RetrogeneDB ID: retro_cjac_3904

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286214.1:68168..68443(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RARRES2
• Ensembl ID: ENSCJAG00000010322
• Aliases: None
• Description: retinoic acid receptor responder (tazarotene induced) 2 [Source:HGNC Symbol;Acc:9868]

Sequence

>retro_cjac_3904
CACGCTCCCATGCAGTCACCTTTTGGGAGACCAGTGTGGATAGCGCCCGTGGACATGCCCTCCAAGTTGGAACACTTGTG
AGGCTGGAATTTAAACTCCAGAAGACAAGGGGTCATAAGAAGGACTGAAAGGAACCCGAGTGTAAAGTAAAGCTCAAAGG
GAAGAAGCGGAAATGCCTGGCCCGTGTCAAACCGGGCTCTGAACAGAAGGTTCTGAGCTGGATGGGTCAATGCCCTATAG
AGGTGCAGGCTCTGCAGGAGTCTGAGGAGCACCAG

Alignment

ORF - retro_cjac_3904 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.54 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HPPVQW-TFQKICVYSAEDTPFPAGIFVRLEFKLQQTDCRKEDWKKPHCKVKPNGRKRKCLACIKLGSEN
          H.P.Q..TF....V.SA.......G..VRLEFKLQ.T...K.D.K.P.CKVK..G.KRKCLA..K.GSE.
Retrocopy HAPMQS<TFWETSVDSARGHALQVGTLVRLEFKLQKTRGHKKD*KEPECKVKLKGKKRKCLARVKPGSEQ

Parental  EVLGRMIHCPTKTQVLREPKEYQ
          .VL..M..CP...Q.L.E..E.Q
Retrocopy KVLSWMGQCPIEVQALQESEEHQ

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	2.26 RPM
SRP051959_heart	0.00 RPM	3.46 RPM
SRP051959_kidney	0.00 RPM	2.06 RPM
SRP051959_liver	0.00 RPM	17.55 RPM
SRP051959_lung	0.00 RPM	3.89 RPM
SRP051959_lymph_node	0.00 RPM	2.44 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.81 RPM
SRP051959_spleen	0.00 RPM	2.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3904 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3904 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3904 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010322	5 retrocopies	retro_cjac_2100, retro_cjac_2706, retro_cjac_3874, retro_cjac_3904 , retro_cjac_4141,
Homo sapiens	ENSG00000106538	13 retrocopies	retro_hsap_1678, retro_hsap_1679, retro_hsap_1680, retro_hsap_1681, retro_hsap_1682, retro_hsap_1683, retro_hsap_2665, retro_hsap_3134, retro_hsap_4327, retro_hsap_4330, retro_hsap_4332, retro_hsap_4792, retro_hsap_743,
Gorilla gorilla	ENSGGOG00000011158	1 retrocopy	retro_ggor_2984,
Macaca mulatta	ENSMMUG00000005232	4 retrocopies	retro_mmul_1555, retro_mmul_1993, retro_mmul_2378, retro_mmul_2554,
Nomascus leucogenys	ENSNLEG00000001362	18 retrocopies	retro_nleu_1108, retro_nleu_1744, retro_nleu_2079, retro_nleu_2944, retro_nleu_2978, retro_nleu_2999, retro_nleu_3000, retro_nleu_3001, retro_nleu_3034, retro_nleu_3036, retro_nleu_3067, retro_nleu_3071, retro_nleu_3072, retro_nleu_3076, retro_nleu_3089, retro_nleu_3092, retro_nleu_3119, retro_nleu_3128,
Pongo abelii	ENSPPYG00000018166	28 retrocopies	retro_pabe_1382, retro_pabe_1383, retro_pabe_1384, retro_pabe_1386, retro_pabe_1387, retro_pabe_1423, retro_pabe_1424, retro_pabe_1425, retro_pabe_1426, retro_pabe_2404, retro_pabe_2591, retro_pabe_2593, retro_pabe_2595, retro_pabe_2596, retro_pabe_2597, retro_pabe_2600, retro_pabe_2604, retro_pabe_2605, retro_pabe_2606, retro_pabe_2608, retro_pabe_3540, retro_pabe_3558, retro_pabe_3559, retro_pabe_3604, retro_pabe_3727, retro_pabe_638, retro_pabe_639, retro_pabe_666,
Pan troglodytes	ENSPTRG00000019854	10 retrocopies	retro_ptro_1095, retro_ptro_1096, retro_ptro_1097, retro_ptro_1098, retro_ptro_1099, retro_ptro_1100, retro_ptro_1795, retro_ptro_2942, retro_ptro_3067, retro_ptro_3188,