RetrogeneDB ID: retro_cjac_3186

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:18514000..18514328(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007832
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C1orf123
• Ensembl ID: ENSCJAG00000004526
• Aliases: None
• Description: chromosome 1 open reading frame 123 [Source:HGNC Symbol;Acc:26059]

Sequence

>retro_cjac_3186
AGTGTGGCACTGGAGCGGGCCGTGGCAGTGCTTCCACGGTCCAGAAGTGCAGGTTGTGTGCAAGAGAAAATTCCATCGAG
ATTTTAAGCAGCACCATCAAGCCTTACAATGCTGAAGACGATGAGAACTTCAAGACAATAGTGGAGTTTGAGTGGGAGGC
CTTGAACCAATTGATTTCCAGCCTCAGGCTGGGTTTGCTGCTGAAGGTGTGGAGTCGGGGACAGTCTTCAGTGACATTAA
TTTGCAGGAGAAGGACTGGACTGACTATGATGAAAAGGCCCAGGAGTCTGTGGGCATCTACGAGGTCACCCACCAGTTTG
TGAAGTGC

Alignment

ORF - retro_cjac_3186 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.18 %
• Parental protein coverage: 69.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVALK-GGRGSASMVQKCKLCARENSIDILSSTIKPYNAEDNENFKTIVEFECR-GLEPVDFQPQAGFAA
          SVAL...GRGSAS.VQKC.LCARENSI.ILSSTIKPYNAED.ENFKTIVEFE...GLEP.DFQPQAGFAA
Retrocopy SVALE<AGRGSASTVQKCRLCARENSIEILSSTIKPYNAEDDENFKTIVEFEWE<GLEPIDFQPQAGFAA

Parental  EGVESGTVFSDINLQEKDWTDYDEKAQESVGIYEVTHQFVKC
          EGVESGTVFSDINLQEKDWTDYDEKAQESVGIYEVTHQFVKC
Retrocopy EGVESGTVFSDINLQEKDWTDYDEKAQESVGIYEVTHQFVKC

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	0.02 RPM	6.06 RPM
SRP051959_heart	0.02 RPM	7.72 RPM
SRP051959_kidney	0.04 RPM	11.83 RPM
SRP051959_liver	0.04 RPM	10.03 RPM
SRP051959_lung	0.05 RPM	8.02 RPM
SRP051959_lymph_node	0.07 RPM	10.43 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.03 RPM
SRP051959_spleen	0.02 RPM	8.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3186 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3186 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3186 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004526	3 retrocopies	retro_cjac_2948, retro_cjac_3149, retro_cjac_3186 ,
Cavia porcellus	ENSCPOG00000011509	1 retrocopy	retro_cpor_1142,
Homo sapiens	ENSG00000162384	1 retrocopy	retro_hsap_192,
Gorilla gorilla	ENSGGOG00000004027	1 retrocopy	retro_ggor_271,
Microcebus murinus	ENSMICG00000006397	1 retrocopy	retro_mmur_1113,
Myotis lucifugus	ENSMLUG00000002439	1 retrocopy	retro_mluc_101,
Mus musculus	ENSMUSG00000028608	1 retrocopy	retro_mmus_975,
Nomascus leucogenys	ENSNLEG00000017988	1 retrocopy	retro_nleu_1001,
Oryctolagus cuniculus	ENSOCUG00000029317	1 retrocopy	retro_ocun_770,
Otolemur garnettii	ENSOGAG00000013324	1 retrocopy	retro_ogar_861,
Ochotona princeps	ENSOPRG00000009003	2 retrocopies	retro_opri_351, retro_opri_711,
Pongo abelii	ENSPPYG00000001336	1 retrocopy	retro_pabe_443,
Pan troglodytes	ENSPTRG00000000752	1 retrocopy	retro_ptro_99,
Rattus norvegicus	ENSRNOG00000012724	3 retrocopies	retro_rnor_1999, retro_rnor_2403, retro_rnor_2705,