RetrogeneDB ID: retro_cjac_2282

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:138360078..138360454(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL5
• Ensembl ID: ENSCJAG00000006777
• Aliases: None
• Description: methyltransferase like 5 [Source:HGNC Symbol;Acc:25006]

Sequence

>retro_cjac_2282
CAGCTGCAATAAGTGGATGGATTCAAATAGCCAGCCTACTTCTAGAATAGTACCCAACCAGGATGCATATTTAAGCTTGT
GTGCTCTATACAATCCTCTACACATGGGATGACATTGAAATTAAAGTGGTTACAGATCTAGAACCTGGTAATGGAGCACT
TAGCATCCCAGCTGCAATGGGAGGAGCAGGATTGTGGTTGTATTGAACATAGATGAAGATGCATTGAAAATATTTAATAG
GAACGTGGAAGAGTTTGAGTCAGGAAATGTTGTTATGTTTTACTGTGATATGTGCTCATAATTTAGTAGAATGTCCAAGT
CATTAGATACAGTCATCATGAATCCTCACTTTGGGACCACATATAATAAAGGAAGT

Alignment

ORF - retro_cjac_2282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.06 %
• Parental protein coverage: 51.64 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLQQVDEFEKP-KLLLEQYPTRPHIAACMLYTIHNTYDDIENKVIADLGCGCGVLSIGSAMLGAGL-CVG
          .LQ.VD.F..P..LLLE.YPTR.HI.AC.LYTI..T.DDIE.KV..DL..G.G.LSI..AM.GAGL..V.
Retrocopy QLQ*VDGFK*P<SLLLE*YPTRMHI*ACVLYTILYTWDDIEIKVVTDLEPGNGALSIPAAMGGAGL<VVV

Parental  FDIDEDALEIFNRNVEEFELTNIDMIQCDVCLLSNRMSKSFDTVIMNPPFGTKNNKGT
          ..IDEDAL.IFNRNVEEFE..N..M..CD.C....RMSKS.DTVIMNP.FGT..NKG.
Retrocopy LNIDEDALKIFNRNVEEFESGNVVMFYCDMCS*FSRMSKSLDTVIMNPHFGTTYNKGS

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	2.46 RPM
SRP051959_heart	0.00 RPM	3.42 RPM
SRP051959_kidney	0.00 RPM	4.50 RPM
SRP051959_liver	0.00 RPM	3.90 RPM
SRP051959_lung	0.02 RPM	2.80 RPM
SRP051959_lymph_node	0.00 RPM	3.58 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.13 RPM
SRP051959_spleen	0.00 RPM	2.94 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2282 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2282 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2282 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2930
Pan troglodytes	retro_ptro_2062
Gorilla gorilla	retro_ggor_2032
Pongo abelii	retro_pabe_2523
Macaca mulatta	retro_mmul_1953

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012438	1 retrocopy	retro_cfam_1726,
Callithrix jacchus	ENSCJAG00000006777	2 retrocopies	retro_cjac_2282 , retro_cjac_729,
Dasypus novemcinctus	ENSDNOG00000013460	2 retrocopies	retro_dnov_1043, retro_dnov_773,
Gorilla gorilla	ENSGGOG00000022484	2 retrocopies	retro_ggor_1064, retro_ggor_2032,
Loxodonta africana	ENSLAFG00000018044	2 retrocopies	retro_lafr_1213, retro_lafr_864,
Tursiops truncatus	ENSTTRG00000002154	2 retrocopies	retro_ttru_251, retro_ttru_38,