RetrogeneDB ID: retro_cjac_3176

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:5041253..5041488(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM6
• Ensembl ID: ENSCJAG00000002482
• Aliases: None
• Description: LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17017]

Sequence

>retro_cjac_3176
AGTCTTCAGAAGCAAACCCCTAGTGACTTCTTAAAGCAAATCATCGGACGACCAGTTGTGGTAAAATCAAATTCTGGAGT
GGATTATCGAGGGGTCCTGGCTTGCCTGGATGCTACATGAATATAGCCTGGAGCAGACAGAGGAACATGTAAATGGACAA
CTGAAGAATAAGTATGGGGACGCATTTATCCAAGGAAACAATGTGTTGTACATCAGTACACAGAAGAGAAGGATG

Alignment

ORF - retro_cjac_3176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.36 %
• Parental protein coverage: 98.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDG-YMNIA-LEQTEEYVNGQLKNKYGDAFIRGNN
          SL.KQTPSDFLKQIIGRPVVVK.NSGVDYRGVLACLD..YMNIA.LEQTEE.VNGQLKNKYGDAFI.GNN
Retrocopy SLQKQTPSDFLKQIIGRPVVVKSNSGVDYRGVLACLDA<YMNIA<LEQTEEHVNGQLKNKYGDAFIQGNN

Parental  VLYISTQKRRM
          VLYISTQKRRM
Retrocopy VLYISTQKRRM

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	0.00 RPM	6.57 RPM
SRP051959_heart	0.00 RPM	5.79 RPM
SRP051959_kidney	0.00 RPM	5.77 RPM
SRP051959_liver	0.00 RPM	6.41 RPM
SRP051959_lung	0.03 RPM	8.82 RPM
SRP051959_lymph_node	0.00 RPM	8.81 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.24 RPM
SRP051959_spleen	0.00 RPM	10.36 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3176 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3176 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002482	4 retrocopies	retro_cjac_1173, retro_cjac_1278, retro_cjac_3176 , retro_cjac_3248,
Callithrix jacchus	ENSCJAG00000002705	2 retrocopies	retro_cjac_1705, retro_cjac_3039,
Dasypus novemcinctus	ENSDNOG00000009322	5 retrocopies	retro_dnov_1118, retro_dnov_176, retro_dnov_2092, retro_dnov_301, retro_dnov_664,
Microcebus murinus	ENSMICG00000000571	1 retrocopy	retro_mmur_1563,
Macaca mulatta	ENSMMUG00000005524	2 retrocopies	retro_mmul_668, retro_mmul_991,
Mus musculus	ENSMUSG00000031683	2 retrocopies	retro_mmus_820, retro_mmus_956,
Otolemur garnettii	ENSOGAG00000026665	1 retrocopy	retro_ogar_233,
Pongo abelii	ENSPPYG00000015105	1 retrocopy	retro_pabe_1994,
Pan troglodytes	ENSPTRG00000016488	1 retrocopy	retro_ptro_1545,
Tarsius syrichta	ENSTSYG00000012759	4 retrocopies	retro_tsyr_1332, retro_tsyr_1727, retro_tsyr_340, retro_tsyr_653,