RetrogeneDB ID: retro_cjac_1409

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:68490597..68491207(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED10
• Ensembl ID: ENSCJAG00000020627
• Aliases: None
• Description: transmembrane emp24-like trafficking protein 10 (yeast) [Source:HGNC Symbol;Acc:16998]

Sequence

>retro_cjac_1409
TTGGCATGGCTGTTTTTATTTCTGCTCAGCTTCAGCTTGGTCCTCACCATCTCCTTCCACCTGCCCATTAACTCCTGAAA
GTGCCTCCGTGAGGAGATCCACAAGGACCTGCTAGTGATGGGCACGTACGAGATCTCCAACTAGTCTGGGGGCACTGGCA
GCCTGCACAGACACCTCAAGGTCACAGATTCTGCTGGCCACATTCTCTACTCCAAGGAGGATGCAACCAAAGGGAAATTC
GCCTTTACTCTGGAAGATTATGACATGTTTGCAGTGTGTTTTGAGAGCAAGGAAACAAGGTGGATACCTGACCAACTCGT
GAGCCTAGACATGAAGCATGGAGTGGAGGCAAAAAAAAAAAAAGATTACAAGGAGATTGCAAAACCCTAGAAGCTTAAGC
CATTATAGGTGGAACTTCAATCCCTGGGCCTCTCAGAATCTATTGTTAATGATTTTCCTAGATGAAGAAGAGCGAGGAGA
GATGTATGATACCAATGAATCAACAAACACTCGAGTCCTGTACTTCAGTGTCTCTTTAATGGTCTGCTTCATTGGATTAG
ATACCTGGCAGGTTTTCTACCTGCGTTGCTTCTTCAAGGCCAAGATGTTG

Alignment

ORF - retro_cjac_1409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.29 %
• Parental protein coverage: 89.78 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LALLLLFLLGPSLVLAISFHLPINSRKCLREEIHKDLLVTGAYEISDQSGGAGGLRSHLKITDSAGHILY
          LA.L.LFLL..SLVL.ISFHLPINS.KCLREEIHKDLLV.G.YEIS..SGG.G.L..HLK.TDSAGHILY
Retrocopy LAWLFLFLLSFSLVLTISFHLPINS*KCLREEIHKDLLVMGTYEISN*SGGTGSLHRHLKVTDSAGHILY

Parental  SKEDATKGKFAFTTEDYDMFEVCFESKGTGRIPDQLVILDMKHGVEAK---NYEEIAKVEKLKPLEVELR
          SKEDATKGKFAFT.EDYDMF.VCFESK.T..IPDQLV.LDMKHGVEAK....Y.EIAK..KLKPL.VEL.
Retrocopy SKEDATKGKFAFTLEDYDMFAVCFESKETRWIPDQLVSLDMKHGVEAKKKKDYKEIAKP*KLKPL*VELQ

Parental  RLEDLSESIVND-FAYMKKREE-EMRDTNESTNTRVLYFSIFSMFCLIGLATWQVFYLRRFFKAKKL
          .L..LSESIVND.F..MKK.EE.EM.DTNESTNTRVLYFS...M.C.IGL.TWQVFYLR.FFKAK.L
Retrocopy SL-GLSESIVND<FS*MKKSEE<EMYDTNESTNTRVLYFSVSLMVCFIGLDTWQVFYLRCFFKAKML

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	43.07 RPM
SRP051959_heart	0.09 RPM	35.50 RPM
SRP051959_kidney	0.02 RPM	40.98 RPM
SRP051959_liver	0.15 RPM	60.65 RPM
SRP051959_lung	0.02 RPM	35.40 RPM
SRP051959_lymph_node	0.02 RPM	33.22 RPM
SRP051959_skeletal_muscle	0.00 RPM	36.10 RPM
SRP051959_spleen	0.02 RPM	42.25 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1409 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1409 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1409 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2701
Pan troglodytes	retro_ptro_1823
Macaca mulatta	retro_mmul_885

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016899	1 retrocopy	retro_acar_187,
Callithrix jacchus	ENSCJAG00000020627	2 retrocopies	retro_cjac_1409 , retro_cjac_4223,
Dasypus novemcinctus	ENSDNOG00000019851	1 retrocopy	retro_dnov_1225,
Echinops telfairi	ENSETEG00000010607	1 retrocopy	retro_etel_1798,
Homo sapiens	ENSG00000170348	2 retrocopies	retro_hsap_2701, retro_hsap_4014,
Gorilla gorilla	ENSGGOG00000007453	1 retrocopy	retro_ggor_2696,
Myotis lucifugus	ENSMLUG00000017125	2 retrocopies	retro_mluc_2079, retro_mluc_2093,
Macaca mulatta	ENSMMUG00000015168	2 retrocopies	retro_mmul_2316, retro_mmul_885,
Mus musculus	ENSMUSG00000021248	2 retrocopies	retro_mmus_1093, retro_mmus_649,
Nomascus leucogenys	ENSNLEG00000016453	2 retrocopies	retro_nleu_2897, retro_nleu_2963,
Oryctolagus cuniculus	ENSOCUG00000004669	1 retrocopy	retro_ocun_875,
Pongo abelii	ENSPPYG00000029389	1 retrocopy	retro_pabe_3296,
Pan troglodytes	ENSPTRG00000006552	2 retrocopies	retro_ptro_1823, retro_ptro_2724,
Rattus norvegicus	ENSRNOG00000007901	2 retrocopies	retro_rnor_1729, retro_rnor_2031,
Ictidomys tridecemlineatus	ENSSTOG00000007392	1 retrocopy	retro_itri_362,
Vicugna pacos	ENSVPAG00000003089	1 retrocopy	retro_vpac_573,