RetrogeneDB ID: retro_cjac_1049

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:79898113..79898941(-)
• Located in intron of: ENSCJAG00000008643

Retrocopy information

• Ensembl ID: ENSCJAG00000008756
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_1049
ATGACAGATCAGGCCTTTGTGACACTGACCACAAACGATGCCTACGCCAAAGGTGCCCTGGTCTTGGACTCATCTCCGAA
ACAGCGCAGGACCACCAGGAAGCTGGTCATGTTTGCCACCCCACAGGTCTCAGACTCCATGAGAAAAGTTTTAGAGACAG
TCTTTGATGAAGTCATTATGGTAGATGTCTTGGACAGTGGTGATTCTGCTCATCTAACCTTAATGAAGAGGCCAGAGTTG
CGTGTCACGCTGACAAAGCTCCACTGCTGGTCACTCACACAGTATTCAAAATGTGTATTCATGGATGCAGGTACTCTGGT
CCTAGCAAATATTGATGATCTTTTTGAGAAAGAAGAATTGTCAGTAGCACCAGACCCAGGGGGGGCCTGACTGCTTTAAT
TCCAGAGTTTTCGTTTATCAGCCTTCAGTTGAAACATATAATTGGCTGTTCGTCTTGCTTCTGAGCAAGGTAGTTTTGAT
GGTGGGGACCAAGGCATACTGAACACATTTTTTAGCAGCTGGGCAACAACAGATATCAGAAAACACCTGCCATTTATTTA
TAACCTAAGCAGCATCTCTATATATTCCTACCTCCCAGCATTTAAAGTGTTTGGTGCAAGTGCGAAAGTTGTGCATTTCC
TGGGAAGAGTCAAACCATGGAATTATACTTATGATCCCAAAACAAAAAGTGTCAAAAGTGAGTCCCATGATCCCAACATG
ACTCATCCAGAGTTTCTTATCTTGTGGTGGAACATCTTTACTACCAACATTTTACCTCTACTTCAACAATTTGGCCTTGT
CAAAGACACCTGCTCATACGTAAATGTG

Alignment

ORF - retro_cjac_1049 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.53 %
• Parental protein coverage: 78.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTDQAFVTLTTNDAYAKGALVLGSSLKQHRTTRKLVVLATPQVSDSMRKVLETVFDEVIVVDVLDSGDSA
          MTDQAFVTLTTNDAYAKGALVL.SS.KQ.RTTRKLV..ATPQVSDSMRKVLETVFDEVI.VDVLDSGDSA
Retrocopy MTDQAFVTLTTNDAYAKGALVLDSSPKQRRTTRKLVMFATPQVSDSMRKVLETVFDEVIMVDVLDSGDSA

Parental  HLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFEREELSAAPDPGW-PDCFNSGVFVY
          HLTLMKRPEL.VTLTKLHCWSLTQYSKCVFMDA.TLVLANIDDLFE.EELS.APDPG..PDCFNS.VFVY
Retrocopy HLTLMKRPELRVTLTKLHCWSLTQYSKCVFMDAGTLVLANIDDLFEKEELSVAPDPGG>PDCFNSRVFVY

Parental  QPSVETYNQL-LHLASEQGSFDGGDQGILNTFFSSWATTDIRKHLPFIYNLSSISIYSYLPAFKVFGASA
          QPSVETYN.L...LASEQGSFDGGDQGILNTFFSSWATTDIRKHLPFIYNLSSISIYSYLPAFKVFGASA
Retrocopy QPSVETYNWL<VRLASEQGSFDGGDQGILNTFFSSWATTDIRKHLPFIYNLSSISIYSYLPAFKVFGASA

Parental  KVVHFLGRVKPWNYTYDPKTKSVKSESHDPNMTHPEFLILWWNIFTTNVLPLLQQFGLVKDTCSYVNV
          KVVHFLGRVKPWNYTYDPKTKSVKSESHDPNMTHPEFLILWWNIFTTN.LPLLQQFGLVKDTCSYVNV
Retrocopy KVVHFLGRVKPWNYTYDPKTKSVKSESHDPNMTHPEFLILWWNIFTTNILPLLQQFGLVKDTCSYVNV

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	0.67 RPM	7.30 RPM
SRP051959_heart	1.40 RPM	28.45 RPM
SRP051959_kidney	0.58 RPM	14.31 RPM
SRP051959_liver	0.37 RPM	5.96 RPM
SRP051959_lung	1.72 RPM	12.30 RPM
SRP051959_lymph_node	0.78 RPM	9.27 RPM
SRP051959_skeletal_muscle	4.02 RPM	152.58 RPM
SRP051959_spleen	1.30 RPM	16.81 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1049 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1049 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1049 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,