RetrogeneDB ID: retro_cjac_3466

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01180829.1:10419..10590(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000020103
• Aliases: None
• Description: None

Sequence

>retro_cjac_3466
TTTCTTTCACAGATAAGTGTTCATAATAACAAATACAGATTAGACTGGGCATGGTAGCTGACCCCTATAATACCAGCACT
TTGAGAGGCTGAGGTGAGTGGATCACGTGAGGTCAGGAGTTCCAGACCAGCCTGGCCAACATGGTGAACCCCTGTCGCTA
CTAAAAAAACA

Alignment

ORF - retro_cjac_3466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.63 %
• Parental protein coverage: 60.64 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FRDQSGQHSETPQASQAWWLMPVIPALWEDEAGGSPEVRSSRPAWPTWQNPISVKNT
          F..Q...H........AW.L.P.IPAL.E.E..GS.EVRSSRPAWPTW..P...K.T
Retrocopy FLSQISVHNNKYRLDWAW*LTPIIPAL*EAEVSGSREVRSSRPAWPTW*TPVATKKT

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	0.04 RPM	0.00 RPM
SRP051959_heart	0.26 RPM	0.00 RPM
SRP051959_kidney	0.04 RPM	0.00 RPM
SRP051959_liver	0.04 RPM	0.02 RPM
SRP051959_lung	0.16 RPM	0.00 RPM
SRP051959_lymph_node	0.27 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.11 RPM	0.00 RPM
SRP051959_spleen	0.11 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3466 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3466 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3466 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020103	14 retrocopies	retro_cjac_3387, retro_cjac_3463, retro_cjac_3466 , retro_cjac_3471, retro_cjac_3522, retro_cjac_3527, retro_cjac_3574, retro_cjac_3575, retro_cjac_3586, retro_cjac_3699, retro_cjac_3705, retro_cjac_3737, retro_cjac_3750, retro_cjac_3753,
Callithrix jacchus	ENSCJAG00000034129	3 retrocopies	retro_cjac_3646, retro_cjac_3740, retro_cjac_3780,
Gorilla gorilla	ENSGGOG00000027169	1 retrocopy	retro_ggor_2832,
Pongo abelii	ENSPPYG00000006176	2 retrocopies	retro_pabe_1259, retro_pabe_739,