RetrogeneDB ID: retro_cjac_1478

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:69561434..69561671(+)
• Located in intron of: ENSCJAG00000012645

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000033635
• Aliases: None
• Description: None

Sequence

>retro_cjac_1478
ATGTCACACAAATAAATTTACTATTTGGACAAATATGATGGCGAGGAGTTTGAGTATGGGCATGTCATGTTGCCCAAGGA
CATAGCCAAGCTGGTCCCTAAAACCCATTTGATGTCTGAATCTGAATGCAGGAATCTTGGCGTTCAGCAGAGTCAGGGTT
GGGTCCATTACATGATCCGTAAACCAGAACCTCACATCTTACTGTTCTGGCACCCACTACCCAAGAAGTCGAAGAAA

Alignment

ORF - retro_cjac_1478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEPHILLFR
          MSHK.IYY.DKYD.EEFEY.HVMLPKDIAKLVPKTHLMSESE.RNLGVQQSQGWVHYMI..PEPHILLF.
Retrocopy MSHK*IYYLDKYDGEEFEYGHVMLPKDIAKLVPKTHLMSESECRNLGVQQSQGWVHYMIRKPEPHILLFW

Parental  RPLPKKPKK
          .PLPKK.KK
Retrocopy HPLPKKSKK

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	0.38 RPM	5.79 RPM
SRP051959_heart	0.42 RPM	2.19 RPM
SRP051959_kidney	0.47 RPM	1.73 RPM
SRP051959_liver	0.26 RPM	3.44 RPM
SRP051959_lung	0.50 RPM	1.64 RPM
SRP051959_lymph_node	0.78 RPM	2.42 RPM
SRP051959_skeletal_muscle	0.37 RPM	0.50 RPM
SRP051959_spleen	0.59 RPM	4.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1478 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1478 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1478 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007792	1 retrocopy	retro_cjac_261,
Callithrix jacchus	ENSCJAG00000033635	10 retrocopies	retro_cjac_13, retro_cjac_1441, retro_cjac_1478 , retro_cjac_1779, retro_cjac_2040, retro_cjac_2212, retro_cjac_2649, retro_cjac_276, retro_cjac_57, retro_cjac_876,
Cavia porcellus	ENSCPOG00000024061	2 retrocopies	retro_cpor_859, retro_cpor_941,
Dipodomys ordii	ENSDORG00000003764	6 retrocopies	retro_dord_25, retro_dord_290, retro_dord_599, retro_dord_64, retro_dord_647, retro_dord_739,
Equus caballus	ENSECAG00000003460	1 retrocopy	retro_ecab_975,
Erinaceus europaeus	ENSEEUG00000015895	1 retrocopy	retro_eeur_302,
Echinops telfairi	ENSETEG00000003337	4 retrocopies	retro_etel_1246, retro_etel_1938, retro_etel_239, retro_etel_497,
Felis catus	ENSFCAG00000001347	1 retrocopy	retro_fcat_1041,
Homo sapiens	ENSG00000173207	1 retrocopy	retro_hsap_27,
Gorilla gorilla	ENSGGOG00000013419	4 retrocopies	retro_ggor_10, retro_ggor_1070, retro_ggor_2739, retro_ggor_659,
Loxodonta africana	ENSLAFG00000032213	1 retrocopy	retro_lafr_243,
Myotis lucifugus	ENSMLUG00000002408	1 retrocopy	retro_mluc_1303,
Mus musculus	ENSMUSG00000028044	1 retrocopy	retro_mmus_280,
Nomascus leucogenys	ENSNLEG00000011532	3 retrocopies	retro_nleu_1098, retro_nleu_2592, retro_nleu_411,
Oryctolagus cuniculus	ENSOCUG00000016204	2 retrocopies	retro_ocun_1389, retro_ocun_18,
Otolemur garnettii	ENSOGAG00000006384	10 retrocopies	retro_ogar_1673, retro_ogar_1703, retro_ogar_1713, retro_ogar_1983, retro_ogar_2317, retro_ogar_245, retro_ogar_3310, retro_ogar_450, retro_ogar_530, retro_ogar_877,
Rattus norvegicus	ENSRNOG00000042561	1 retrocopy	retro_rnor_97,
Sorex araneus	ENSSARG00000012383	2 retrocopies	retro_sara_667, retro_sara_77,
Sarcophilus harrisii	ENSSHAG00000004796	1 retrocopy	retro_shar_786,
Sus scrofa	ENSSSCG00000029737	1 retrocopy	retro_sscr_730,
Vicugna pacos	ENSVPAG00000012182	1 retrocopy	retro_vpac_532,