RetrogeneDB ID: retro_cjac_1112

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:88931400..88931720(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BOLA3
• Ensembl ID: ENSCJAG00000017844
• Aliases: None
• Description: bolA homolog 3 (E. coli) [Source:HGNC Symbol;Acc:24415]

Sequence

>retro_cjac_1112
ATGGTAGCATGGAGCCCAGCAGCAGCAGTGCCTCTGTTCTGCAGGATCCGTGGGCTTCTTCTTCACTGTGTCCATCATAT
GTTTGCCTCCCAGACTGAGAGGGAGCTCAGACTGATCCAGATTCTAAAAAGTTTCCTTGAGATACAGCTGTCAAAGTCAC
TCACATTTCAGGAGGTTGTAGGGCGATGTATAAAATTAAAATTGAATCATAAGAATTTAAGAAGATAACTGTTCAGCAGC
ACCAGATGGTTAATCAGGCCCTAAAAGAAGAAATCGAAGGGATGCATGGATTGTGGATATTTACCTCTGTCCCCAAACAC

Alignment

ORF - retro_cjac_1112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAWSPAAAAPLLRGIRGLPLHCVHRMFASQTEGELRVTQILKEKFPQATAIKVTDISGGCGAMYEIKI-
          M.AWSPAAA.PL...IRGL.LHCVH.MFASQTE.ELR..QILK..F......K........G.....K..
Retrocopy MVAWSPAAAVPLFCRIRGLLLHCVHHMFASQTERELRLIQILK-SFLEIQLSKSLTFQEVVGRCIKLKL<

Parental  ESEEFKEKRTVQQHQMVNQALKEEIKGMHGLRIFTSVPKH
          ES.EFK.K.TVQQHQMVNQALKEEI.GMHGL.IFTSVPKH
Retrocopy ES*EFK-KITVQQHQMVNQALKEEIEGMHGLWIFTSVPKH

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	0.98 RPM
SRP051959_heart	0.00 RPM	2.39 RPM
SRP051959_kidney	0.00 RPM	2.44 RPM
SRP051959_liver	0.00 RPM	1.39 RPM
SRP051959_lung	0.00 RPM	0.59 RPM
SRP051959_lymph_node	0.00 RPM	0.71 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.07 RPM
SRP051959_spleen	0.00 RPM	0.59 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1112 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1112 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008739	1 retrocopy	retro_cfam_1574,
Callithrix jacchus	ENSCJAG00000017844	1 retrocopy	retro_cjac_1112 ,
Dasypus novemcinctus	ENSDNOG00000008309	2 retrocopies	retro_dnov_2474, retro_dnov_510,
Homo sapiens	ENSG00000163170	3 retrocopies	retro_hsap_1959, retro_hsap_3383, retro_hsap_4148,
Gorilla gorilla	ENSGGOG00000024505	4 retrocopies	retro_ggor_1423, retro_ggor_1424, retro_ggor_2290, retro_ggor_2786,
Myotis lucifugus	ENSMLUG00000016364	1 retrocopy	retro_mluc_1407,
Macaca mulatta	ENSMMUG00000015207	2 retrocopies	retro_mmul_1181, retro_mmul_2109,
Mustela putorius furo	ENSMPUG00000007813	1 retrocopy	retro_mputfur_1519,
Mus musculus	ENSMUSG00000045160	1 retrocopy	retro_mmus_1648,
Nomascus leucogenys	ENSNLEG00000000320	4 retrocopies	retro_nleu_1391, retro_nleu_1567, retro_nleu_2604, retro_nleu_971,
Oryctolagus cuniculus	ENSOCUG00000016658	1 retrocopy	retro_ocun_51,
Otolemur garnettii	ENSOGAG00000003502	1 retrocopy	retro_ogar_1839,
Pongo abelii	ENSPPYG00000012285	2 retrocopies	retro_pabe_1618, retro_pabe_3461,
Pan troglodytes	ENSPTRG00000012078	3 retrocopies	retro_ptro_1309, retro_ptro_2299, retro_ptro_2820,
Sorex araneus	ENSSARG00000001754	1 retrocopy	retro_sara_83,
Sus scrofa	ENSSSCG00000008291	1 retrocopy	retro_sscr_750,
Tursiops truncatus	ENSTTRG00000006698	3 retrocopies	retro_ttru_1149, retro_ttru_1493, retro_ttru_254,