RetrogeneDB ID: retro_cjac_1642

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:35253644..35253944(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP14
• Ensembl ID: ENSCJAG00000020912
• Aliases: None
• Description: signal recognition particle 14kDa (homologous Alu RNA binding protein) [Source:HGNC Symbol;Acc:11299]

Sequence

>retro_cjac_1642
ATGGTGCTACTGGAGAGCAAGCAGTTCCTAACGGAGCTGATCGGACTCTTCCAGAAGTGCCAGCCACCAGGTAGCATGTA
TATCACCTCGAAGAAGTCTGATGGTTGAACCAAACCCATTCTAAAGAAAGGTTCTGCTGTGGATTTTGAGTCTTTAGACT
GGTGTCTGTTAAGAGCTGCTGATGGGAAAAAGAAGATTAGCACTATGGTGAGCTCCAAAGAAGTAAATAAGATCTGAATG
GCTTATTCAAACCTACCACAAACTAACATGGGTGGGCTGAAGAAGAGGGACAAAAAGAAC

Alignment

ORF - retro_cjac_1642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.27 %
• Parental protein coverage: 74.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVLLESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPIPKKGTVEGFEPADNKCLLRATDGKKKISTV
          MVLLES.QFLTEL..LFQKC...GS.YIT.KK.DG.TKPI.KKG....FE..D..CLLRA.DGKKKIST.
Retrocopy MVLLESKQFLTELIGLFQKCQPPGSMYITSKKSDG*TKPILKKGSAVDFESLD-WCLLRAADGKKKISTM

Parental  VSSKEVNKFQMAYSNLLRANMDGLKKRDKKN
          VSSKEVNK..MAYSNL...NM.GLKKRDKKN
Retrocopy VSSKEVNKI*MAYSNLPQTNMGGLKKRDKKN

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	0.04 RPM	19.99 RPM
SRP051959_heart	0.07 RPM	28.36 RPM
SRP051959_kidney	0.02 RPM	31.42 RPM
SRP051959_liver	0.09 RPM	28.27 RPM
SRP051959_lung	0.07 RPM	28.55 RPM
SRP051959_lymph_node	0.02 RPM	22.83 RPM
SRP051959_skeletal_muscle	0.11 RPM	38.65 RPM
SRP051959_spleen	0.02 RPM	26.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1642 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1642 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1642 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_573

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017231	1 retrocopy	retro_amel_1566,
Canis familiaris	ENSCAFG00000029889	2 retrocopies	retro_cfam_210, retro_cfam_40,
Choloepus hoffmanni	ENSCHOG00000005321	2 retrocopies	retro_chof_212, retro_chof_2659,
Callithrix jacchus	ENSCJAG00000020912	3 retrocopies	retro_cjac_1642 , retro_cjac_171, retro_cjac_3057,
Cavia porcellus	ENSCPOG00000008994	2 retrocopies	retro_cpor_1071, retro_cpor_462,
Dasypus novemcinctus	ENSDNOG00000011147	3 retrocopies	retro_dnov_1303, retro_dnov_2164, retro_dnov_2599,
Equus caballus	ENSECAG00000000319	1 retrocopy	retro_ecab_817,
Erinaceus europaeus	ENSEEUG00000012759	1 retrocopy	retro_eeur_357,
Echinops telfairi	ENSETEG00000011870	1 retrocopy	retro_etel_1094,
Felis catus	ENSFCAG00000030207	2 retrocopies	retro_fcat_1425, retro_fcat_1684,
Homo sapiens	ENSG00000140319	3 retrocopies	retro_hsap_1765, retro_hsap_811, retro_hsap_949,
Gorilla gorilla	ENSGGOG00000009921	1 retrocopy	retro_ggor_665,
Microcebus murinus	ENSMICG00000007637	1 retrocopy	retro_mmur_487,
Myotis lucifugus	ENSMLUG00000010531	5 retrocopies	retro_mluc_1489, retro_mluc_2284, retro_mluc_2545, retro_mluc_375, retro_mluc_384,
Macaca mulatta	ENSMMUG00000016061	4 retrocopies	retro_mmul_1228, retro_mmul_1740, retro_mmul_573, retro_mmul_780,
Monodelphis domestica	ENSMODG00000029204	1 retrocopy	retro_mdom_1806,
Mustela putorius furo	ENSMPUG00000008324	1 retrocopy	retro_mputfur_376,
Nomascus leucogenys	ENSNLEG00000002457	2 retrocopies	retro_nleu_246, retro_nleu_2831,
Otolemur garnettii	ENSOGAG00000029070	2 retrocopies	retro_ogar_2839, retro_ogar_40,
Ochotona princeps	ENSOPRG00000008599	1 retrocopy	retro_opri_619,
Pongo abelii	ENSPPYG00000006342	3 retrocopies	retro_pabe_1534, retro_pabe_262, retro_pabe_811,
Pan troglodytes	ENSPTRG00000006911	3 retrocopies	retro_ptro_1181, retro_ptro_564, retro_ptro_656,
Pteropus vampyrus	ENSPVAG00000002186	2 retrocopies	retro_pvam_152, retro_pvam_323,
Rattus norvegicus	ENSRNOG00000007512	1 retrocopy	retro_rnor_2702,
Ictidomys tridecemlineatus	ENSSTOG00000015627	9 retrocopies	retro_itri_1334, retro_itri_1501, retro_itri_1633, retro_itri_382, retro_itri_432, retro_itri_707, retro_itri_710, retro_itri_799, retro_itri_824,
Tupaia belangeri	ENSTBEG00000016637	1 retrocopy	retro_tbel_196,
Tarsius syrichta	ENSTSYG00000009467	4 retrocopies	retro_tsyr_1283, retro_tsyr_1985, retro_tsyr_60, retro_tsyr_73,
Tursiops truncatus	ENSTTRG00000000036	5 retrocopies	retro_ttru_1185, retro_ttru_1288, retro_ttru_594, retro_ttru_74, retro_ttru_782,
Vicugna pacos	ENSVPAG00000010282	1 retrocopy	retro_vpac_20,