RetrogeneDB ID: retro_cjac_3243

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:91245974..91246924(+)
• Located in intron of: ENSCJAG00000001995

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX5
• Ensembl ID: ENSCJAG00000004947
• Aliases: None
• Description: None

Sequence

>retro_cjac_3243
CTGCAGATTCCGCCTGGGCCTACGAAGCCCAACTTCCATGGTCCTCGAGAGAAGATGCAGAAACAGGGAGAAGGTGGAGG
GTCTGTGACCAAAGAAGAGTTTGCCAAGATGAAACCAAAACTGGAAGCTGAGTATCTCACTGTTTTTCCAAAGACTGTGT
CCTCCCATGAAGTCTTTCTTCAGCAGCTTTCTTCTCACCCTGTTCTCAGTAAAGGTCGCAACTTTCATGTTTTCCTGGAA
TACGATCAGAATCTAAGTGTTAGGAGGAAAAATGCTAAGGAGATATTTGGTGGCTTCTTCAAAAGTGTGGTGAAAAGTGC
TGATGAAGCCCTTTTTGCTGGAGTTAAGGAAGTAGATGACTTCTTTGAGCAAGAGAACAACTTCCTTATTAACTATCATA
ATAGGATCAAAGATTCTTGTGTGAAAGCTGACAAAATGACCAGATCTCATAAAAATGTTGCTGATGACTGAACGTACACT
GCAGCCTGCTTATATAACCTGGCCTTAGGAAAGCCCACAGTCATCAAAAAGTACCTTTTGAAGGTTGCTGAGGTATTTGA
AAAACTTAGGAAAGTAGAGGGTCAAGTCTCATCAGATGAAGATTTAACGCTAACAGAGCTCCTCTGATACTACATGCTCA
GCATCAAAGCTGCCAAGGCTCTCTTATACAGATGCACCAAAGCCCTCATTGACTGTGAGAACTCAAACAAAGCTCTGGGT
AAGACCCGGTTAAAGAGCAAAGATGTCAAGTTGGTTGAGGCACACCAGCAGGAGTGCTGCCAGAAATTTGAACAGCTTTC
TGAATCTGCAAAAGAAGAACTAATAAATTCAAATGAAAGAGAGTGGCAGTATTTAGAAAGAATTTAATTGAAATGTCTGA
ACTGGAAATAAAACATGCCAGGAACAGTGTCTCCCTTTTGCAGAATTGTATTGACTTGTTCAAGAATAAC

Alignment

ORF - retro_cjac_3243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.96 %
• Parental protein coverage: 78.47 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQELEAEYLAVFKKTVSSHEVFLQRLASHPVLS
          L.IPP.PTKP.F.GPREKMQK.GEG.GS.TKEEFAKMK..LEAEYL.VF.KTVSSHEVFLQ.L.SHPVLS
Retrocopy LQIPPGPTKPNFHGPREKMQKQGEGGGSVTKEEFAKMKPKLEAEYLTVFPKTVSSHEVFLQQLSSHPVLS

Parental  KDRNFHVFLEYDQDLSVRRKNTKEMFGGFFKSVVKSADEVLFTGVKEVDDFFEQEKNFLINYYNRIKDSC
          K.RNFHVFLEYDQ.LSVRRKN.KE.FGGFFKSVVKSADE.LF.GVKEVDDFFEQE.NFLINY.NRIKDSC
Retrocopy KGRNFHVFLEYDQNLSVRRKNAKEIFGGFFKSVVKSADEALFAGVKEVDDFFEQENNFLINYHNRIKDSC

Parental  VKADKMTRSHKNVADDYIHTAACLHSLALEEPTVIKNSLRQVAELFEKLRKVEGRVSSDEDLKLTELLRY
          VKADKMTRSHKNVADD...TAACL..LAL..PTVIK..L..VAE.FEKLRKVEG.VSSDEDL.LTELL.Y
Retrocopy VKADKMTRSHKNVADD*TYTAACLYNLALGKPTVIKKYLLKVAEVFEKLRKVEGQVSSDEDLTLTELL*Y

Parental  YMLNIEAAKDLLYRRTKALIDYENSNKALDKARLKSKDVKLAEAHQQECCQKFEQLSESAKEELIN-FKR
          YML.I.AAK.LLYR.TKALID.ENSNKAL.K.RLKSKDVKL.EAHQQECCQKFEQLSESAKEELIN.FK.
Retrocopy YMLSIKAAKALLYRCTKALIDCENSNKALGKTRLKSKDVKLVEAHQQECCQKFEQLSESAKEELIN<FK*

Parental  KRVAAFRKNLVEMSELEIKHAKNNVSLLQSCIDLFKNN
          KRVA.FRKNL.EMSELEIKHA.N.VSLLQ.CIDLFKNN
Retrocopy KRVAVFRKNLIEMSELEIKHARNSVSLLQNCIDLFKNN

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	32.28 RPM
SRP051959_heart	0.02 RPM	19.33 RPM
SRP051959_kidney	0.00 RPM	59.53 RPM
SRP051959_liver	0.00 RPM	45.81 RPM
SRP051959_lung	0.07 RPM	36.78 RPM
SRP051959_lymph_node	0.00 RPM	43.83 RPM
SRP051959_skeletal_muscle	0.00 RPM	14.54 RPM
SRP051959_spleen	0.02 RPM	54.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3243 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3243 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3243 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1051
Pan troglodytes	retro_ptro_717
Gorilla gorilla	retro_ggor_829
Pongo abelii	retro_pabe_877
Macaca mulatta	retro_mmul_832

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010128	2 retrocopies	retro_chof_1478, retro_chof_2166,
Callithrix jacchus	ENSCJAG00000004947	2 retrocopies	retro_cjac_2192, retro_cjac_3243 ,
Homo sapiens	ENSG00000089006	2 retrocopies	retro_hsap_1051, retro_hsap_2945,
Gorilla gorilla	ENSGGOG00000008953	1 retrocopy	retro_ggor_829,
Macropus eugenii	ENSMEUG00000009110	1 retrocopy	retro_meug_475,
Macaca mulatta	ENSMMUG00000011476	2 retrocopies	retro_mmul_1746, retro_mmul_832,
Nomascus leucogenys	ENSNLEG00000009714	1 retrocopy	retro_nleu_2071,
Oryctolagus cuniculus	ENSOCUG00000017072	1 retrocopy	retro_ocun_1323,
Otolemur garnettii	ENSOGAG00000006157	1 retrocopy	retro_ogar_1203,
Pongo abelii	ENSPPYG00000010730	2 retrocopies	retro_pabe_2442, retro_pabe_877,
Pan troglodytes	ENSPTRG00000013278	2 retrocopies	retro_ptro_2052, retro_ptro_717,
Sus scrofa	ENSSSCG00000007088	1 retrocopy	retro_sscr_593,
Ictidomys tridecemlineatus	ENSSTOG00000015416	1 retrocopy	retro_itri_1176,
Tursiops truncatus	ENSTTRG00000016432	1 retrocopy	retro_ttru_410,