RetrogeneDB ID: retro_cjac_846

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:36291695..36292007(+)
• Located in intron of: ENSCJAG00000000566

Retrocopy information

• Ensembl ID: ENSCJAG00000023196
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000014940
• Aliases: None
• Description: None

Sequence

>retro_cjac_846
ATGTCTCTCACTATTTTGCTGGTACAGCCTGCCAAGAGGCCAGAAGGCAGAACTTATGCAGACTATGAATCTGTGAATGA
ATGCATGGAAGGCATTTGTAAAATGTATGAAGAACATCTGAAAAGAAAGAATCCCAACAGTCCTTCTATCACATATGACA
TCAGTCAACTGTTTGATTTCATTGATGATCTGGCAGACCGCAGCTGCCTGGTTTACCGGGCTGATACCCAGACATACCAG
CCTTATAACAAAGACTGGATTAAAGAGAAGATCTACATGCTCCTTCATCGGCAGGCCCAATAGGGTGGGAAA

Alignment

ORF - retro_cjac_846 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNPNSPSITYDISQLFDFIDDLADLSCL
          MS.TILLVQP.KRPEGRTYADYESVNECMEG.CKMYEEHLKR.NPNSPSITYDISQLFDFIDDLAD.SCL
Retrocopy MSLTILLVQPAKRPEGRTYADYESVNECMEGICKMYEEHLKRKNPNSPSITYDISQLFDFIDDLADRSCL

Parental  VYRADTQTYQPYNKDWIKEKIYVLLRRQAQQAGK
          VYRADTQTYQPYNKDWIKEKIY.LL.RQAQ..GK
Retrocopy VYRADTQTYQPYNKDWIKEKIYMLLHRQAQ*GGK

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	0.60 RPM	17.35 RPM
SRP051959_heart	0.35 RPM	14.82 RPM
SRP051959_kidney	0.58 RPM	18.55 RPM
SRP051959_liver	0.26 RPM	20.38 RPM
SRP051959_lung	0.34 RPM	17.00 RPM
SRP051959_lymph_node	0.05 RPM	17.44 RPM
SRP051959_skeletal_muscle	0.13 RPM	12.73 RPM
SRP051959_spleen	0.34 RPM	18.78 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_846 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_846 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_846 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014529	1 retrocopy	retro_amel_1906,
Bos taurus	ENSBTAG00000017798	4 retrocopies	retro_btau_1260, retro_btau_438, retro_btau_651, retro_btau_795,
Callithrix jacchus	ENSCJAG00000014940	2 retrocopies	retro_cjac_209, retro_cjac_846 ,
Dipodomys ordii	ENSDORG00000006912	3 retrocopies	retro_dord_250, retro_dord_406, retro_dord_562,
Equus caballus	ENSECAG00000019178	1 retrocopy	retro_ecab_45,
Erinaceus europaeus	ENSEEUG00000007758	6 retrocopies	retro_eeur_105, retro_eeur_108, retro_eeur_115, retro_eeur_116, retro_eeur_185, retro_eeur_546,
Echinops telfairi	ENSETEG00000016172	5 retrocopies	retro_etel_1122, retro_etel_1451, retro_etel_715, retro_etel_716, retro_etel_975,
Homo sapiens	ENSG00000100632	2 retrocopies	retro_hsap_3594, retro_hsap_3799,
Gorilla gorilla	ENSGGOG00000004751	2 retrocopies	retro_ggor_2424, retro_ggor_2553,
Macropus eugenii	ENSMEUG00000014602	3 retrocopies	retro_meug_1469, retro_meug_498, retro_meug_64,
Microcebus murinus	ENSMICG00000009623	1 retrocopy	retro_mmur_74,
Myotis lucifugus	ENSMLUG00000011879	1 retrocopy	retro_mluc_142,
Macaca mulatta	ENSMMUG00000021571	1 retrocopy	retro_mmul_1649,
Mus musculus	ENSMUSG00000021131	4 retrocopies	retro_mmus_1576, retro_mmus_2599, retro_mmus_3184, retro_mmus_39,
Nomascus leucogenys	ENSNLEG00000001514	2 retrocopies	retro_nleu_1128, retro_nleu_1604,
Oryctolagus cuniculus	ENSOCUG00000004636	1 retrocopy	retro_ocun_42,
Otolemur garnettii	ENSOGAG00000029388	5 retrocopies	retro_ogar_1170, retro_ogar_1537, retro_ogar_2710, retro_ogar_625, retro_ogar_854,
Ochotona princeps	ENSOPRG00000000086	2 retrocopies	retro_opri_1140, retro_opri_519,
Pongo abelii	ENSPPYG00000005939	2 retrocopies	retro_pabe_2954, retro_pabe_3104,
Pan troglodytes	ENSPTRG00000006482	2 retrocopies	retro_ptro_2433, retro_ptro_2577,
Rattus norvegicus	ENSRNOG00000004883	3 retrocopies	retro_rnor_1721, retro_rnor_2670, retro_rnor_308,
Sorex araneus	ENSSARG00000005558	11 retrocopies	retro_sara_114, retro_sara_127, retro_sara_151, retro_sara_221, retro_sara_251, retro_sara_295, retro_sara_298, retro_sara_490, retro_sara_56, retro_sara_58, retro_sara_66,
Sus scrofa	ENSSSCG00000002307	1 retrocopy	retro_sscr_748,
Tursiops truncatus	ENSTTRG00000013963	2 retrocopies	retro_ttru_1671, retro_ttru_614,
Vicugna pacos	ENSVPAG00000006444	1 retrocopy	retro_vpac_423,