RetrogeneDB ID: retro_cjac_4223

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:128355914..128356587(-)
• 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_4223
GAATGAGTCTCCAGCACCATGTCTGGTTTGTCTGACCCACCAGCCCAGCGTGGCCCCTGTCCATTGGTGTTGCTGCTTTT
ATTCCGGCTCAGCCCCAGCTTGGTCCTTGTCATCTCCTTCGATCTGCCCGTTAACTCTTGCAAGTGCCTCCATGAGGAGA
TCCACAAGGACCTGCTAGTGACAGGTGCGTACGAGATCTCCGACCAGTCTGGGGGTGCTGGTGGCCTACGCAGCCACCAC
AAGATCACAGAATCTGCTGGCCATATTTTCTACTCCAAAGAGGATGCAACCAAGGAGAAATCTGCCTTTACCACTGAAGA
TTATGACACATTTGAAGTGTGTTTTGAGAGCAAGGGAACAGGACAGATACCTGACCAACTCATGATCCTAGACATGAAGC
ATGGAGTGGAGGCGAAAAATTAGGAAGAGATTGCAAAAGTTGAGAAGCTCAAACCATTAGAGGTAGAGCTGCGATGCCTA
GAAGACCTTTCGGAATCTATTGTTAATGATTTGCCTACATGAAGAAGAGAGAAGAAGAAATGCGTGATATATCAATGAGT
CAACGAACACTGGGGTCCTATACTTCAACATTTTCAATGTTCTGCCTTATTGACTAGCCACCTGGCAGGTCTGCTACCAG
CGATGCTTCTTCAAGTCCAAGAAGTTGATTGAG

Alignment

ORF - retro_cjac_4223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ERVSSTMSGLSGPPARRGPRPLALLLLFLLGPSLVLAISFHLPINSRKCLREEIHKDLLVTGAYEISDQS
          E.VSSTMSGLS.PPA.RGP.PL.LLLLF.L.PSLVL.ISF.LP.NS.KCL.EEIHKDLLVTGAYEISDQS
Retrocopy E*VSSTMSGLSDPPAQRGPCPLVLLLLFRLSPSLVLVISFDLPVNSCKCLHEEIHKDLLVTGAYEISDQS

Parental  GGAGGLRSHLKITDSAGHILYSKEDATKGKFAFTTEDYDMFEVCFESKGTGRIPDQLVILDMKHGVEAKN
          GGAGGLRSH.KIT.SAGHI.YSKEDATK.K.AFTTEDYD.FEVCFESKGTG.IPDQL.ILDMKHGVEAKN
Retrocopy GGAGGLRSHHKITESAGHIFYSKEDATKEKSAFTTEDYDTFEVCFESKGTGQIPDQLMILDMKHGVEAKN

Parental  YEEIAKVEKLKPLEVELRRLEDLSESIVND-FAYMKKREEEMRDTNESTNTRVLYFSIFSMFCLIG-LAT
          .EEIAKVEKLKPLEVELR.LEDLSESIVND.FAYMKKREEEMRD...S..T...Y.S.FSMFCLI..LAT
Retrocopy *EEIAKVEKLKPLEVELRCLEDLSESIVND<FAYMKKREEEMRDISMSQRTLGSYTSTFSMFCLID<LAT

Parental  WQVFYLRRFFKAKKLIE
          WQV.Y.R.FFK.KKLIE
Retrocopy WQVCYQRCFFKSKKLIE

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

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4223 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4223 has 0 orthologous retrocopies within eutheria group .

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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,