RetrogeneDB ID: retro_cjac_2915

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:90470277..90471104(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GYG1
• Ensembl ID: ENSCJAG00000001467
• Aliases: None
• Description: None

Sequence

>retro_cjac_2915
ATGACAGATCAGGCCTTTGTGACATTGATCACAAATGATGCCTACGCCAAAGGTGCCCTGATCCTGGGCTCATCTCTGAA
ACAGCACAGGACCACCAGGAGGCTGGTCATGCTTGCCACCCTGCAGGTCTCAGACTCCATGAGAAAAGTTTTAGAGACAG
TCTTTGATGAAGTCATCATGGTAGATGTCTTAGACAGTGGCAATTCTACTCATCTAACCTTAATGAAGAGGCCAGAGTTG
GGTGTTATGCTGGCAAAACTCCACTGCTGGTTTCTTACACAGTATTCAAAATGTGTATTCATGGATACAGATACTCTAGT
CCTAGCAAATATTGATGATCTTTTTGAGAGAGAAGAATTGTCAGCGGCACCTGACCCAGAATGGCCTGACTGCTTCAATT
CTGGAGTCATTTATCAGCCTTCAGTAGACACATATAATCAGCTGTTGAGTCTTGCTTCTGAGCAAGGTAGTTTTGATGGT
GGGGACCAAGGCATACTGAACATGTTTTTTAGCAGCTGGGTGACAACAGATATCAGAAAATATCTGCCATTTATTTATAA
CCTAAGCTGGATCTCTGTATACTCTTACTTCCCAGCATTTTAAGTGTTTGGGACAAGTGCCAAAGTTGTGCATTTCCTGG
GACAAGTCAAACCATGGAATTATACTTATGATCCCAAAACAAAAAGTGTCAAAAGTGAGTCCCAGGATCCCAATGTGACT
CATTCAGAGTTTCTCATCATCTGTGGTAGAACATCTTTACCACCAGTATTTTACATCTGCTTCAACAATTTGGCCTTGTC
AAAGACACCTGCTCATATGTAAATGTG

Alignment

ORF - retro_cjac_2915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.05 %
• Parental protein coverage: 78.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTDQAFVTLTTNDAYAKGALVLGSSLKQHRTTRKLVVLATPQVSDSMRKVLETVFDEVIVVDVLDSGDSA
          MTDQAFVTL.TNDAYAKGAL.LGSSLKQHRTTR.LV.LAT.QVSDSMRKVLETVFDEVI.VDVLDSG.S.
Retrocopy MTDQAFVTLITNDAYAKGALILGSSLKQHRTTRRLVMLATLQVSDSMRKVLETVFDEVIMVDVLDSGNST

Parental  HLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFEREELSAAPDPGWPDCFNSGVFVYQ
          HLTLMKRPELGV.L.KLHCW.LTQYSKCVFMD.DTLVLANIDDLFEREELSAAPDP.WPDCFNSGV..YQ
Retrocopy HLTLMKRPELGVMLAKLHCWFLTQYSKCVFMDTDTLVLANIDDLFEREELSAAPDPEWPDCFNSGV-IYQ

Parental  PSVETYNQLLHLASEQGSFDGGDQGILNTFFSSWATTDIRKHLPFIYNLSSISIYSYLPAFKVFGASAKV
          PSV.TYNQLL.LASEQGSFDGGDQGILN.FFSSW.TTDIRK.LPFIYNLS.IS.YSY.PAF.VFG.SAKV
Retrocopy PSVDTYNQLLSLASEQGSFDGGDQGILNMFFSSWVTTDIRKYLPFIYNLSWISVYSYFPAF*VFGTSAKV

Parental  VHFLGRVKPWNYTYDPKTKSVKSESHDPNMTHPEFLIL-WW-NIFTTNVLPLLQQFGLVKDTCSYVNV
          VHFLG.VKPWNYTYDPKTKSVKSES.DPN.TH.EFLI...W.NIFTT..L.LLQQFGLVKDTCSYVNV
Retrocopy VHFLGQVKPWNYTYDPKTKSVKSESQDPNVTHSEFLII<LW*NIFTTSILHLLQQFGLVKDTCSYVNV

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	7.30 RPM
SRP051959_heart	0.00 RPM	28.45 RPM
SRP051959_kidney	0.02 RPM	14.31 RPM
SRP051959_liver	0.00 RPM	5.96 RPM
SRP051959_lung	0.00 RPM	12.30 RPM
SRP051959_lymph_node	0.09 RPM	9.27 RPM
SRP051959_skeletal_muscle	0.00 RPM	152.58 RPM
SRP051959_spleen	0.00 RPM	16.81 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2915 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2915 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2915 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001467	2 retrocopies	retro_cjac_1049, retro_cjac_2915 ,
Danio rerio	ENSDARG00000011934	1 retrocopy	retro_drer_23,
Homo sapiens	ENSG00000163754	2 retrocopies	retro_hsap_1222, retro_hsap_159,
Myotis lucifugus	ENSMLUG00000006382	1 retrocopy	retro_mluc_2351,
Macaca mulatta	ENSMMUG00000005521	2 retrocopies	retro_mmul_1297, retro_mmul_376,
Nomascus leucogenys	ENSNLEG00000002557	2 retrocopies	retro_nleu_1556, retro_nleu_693,
Oryctolagus cuniculus	ENSOCUG00000003516	1 retrocopy	retro_ocun_1766,
Pongo abelii	ENSPPYG00000025899	2 retrocopies	retro_pabe_1015, retro_pabe_1080,
Pan troglodytes	ENSPTRG00000015509	1 retrocopy	retro_ptro_836,