RetrogeneDB ID: retro_cjac_2149

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:75137591..75138095(+)
• Located in intron of: ENSCJAG00000003361

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000012084
• Aliases: None
• Description: None

Sequence

>retro_cjac_2149
AAGGAAAAATTTGAGGGCCTCTTCTGGACTTATGATGACTGTGTGACGTTCCAGCTATTTAAGAGTTTCAGACGTGTCCG
CATAAACTTCAGCAATCCTAAATCTGCAGCCCGAGCTAGGATAGAGCTTCATGAAACCCAATTCAGAGGGAAAAAATTAA
AACTCTACTTTGCACAGGTTCAGACTCCAGAGACAGATGGAGACAAACTGCACTTGGCTCCACCCCAGCCTGCCAAACAA
TTTCTCATATCGCTCCCTTCCTCCCCACCTGTCGGCTGGCAGCCCATCAATGCCACTCCCGTCCTCAACTACGACCTCCT
CTATGCTGCGGCCAAACTAGGACCAGGAGAGAAGTATGAGCTCCATGCAGGGACTGAGTCCACCCCAAGTGTCGTCGTGC
ACATGTGCGACAGTGACATAGAGGAAGAAGAGGACCCAAAGACTTCCCCAAAGCCAAAAATCATCCAGACTCGGCGTCCT
GGCCTGCCACCCTCCATGTCCAAC

Alignment

ORF - retro_cjac_2149 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.45 %
• Parental protein coverage: 88.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEKFEGLFRTYDDCVTFQLFKSFRRVRINFSNPKSAARARIELHETQFRGKKLKLYFAQVQTPETDGDKL
          KEKFEGLF.TYDDCVTFQLFKSFRRVRINFSNPKSAARARIELHETQFRGKKLKLYFAQVQTPETDGDKL
Retrocopy KEKFEGLFWTYDDCVTFQLFKSFRRVRINFSNPKSAARARIELHETQFRGKKLKLYFAQVQTPETDGDKL

Parental  HLAPPQPAKQFLISPPSSPPVGWQPINDATPVLNYDLLYAVAKLGPGEKYELHAGTESTPSVVVHVCDSD
          HLAPPQPAKQFLIS.PSSPPVGWQPIN.ATPVLNYDLLYA.AKLGPGEKYELHAGTESTPSVVVH.CDSD
Retrocopy HLAPPQPAKQFLISLPSSPPVGWQPIN-ATPVLNYDLLYAAAKLGPGEKYELHAGTESTPSVVVHMCDSD

Parental  IEEEEDPKTSPKPKIIQTRRPGLPPSVSN
          IEEEEDPKTSPKPKIIQTRRPGLPPS.SN
Retrocopy IEEEEDPKTSPKPKIIQTRRPGLPPSMSN

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	0.29 RPM	1.71 RPM
SRP051959_heart	0.21 RPM	39.94 RPM
SRP051959_kidney	0.24 RPM	5.26 RPM
SRP051959_liver	0.22 RPM	0.41 RPM
SRP051959_lung	0.39 RPM	3.22 RPM
SRP051959_lymph_node	0.55 RPM	1.19 RPM
SRP051959_skeletal_muscle	0.02 RPM	3.45 RPM
SRP051959_spleen	0.34 RPM	4.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2149 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2149 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2149 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002838	2 retrocopies	retro_cjac_4016, retro_cjac_437,
Callithrix jacchus	ENSCJAG00000012084	1 retrocopy	retro_cjac_2149 ,