RetrogeneDB ID: retro_cjac_2299

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:177391590..177392303(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9orf78
• Ensembl ID: ENSCJAG00000020318
• Aliases: None
• Description: chromosome 9 open reading frame 78 [Source:HGNC Symbol;Acc:24932]

Sequence

>retro_cjac_2299
ATGGGTGCTATGGCCCTGCTTTTGGGAAAGAAGATACAAGAAGAGCCCACTCTAGTGAAAGATCCCTTTCAGATGAAAAC
AGCTGGTATGGTGGATATGAAGAAACTGAAGAAAAGGGGCAAAGATAAAATCAGTGAAGAGGAAGACTGTCACTTGGGGA
CATCATTTTCTGCAGAAACCAACTGAAGGGTTGAGGATGCAGACATGATGAAGTACACTGAGGCAGAGCTAAAGAAGACG
AAAGGGATCATGGAACATGAGGAAGAGAAAGTCAAGCCAAGGAATGCAGGACTTTATGAACTTCCAGAAAACACCCACAT
TTCCGCAGCAAAGAAGAACAAGGAGATGTTTTCCAACCAGATGCTGCATGGCATTCCTGAGTTAGACCTCGGCATCAGTG
CTAGAATAAAAAATATTTCTGTAGAGGATGCCAAGGCCCATCTGCTGGCAGAGCAGCAGAATAAGAAAAAAAAGACAGCG
AGCTATCCTTCATGCCTGCCAACATGGCTATGAATTACAACAAATTTTATCATGAGGAGCTCAACATGCCCATATAGAGA
AACACAGAAGAAACCAAAACCAGACTCTTGAGAGTAGGCCACCTAGAGAAGCCAGAGGCTGAGAGGTCTCCTCCTAAGTG
CAAACATCCTGGTAAGCAGAAGGCCACTTACGATTGTCATTATGAAAAGGTCGAGAAGATGAACAGGCTGTAC

Alignment

ORF - retro_cjac_2299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.16 %
• Parental protein coverage: 84.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSAVALLVGEKVQEETTLVDDPFQMKTGGMVDMKKLKERGKDKISDEEDLHLGTSFSAETNRRDEDADMM
          ..A.ALL.G.K.QEE.TLV.DPFQMKT.GMVDMKKLK.RGKDKIS.EED.HLGTSFSAETN.R.EDADMM
Retrocopy MGAMALLLGKKIQEEPTLVKDPFQMKTAGMVDMKKLKKRGKDKISEEEDCHLGTSFSAETN*RVEDADMM

Parental  KYIETELKKRKGIVEHEEQKVKPKNAEDCLYELPENIRVSSAKKTEEMLSNQMLSGIPEVDLGIDAKIKN
          KY.E.ELKK.KGI.EHEE.KVKP.NA...LYELPEN...S.AKK..EM.SNQML.GIPE.DLGI.A.IKN
Retrocopy KYTEAELKKTKGIMEHEEEKVKPRNAG--LYELPENTHISAAKKNKEMFSNQMLHGIPELDLGISARIKN

Parental  IISTEDAKARLLAEQQNKKKDSETSFVPTNMAVNYVQHNRFYHEELNAPIRRNKEEP-KARPLRVGDTEK
          .IS.EDAKA.LLAEQQNKKK...T...P............F.......P.R.....P.K.R.LRVG..EK
Retrocopy -ISVEDAKAHLLAEQQNKKK--KTASYPSCLPTWL*ITTNFIMRSSTCPYRETQKKP<KTRLLRVGHLEK

Parental  PEPERSPPNRKRPANEKATDDYHYEKFKKMNRRY
          PE.ERSPP..K.P...KAT.D.HYEK..KMNR.Y
Retrocopy PEAERSPPKCKHPGKQKATYDCHYEKVEKMNRLY

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	8.23 RPM
SRP051959_heart	0.00 RPM	10.61 RPM
SRP051959_kidney	0.02 RPM	16.84 RPM
SRP051959_liver	0.00 RPM	13.67 RPM
SRP051959_lung	0.00 RPM	14.17 RPM
SRP051959_lymph_node	0.00 RPM	11.78 RPM
SRP051959_skeletal_muscle	0.00 RPM	21.75 RPM
SRP051959_spleen	0.00 RPM	13.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2299 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2299 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2299 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2913
Pan troglodytes	retro_ptro_1969
Pongo abelii	retro_pabe_2426
Macaca mulatta	retro_mmul_1870

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019979	1 retrocopy	retro_cfam_116,
Choloepus hoffmanni	ENSCHOG00000013895	3 retrocopies	retro_chof_1103, retro_chof_1747, retro_chof_978,
Callithrix jacchus	ENSCJAG00000020318	3 retrocopies	retro_cjac_1757, retro_cjac_2299 , retro_cjac_2778,
Dasypus novemcinctus	ENSDNOG00000019214	1 retrocopy	retro_dnov_1540,
Homo sapiens	ENSG00000136819	3 retrocopies	retro_hsap_2872, retro_hsap_2913, retro_hsap_320,
Gorilla gorilla	ENSGGOG00000013358	1 retrocopy	retro_ggor_1990,
Macropus eugenii	ENSMEUG00000010524	3 retrocopies	retro_meug_1046, retro_meug_1241, retro_meug_508,
Macaca mulatta	ENSMMUG00000003795	2 retrocopies	retro_mmul_1460, retro_mmul_1870,
Monodelphis domestica	ENSMODG00000006832	1 retrocopy	retro_mdom_518,
Nomascus leucogenys	ENSNLEG00000017658	3 retrocopies	retro_nleu_1763, retro_nleu_614, retro_nleu_823,
Otolemur garnettii	ENSOGAG00000009770	1 retrocopy	retro_ogar_1015,
Pongo abelii	ENSPPYG00000019685	1 retrocopy	retro_pabe_2426,
Pan troglodytes	ENSPTRG00000021465	3 retrocopies	retro_ptro_1943, retro_ptro_1969, retro_ptro_258,
Sarcophilus harrisii	ENSSHAG00000012313	1 retrocopy	retro_shar_746,