RetrogeneDB ID: retro_cjac_1177

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:4503122..4504153(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTA3
• Ensembl ID: ENSCJAG00000014614
• Aliases: None
• Description: None

Sequence

>retro_cjac_1177
ATGGTGGCCAACATGTACCAGGTCAGAGATTATGTGTACTTTGAGAATTCCTCCAGCAACCTATACCTAATGAGAAGGAT
AGAAGAACTCAACAAGACTGCAAGTGGCAACGTGGAAGCAAAAGTAGTATGCTTTTATAGACGACGCGATATTTCCAACA
CACCTATAATGCTCGCAGATAAGCATGCTAAAGAAATTGAGGAAGAATCTGAAACAACAGTTGAGGCTGACTTGACTGAT
AAGCAGAAACATCAGTTGAAACATAGAGAACTCTTTTTGTCACGCCAGTATGAATCTCTGCCTACAACACATATCAGGGG
AAAGTGCAGTGTTGCCCTTCTGAATGAGACAGAATCCGTATTGTCCTATCTTGATAAAGAGGATACCTTCTACTCATTTG
GTCTATGACCCCTCATTGAAAACACTATTAGCTGACAGGTGAAATCAGAGTGGGACCTTGAGATCAAGCAGACATTCCAG
AAATGCTGTTAGAAGGAGAATCAGATGAGAGGGAACAGTCAAAATTGGAAGTTAAAGTTTGGGATCCAAATAGCCCACTT
ACGGATGGACAGACTGACCAGTTTTTAGTTGTAGCACGTGCTGTTGGGACATTTGCTAGAGCCCTGGATTGCAGCAGTTC
TGTGAGGCAGCCTAGTTTGCATATGAGTGCTGTTGCAGCTTCCTGAGACATTACCTTGTTTCATGCTGTGGATACATTGT
ATAGACACAGCTATGATTTGAGCAGTGCCATTAGTGTCTTAGTACCACTTGGAGGACCTGTTTTTTGCAGAGATGAAATG
GAGGAATGGTCAGCCTCTGAAGCTAGCTTATTTGAAGAGGCACTGGAAAAATATGGCAAAGACTTCAATGATATATGGCA
AGATTTTCTTCCTTGGAAATCATTGACTAGCATCATTGAAGATTACTACATGTGGAAAACTACTGACAGATATGTGCAAC
AGAAACGTCTAAAAGCAGCAGAAGCTGAGAGTAAACTGAAACAAGTATATATCCCAACTTACCAAATCCCA

Alignment

ORF - retro_cjac_1177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.88 %
• Parental protein coverage: 58.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAANMYRVGDYVYFENSSSNPYLIRRIEELNKTASGNVEAKVVCFYRRRDISNTLIMLADKHAKEIEEES
          M.ANMY.V.DYVYFENSSSN.YL.RRIEELNKTASGNVEAKVVCFYRRRDISNT.IMLADKHAKEIEEES
Retrocopy MVANMYQVRDYVYFENSSSNLYLMRRIEELNKTASGNVEAKVVCFYRRRDISNTPIMLADKHAKEIEEES

Parental  EITVEADLTDKQKHQLKHRELFLSRQYESLPATHIRGKCSVALLNETESVLSYLDKEDTFFYSLVYDPSL
          E.TVEADLTDKQKHQLKHRELFLSRQYESLP.THIRGKCSVALLNETESVLSYLDKEDTF.YS....P..
Retrocopy ETTVEADLTDKQKHQLKHRELFLSRQYESLPTTHIRGKCSVALLNETESVLSYLDKEDTF-YSFGL*PLI

Parental  KTLLADK-GEIRVGPRYQADIPEMLLEGESDEREQSKLEVKVWDPNSPLTDRQIDQFLVVARAVGTFARA
          ........GEIRVGP..QADIPEMLLEGESDEREQSKLEVKVWDPNSPLTD.Q.DQFLVVARAVGTFARA
Retrocopy ENTIS*Q<GEIRVGP*DQADIPEMLLEGESDEREQSKLEVKVWDPNSPLTDGQTDQFLVVARAVGTFARA

Parental  LDCSSSVRQPSLHMSAAAASRDITLFHAMDTLYRHSYDLSSAISVLVPLGGPVLCRDEMEEWSASEASLF
          LDCSSSVRQPSLHMSA.AAS.DITLFHA.DTLYRHSYDLSSAISVLVPLGGPV.CRDEMEEWSASEASLF
Retrocopy LDCSSSVRQPSLHMSAVAAS*DITLFHAVDTLYRHSYDLSSAISVLVPLGGPVFCRDEMEEWSASEASLF

Parental  EEALEKYGKDFNDIRQDFLPWKSLTSIIEYYYMWKTTDRYVQQKRLKAAEAESKLKQVYIPTYSKP
          EEALEKYGKDFNDI.QDFLPWKSLTSIIE.YYMWKTTDRYVQQKRLKAAEAESKLKQVYIPTY..P
Retrocopy EEALEKYGKDFNDIWQDFLPWKSLTSIIEDYYMWKTTDRYVQQKRLKAAEAESKLKQVYIPTYQIP

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	8.10 RPM
SRP051959_heart	0.00 RPM	5.98 RPM
SRP051959_kidney	0.00 RPM	7.28 RPM
SRP051959_liver	0.02 RPM	4.46 RPM
SRP051959_lung	0.00 RPM	6.15 RPM
SRP051959_lymph_node	0.00 RPM	4.59 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.73 RPM
SRP051959_spleen	0.00 RPM	4.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1177 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1177 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014614	1 retrocopy	retro_cjac_1177 ,
Homo sapiens	ENSG00000057935	1 retrocopy	retro_hsap_2337,
Gorilla gorilla	ENSGGOG00000006895	1 retrocopy	retro_ggor_1773,
Nomascus leucogenys	ENSNLEG00000016680	1 retrocopy	retro_nleu_1688,
Pan troglodytes	ENSPTRG00000011867	1 retrocopy	retro_ptro_1708,