RetrogeneDB ID: retro_cjac_3312

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:67885634..67886301(-)
• Located in intron of: ENSCJAG00000019176

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM213A
• Ensembl ID: ENSCJAG00000003657
• Aliases: None
• Description: family with sequence similarity 213, member A [Source:HGNC Symbol;Acc:28651]

Sequence

>retro_cjac_3312
GTTGAAAACCCAAAGTGCTTCTCTGTGGGAATGTGGTCCATTGGTACAGGAGCCTGGAAGCTACTGCCTTGGCATTGCCG
CTTCCAACACAGATGTGTTTTTGTCCAACCCCTGGAAGGAGGTGCTGGAGTACCTGGAGAATACAGACCTGAAAACACTG
GAGAAGTAACCAGCAACTTTCAAAGCAAAGGAGCTATGGGGAGAAAATGGAGTTGTGCTTGTGGCTGTGCCAGGCTGTTT
TCTCTGACAAGAAGAAACTGCAGACCTGTTCTCCCTGAAACTCAAGTTGGACGAGCTGGGGTTCCTCCTCTACGCAGGGG
TTAATGAGCAGATCAGGACTGACATAAAGGTTTTCCAGCCTCGTTTCCAAAGAGAAATCTTCCTGGATGCTAATAAAAAG
TTCTATGATCTATAAAGACAGAATATATTGTTTATGGGATTTCGCCCTCTGGGAGTGTGGTACAACTATATCCAGCCTGG
AATCAAGGCTTCTCTGGAAACCTGGAATAACAAGGCTTCATTCTTAGGGGAGTTTTTTCAGTGGGGTCAGGAAAGCAGGG
GATTCTTGAGCATGGAGAAAAAGAATATGGAGACAAAGTAAACTCACTTTCTGTTCTGGGAGCTGCTAGGAAGACCTAAA
CCAGAGACTTTAGCCTCAGAGAACAAA

Alignment

ORF - retro_cjac_3312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.22 %
• Parental protein coverage: 98.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LQDPSFFTMGMWSIGAGA-LGAAALALLL-ANTDVFLSKPQKAALEYLEDIDLKTLENALEPRTLKAKEL
          ...P..F..GMWSIG.GA.L.A.ALAL.L..NTDVFLS.P.K..LEYLE..DLKTLE....P.T.KAKEL
Retrocopy VENPKCFSVGMWSIGTGA<LEATALALPL<SNTDVFLSNPWKEVLEYLENTDLKTLEK*--PATFKAKEL

Parental  WEKNGAVIMAVRRPGCFLCREEAADLSSLKPKLDELGVPLYAVVKEHIKTEVKDFQPYFKGEVFLDEKKK
          W..NG.V..AV..PGCFL..EE.ADL.SLK.KLDELG..LYA.V.E.I.T..K.FQP.F..E.FLD..KK
Retrocopy WGENGVVLVAV--PGCFL*QEETADLFSLKLKLDELGFLLYAGVNEQIRTDIKVFQPRFQREIFLDANKK

Parental  FYGPQRRKMMFMGFIRLGVWYNF-FRAWNGGFSGNLEGEGFVLGGVFVVGSGKQGILLEHREKEFGDKVN
          FY...R....FMGF..LGVWYN....AWN.GFSGNLE..GF.L.GVF.VGSGKQGI.LEH.EKE.GDKVN
Retrocopy FYDL*RQNILFMGFRPLGVWYNY<YPAWNQGFSGNLE*QGFILRGVFSVGSGKQGI-LEHGEKEYGDKVN

Parental  LLSVLEAAKMI-KPQTLASEQK
          .LSVL.AA....KP.TLASE.K
Retrocopy SLSVLGAARKT>KPETLASENK

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	8.96 RPM
SRP051959_heart	0.11 RPM	14.15 RPM
SRP051959_kidney	0.00 RPM	65.34 RPM
SRP051959_liver	0.02 RPM	65.24 RPM
SRP051959_lung	0.00 RPM	7.76 RPM
SRP051959_lymph_node	0.09 RPM	5.14 RPM
SRP051959_skeletal_muscle	0.02 RPM	12.82 RPM
SRP051959_spleen	0.08 RPM	13.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3312 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3312 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3312 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1135
Pan troglodytes	retro_ptro_774
Gorilla gorilla	retro_ggor_886
Pongo abelii	retro_pabe_944
Macaca mulatta	retro_mmul_881

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000813	1 retrocopy	retro_chof_878,
Callithrix jacchus	ENSCJAG00000003657	1 retrocopy	retro_cjac_3312 ,
Dasypus novemcinctus	ENSDNOG00000001981	3 retrocopies	retro_dnov_1843, retro_dnov_1901, retro_dnov_868,
Homo sapiens	ENSG00000122378	2 retrocopies	retro_hsap_1135, retro_hsap_4076,
Gorilla gorilla	ENSGGOG00000013246	2 retrocopies	retro_ggor_2733, retro_ggor_886,
Microcebus murinus	ENSMICG00000007485	2 retrocopies	retro_mmur_1346, retro_mmur_1481,
Macaca mulatta	ENSMMUG00000021773	3 retrocopies	retro_mmul_2351, retro_mmul_2409, retro_mmul_881,
Mus musculus	ENSMUSG00000021792	1 retrocopy	retro_mmus_2227,
Otolemur garnettii	ENSOGAG00000013638	7 retrocopies	retro_ogar_2126, retro_ogar_2435, retro_ogar_2562, retro_ogar_3327, retro_ogar_420, retro_ogar_580, retro_ogar_784,
Procavia capensis	ENSPCAG00000009696	1 retrocopy	retro_pcap_281,
Pongo abelii	ENSPPYG00000025862	4 retrocopies	retro_pabe_3345, retro_pabe_643, retro_pabe_738, retro_pabe_944,
Pan troglodytes	ENSPTRG00000002685	2 retrocopies	retro_ptro_2763, retro_ptro_774,
Rattus norvegicus	ENSRNOG00000011140	1 retrocopy	retro_rnor_1517,