RetrogeneDB ID: retro_cjac_518

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:42254952..42255525(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMS
• Ensembl ID: ENSCJAG00000033933
• Aliases: None
• Description: spermine synthase [Source:HGNC Symbol;Acc:11123]

Sequence

>retro_cjac_518
GCTGATGATGAGACCATTCTAAAAGGCCTCTAGTCCATTTTCCAGGAGCAGGGGATGGTGGAGTCGGTGCACACCTGGCA
GGACCGTGGCTATTTAGCAACCTACACAAACAAGAATGGCAGCTTTGCCAATTTGAGAATTTACCCACATGGATTGGTGT
TGCTGGACCTTCAGAGTTACAATAGTGATGCACAAGGCAAAGAAAAGAGCAACAGTATTGGGAACAAAGTCGAAGAAAGA
CTGAAAGAATCGAGTCAGGACAGTACTGGGCAGGTGAAATGATTACCACTCCCAGTTCAAGGAAGAGCCATGGACAGATA
GTAGCCCACCGCCAGTGGGTGCCTTGTTGAATATGACATAGATGAAGTGGTGTATGACAAAGATTCACCTTACCAAAATA
TAAAAACTCTACAGTTGAAGCCGTTTGGAAATATTCTCATCCTTAGTGGGGATGTTAATTTGGCAGAGAGTGATTTGGCC
TATACCCGGGCCATCATGGGCAGTGGCAAAGAAGATTACGCTGCCCAAGATGTACTCATTCTGGGAGGCAGGTCTGGGGA
CATATTATGTGAA

Alignment

ORF - retro_cjac_518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.2 %
• Parental protein coverage: 56.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADGETILKGLQSIFQEQGMAESVHTWQDHGYLATYTNKNGSFANLRIYPHGLVLLDLQSYDGDAQGKEEI
          AD.ETILKGL.SIFQEQGM.ESVHTWQD.GYLATYTNKNGSFANLRIYPHGLVLLDLQSY..DAQGKE..
Retrocopy ADDETILKGL*SIFQEQGMVESVHTWQDRGYLATYTNKNGSFANLRIYPHGLVLLDLQSYNSDAQGKEKS

Parental  DSILNKVEERMKELSQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSK
          .SI.NKVEER.KE.SQDSTG.VK.LP..V.G.A.DR..PTA.G.LVEYDIDEVVYD.DSPYQNIK.L..K
Retrocopy NSIGNKVEERLKESSQDSTGQVK*LPLPVQGRAMDR**PTASGCLVEYDIDEVVYDKDSPYQNIKTLQLK

Parental  QFGNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCE
          .FGNILILSGDVNLAESDLAYTRAIMGSGKEDY...DVLILGG..G.ILCE
Retrocopy PFGNILILSGDVNLAESDLAYTRAIMGSGKEDYAAQDVLILGGRSGDILCE

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	0.02 RPM	11.27 RPM
SRP051959_heart	0.00 RPM	21.66 RPM
SRP051959_kidney	0.02 RPM	18.95 RPM
SRP051959_liver	0.00 RPM	11.85 RPM
SRP051959_lung	0.00 RPM	10.44 RPM
SRP051959_lymph_node	0.00 RPM	11.14 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.82 RPM
SRP051959_spleen	0.00 RPM	11.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_518 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_518 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_518 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018382	1 retrocopy	retro_btau_1412,
Canis familiaris	ENSCAFG00000013284	3 retrocopies	retro_cfam_1076, retro_cfam_1995, retro_cfam_613,
Callithrix jacchus	ENSCJAG00000033933	1 retrocopy	retro_cjac_518 ,
Cavia porcellus	ENSCPOG00000006176	2 retrocopies	retro_cpor_729, retro_cpor_889,
Echinops telfairi	ENSETEG00000010098	2 retrocopies	retro_etel_1066, retro_etel_1540,
Gorilla gorilla	ENSGGOG00000003123	3 retrocopies	retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Microcebus murinus	ENSMICG00000000192	3 retrocopies	retro_mmur_1421, retro_mmur_1484, retro_mmur_699,
Myotis lucifugus	ENSMLUG00000013185	3 retrocopies	retro_mluc_471, retro_mluc_530, retro_mluc_92,
Monodelphis domestica	ENSMODG00000007897	1 retrocopy	retro_mdom_412,
Mus musculus	ENSMUSG00000071708	6 retrocopies	retro_mmus_2162, retro_mmus_2170, retro_mmus_2837, retro_mmus_3502, retro_mmus_3628, retro_mmus_994,
Nomascus leucogenys	ENSNLEG00000009955	4 retrocopies	retro_nleu_1664, retro_nleu_2200, retro_nleu_2208, retro_nleu_2755,
Oryctolagus cuniculus	ENSOCUG00000006016	2 retrocopies	retro_ocun_1458, retro_ocun_1918,
Pteropus vampyrus	ENSPVAG00000016785	1 retrocopy	retro_pvam_524,
Rattus norvegicus	ENSRNOG00000007688	2 retrocopies	retro_rnor_1934, retro_rnor_938,
Tupaia belangeri	ENSTBEG00000012109	3 retrocopies	retro_tbel_1630, retro_tbel_1893, retro_tbel_3570,
Vicugna pacos	ENSVPAG00000007543	1 retrocopy	retro_vpac_50,