RetrogeneDB ID: retro_cjac_184

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:60686208..60687351(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022875
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000012536
• Aliases: None
• Description: None

Sequence

>retro_cjac_184
ATGAGTGAGACGGTCATCTGTTCCAGCCGGGCCACTGTGATGGTTTATGATGACGGCAACAAGCGATGGGTCCCTGCTCG
CATGGGTCCTCAGGCCTTCAGCCACGTCCAGATCTACCACAACCCCACAGCCAATTCCTTCTGCGTGGTGGGTCGGAAGA
TGCAGCCTGACCAGCAGGTGGTCATCAACTGTGCCATCGTCCAGGGCGTCAAGTATAATCAAGCCACCCCTAATTTCCAT
CAGTGGCGCGATGCCCGCCGGGTCTGGGGCCTCAACTTCAGCAGCAAGGAGGATGCCGCCCAGTTTGCTGCGGGCATGGC
CAGTGCCCTAGAGGCGTTGGAAGGAGGTGGGTCCCCTCCACCGCCAGCACCTCCTGCCTGGTCGGTCCTCAAGGGCCCCT
CCCCGGAGGAGGTGGAGCAGCAGAAAAGGCCCCAGCCCGGCCCGACAGAGCATGTAGAGCGCCGTGTCTCCAATGCAGGA
GGCCCACCTGCTCCCCCTGCTGGGGGTCCACACCCACCACCAGGACCTCCCCCTCCTCCAGGTCCTCCCCTACCCCCAGG
TTTGCCTCCCTCGGGGGTCCCAGCTGCAGCACACGGAGCTGGGGGAGGACCACCCCCTGCACCCCCTCTCCCAGCAGCAC
AGGGCCCCAGTGGTGGGGGGACTGGGGCCCCAGGCCTGGCTGCAGCTATTGCTGGAGCCAAACTCAGGAAAGTCAGCAAG
CAGGAGGAATCCTCAGCAGGGCCCGTAGCCCCCAAAGCTGAGAGCGGTCGAAGCGGAGGTGGGGGACTCATGGAAGAGAT
GAACGCCATGCTGGCCCGGAGAAGGAAAGCCACACAGGTTGGGGAGAAAACTCCCAAGGATGAATCTGCCAATCAGGAGG
AGCCAGAGGCCAGAGTCCTAGCCCAGAGTGAATCTGTGTGGAGACCCTGGGAGAAGAACAGCACAACCTTGCCAAGGATG
AAGTTGTCTTCTTCGGTCACCACTTCTGAGACCCACCCCTACACGCCCAGCTCCGGCGATGACTCGGACCTAGAGAGGGT
GAAACAGGAGCTTCTGGAAGAGGTGAAGAAGGAATTGCAGAAAGTGAAAGAGGAAATCATTGAAGCCTTTGTCCAGGAGC
TGAGGAAGCGGGGTTCTCCCTGA

Alignment

ORF - retro_cjac_184 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.54 %
• Parental protein coverage: 55.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPPAPPAGGLPPSGVPAAAHGSGGGPPPAPPLPAAQGPSGGGTGAPGLAAAIAGAKLRKVSKQEESSAGP
          GPP.PP..GLPPSGVPAAAHG.GGGPPPAPPLPAAQGPSGGGTGAPGLAAAIAGAKLRKVSKQEESSAGP
Retrocopy GPPLPP--GLPPSGVPAAAHGAGGGPPPAPPLPAAQGPSGGGTGAPGLAAAIAGAKLRKVSKQEESSAGP

Parental  VAPKAESGRSGGGGLMEEMNAMLARRRKATQVGEKTPKDESANQEEPEARVPAQSESVRRPWEKNSTTLP
          VAPKAESGRSGGGGLMEEMNAMLARRRKATQVGEKTPKDESANQEEPEARV.AQSESV.RPWEKNSTTLP
Retrocopy VAPKAESGRSGGGGLMEEMNAMLARRRKATQVGEKTPKDESANQEEPEARVLAQSESVWRPWEKNSTTLP

Parental  RMKSSSSVTTSETHPCTPSSGDDSDLERVKQELLEAVKKELQKVKEEIIEAFVQELRKRGSP
          RMK.SSSVTTSETHP.TPSSGDDSDLERVKQELLE.VKKELQKVKEEIIEAFVQELRKRGSP
Retrocopy RMKLSSSVTTSETHPYTPSSGDDSDLERVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSP

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	1.80 RPM	13.98 RPM
SRP051959_heart	1.07 RPM	5.67 RPM
SRP051959_kidney	1.15 RPM	4.75 RPM
SRP051959_liver	0.65 RPM	2.90 RPM
SRP051959_lung	1.63 RPM	11.14 RPM
SRP051959_lymph_node	2.21 RPM	15.55 RPM
SRP051959_skeletal_muscle	0.59 RPM	2.42 RPM
SRP051959_spleen	1.79 RPM	11.81 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_184 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_184 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012536	1 retrocopy	retro_cjac_184 ,
Ictidomys tridecemlineatus	ENSSTOG00000027705	1 retrocopy	retro_itri_333,