RetrogeneDB ID: retro_cjac_2080

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:47682192..47682786(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023199
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000010909
• Aliases: None
• Description: None

Sequence

>retro_cjac_2080
AGGTTCCGGTTCTATGGTGATCTGGACTGTCCCGACTGGGTCCTGGCAGAGATCAGCACGCTGGCCAAGACGTCCTCTGT
GAAGTTGCGGCTGCTCTGCAGCCAGGTACTAAAGGGCCTGCTGGGACAGGGGACTGATTATGAGAAGATCCTGAAGCTCA
TGGCTGACACCAAGTTTGAGTCAGGCGATGTGAAGGCCACAGTGGCAGTGCTGAGCTTCATCCTCTCCAGTGCGGCCAAG
CACAGTGTTGATGGCGAATCCTTATCCAGCGAACTGCAGCAGCTGGGGCTGCCCACAGAGCACGCCGCCGGCCTGTGCCG
CTGTTACCAGGAGAAGCAAATTCCCTGGCAGAAGCACTTGTGGGTCTGCAGCCTACGCACAAACAGGTTGGCAGGTGCAG
GCTGGCGGGCAGACTACACCCTGAGCTCCAGCCTGCTGCAGTCTGTGGAAGAGCCTATGGTGCACCTGCGCCTGGAGGTG
GCAGCTGCCCCAGGTACCCCAGCCCAGCCTGTTGCCATGTCCCTCTCAGCAGACAAGTTCCAGGTCCTCCTGGCAGAGCT
GAAGCAGGCCCAGACCCTGATGAGCTCCCTGGGC

Alignment

ORF - retro_cjac_2080 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.44 %
• Parental protein coverage: 99.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RFRFCGDLDCPDWVLAEISTLAKMSSVKLRLLCSQVLKELLGQGTDYEKILKLTADTKFESGDVKATVAV
          RFRF.GDLDCPDWVLAEISTLAK.SSVKLRLLCSQVLK.LLGQGTDYEKILKL.ADTKFESGDVKATVAV
Retrocopy RFRFYGDLDCPDWVLAEISTLAKTSSVKLRLLCSQVLKGLLGQGTDYEKILKLMADTKFESGDVKATVAV

Parental  LSFILSSAAKHSVDGESLSSELQQLGLPKEHAASLCRCYEEKQIPLQKHLRVCSLRTNRLAGVGWRVDYT
          LSFILSSAAKHSVDGESLSSELQQLGLP.EHAA.LCRCY.EKQIP.QKHL.VCSLRTNRLAG.GWR.DYT
Retrocopy LSFILSSAAKHSVDGESLSSELQQLGLPTEHAAGLCRCYQEKQIPWQKHLWVCSLRTNRLAGAGWRADYT

Parental  LSSSLLQSVEEPMVHLRLEVAAAPGTPAQPVAMSLSADKFQVLLAELKQAQTLMSSLG
          LSSSLLQSVEEPMVHLRLEVAAAPGTPAQPVAMSLSADKFQVLLAELKQAQTLMSSLG
Retrocopy LSSSLLQSVEEPMVHLRLEVAAAPGTPAQPVAMSLSADKFQVLLAELKQAQTLMSSLG

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	0.16 RPM	7.10 RPM
SRP051959_heart	0.07 RPM	7.07 RPM
SRP051959_kidney	0.22 RPM	20.94 RPM
SRP051959_liver	0.02 RPM	6.06 RPM
SRP051959_lung	0.08 RPM	9.44 RPM
SRP051959_lymph_node	0.09 RPM	9.59 RPM
SRP051959_skeletal_muscle	0.07 RPM	7.45 RPM
SRP051959_spleen	0.02 RPM	10.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2080 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2080 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2080 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010909	1 retrocopy	retro_cjac_2080 ,
Dasypus novemcinctus	ENSDNOG00000013425	1 retrocopy	retro_dnov_1860,
Loxodonta africana	ENSLAFG00000006259	1 retrocopy	retro_lafr_1099,