.95 RPM
SRP051959_heart	0.04 RPM	2.98 RPM
SRP051959_kidney	0.13 RPM	8.30 RPM
SRP051959_liver	0.39 RPM	27.27 RPM
SRP051959_lung	0.03 RPM	4.67 RPM
SRP051959_lymph_node	0.05 RPM	4.77 RPM
SRP051959_skeletal_muscle	0.02 RPM	1.35 RPM
SRP051959_spleen	0.00 RPM	4.22 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_194 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_194 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_194 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017286	1 retrocopy	retro_cjac_194 ,
Macropus eugenii	ENSMEUG00000016403	1 retrocopy	retro_meug_1949,
Monodelphis domestica	ENSMODG00000005721	1 retrocopy	retro_mdom_12,
Mus musculus	ENSMUSG00000008393	1 retrocopy	retro_mmus_88,
Rattus norvegicus	ENSRNOG00000002610	1 retrocopy	retro_rnor_1025,