RetrogeneDB ID: retro_cjac_1948

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:116418903..116419450(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000000472
• Aliases: None
• Description: None

Sequence

>retro_cjac_1948
TCCTCCACTTTGTGATGCTTTGTGAAGGGATAGTTTCATGAGTACCAGGAGAAGCACAATCAGAGCAGCCTTCCTCACAC
AGACTGTGTGCTTGGACAACACAACAGTCAGGTTTGAGATCTGGGAAAGGGTTGGACAGGAGCGGTATCACAGCCTGGCC
CCCATATACTCTCGGGGGGCCCAGGCTGCCATCATGGTCTACGTCATCACCAACACAGATACATTTGCCCTAGCCAAGAA
CTGGGTGAAGGAGCTACCGAGGCAGGCCAGCCCCAACATGGTTTTTGCACTCATAGGTAACAAGGCAGACCTGGCCAGCA
GGAGAGCCCTGGAATTCCAGGAAGCACAAGCCTATGCAGACAACCACAGTTTGCTGTTCATGGAGACATCAGCAAAGGCT
GCAATGAATGTGAATGAAATTTTTATGGCAATAGCCAAAAAGCTTCCTAAGAACAAGCCCTAGAATGCATCTGGCACTCC
AGTCGGAAACTGAGGTGTGGACCTCCAAGAGAATCATCCGGTCAGCACCAGCCAGTGCTGCAGAAAT

Alignment

ORF - retro_cjac_1948 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.14 %
• Parental protein coverage: 84.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSLVLRFVKGQFHEYQE-STIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDI
          SS....FVKG.FHEYQE.STI.AAFLTQTVCLD.TTV.FEIW...GQERYHSLAP.Y.RGAQAAI.VY.I
Retrocopy SSTL*CFVKG*FHEYQE>STIRAAFLTQTVCLDNTTVRFEIWERVGQERYHSLAPIYSRGAQAAIMVYVI

Parental  TNTDTFARAKNWVKELQRQASPNIVIALAGNKADLASKRAVEFQXAQAYADDNSLLFMETSAKTAMNVNE
          TNTDTFA.AKNWVKEL.RQASPN.V.AL.GNKADLAS.RA.EFQ.AQAYAD..SLLFMETSAK.AMNVNE
Retrocopy TNTDTFALAKNWVKELPRQASPNMVFALIGNKADLASRRALEFQEAQAYADNHSLLFMETSAKAAMNVNE

Parental  IFMALAKKLPKNEPQNAAGAPGRNRGVDLQESNPASRSQCCSN
          IFMA.AKKLPKN.P.NA.G.P..N.GVDLQE..P.S.SQCC.N
Retrocopy IFMAIAKKLPKNKP*NASGTPVGN*GVDLQENHPVSTSQCCRN

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	22.41 RPM
SRP051959_heart	0.00 RPM	13.19 RPM
SRP051959_kidney	0.00 RPM	31.28 RPM
SRP051959_liver	0.00 RPM	26.27 RPM
SRP051959_lung	0.00 RPM	26.78 RPM
SRP051959_lymph_node	0.00 RPM	19.68 RPM
SRP051959_skeletal_muscle	0.00 RPM	16.14 RPM
SRP051959_spleen	0.00 RPM	33.51 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1948 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1948 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1948 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006003	1 retrocopy	retro_amel_543,
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948 ,
Callithrix jacchus	ENSCJAG00000003731	1 retrocopy	retro_cjac_3268,
Callithrix jacchus	ENSCJAG00000004529	2 retrocopies	retro_cjac_1178, retro_cjac_1179,
Callithrix jacchus	ENSCJAG00000007527	2 retrocopies	retro_cjac_1215, retro_cjac_1879,
Callithrix jacchus	ENSCJAG00000019039	2 retrocopies	retro_cjac_1715, retro_cjac_842,
Cavia porcellus	ENSCPOG00000011190	2 retrocopies	retro_cpor_333, retro_cpor_473,
Dipodomys ordii	ENSDORG00000006819	1 retrocopy	retro_dord_428,
Gorilla gorilla	ENSGGOG00000005472	1 retrocopy	retro_ggor_2182,
Macropus eugenii	ENSMEUG00000005614	1 retrocopy	retro_meug_2118,
Macaca mulatta	ENSMMUG00000014761	1 retrocopy	retro_mmul_2022,
Monodelphis domestica	ENSMODG00000014792	1 retrocopy	retro_mdom_1399,
Otolemur garnettii	ENSOGAG00000009456	2 retrocopies	retro_ogar_2175, retro_ogar_985,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,
Pan troglodytes	ENSPTRG00000009194	1 retrocopy	retro_ptro_2237,
Rattus norvegicus	ENSRNOG00000018568	2 retrocopies	retro_rnor_393, retro_rnor_73,
Tupaia belangeri	ENSTBEG00000007092	1 retrocopy	retro_tbel_4668,