RetrogeneDB ID: retro_cjac_2243

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:77306094..77306751(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOR1A
• Ensembl ID: ENSCJAG00000020346
• Aliases: None
• Description: None

Sequence

>retro_cjac_2243
ATATTTACGGAGAATATTTATGAGTGTGGTTTCAACGGTGACTATGTCCACCTGTTTGTGGCCACACTGCACTTTCCACA
TGCCTCAAACATCACCTAGTACAAGGACCAGTTACAGTTGTGGATTTGAGGCAATGTGAGCGCCTGTGTGAGGTCCATCT
TCGTATTTGATGAAATGGATAAGATGCATGCAGGTCTCATACATGCCATCAAGCCTTTCCTTGACTACTAAGACCTGGTG
GATGGGGTCTCCTACCAGAAAGCCATCTTCATATATCTCAGCAATGCTGGAGCAGAAATGATCACAGATGTGGCTTTAGA
TTTCTGGAGGAGTGGAAAGCAGAGGGAAGACATCAAGCTCAAAGACATTGAACACGCCTTGTCTGCCTCAGTTTTCAATA
ACAAAAACAGTGGCTTTTGGCACCGCAGCTTAATTGACCGGAACCTCATTGATTATTTTGTTCCCTTCCTCCCTCTGGAA
TACAAACACCTAAAAATGTGTATCAGAGTCAAAATGCAGTCCCGAGGCTACGACATCGATGAAGACATTGTAAGCAGAGT
GGCTGAGGAGATGACATTTTTCCCCAAAGAGGAGAGAATATTCTAGGATAAAGGCTGCAAAACTGTGTTTACCAAGTTAG
ATTATTACTACGATGAT

Alignment

ORF - retro_cjac_2243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.78 %
• Parental protein coverage: 60.16 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IIAENIYEGGLNSDYVHLFVATLHFPHASNITLYKDQLQLWIRGNVSACARSIFIFDEMDKMHAGLIDAI
          I..ENIYE.G.N.DYVHLFVATLHFPHASNIT.YKDQLQLWI.GNVSAC.RSIF.FDEMDKMHAGLI.AI
Retrocopy IFTENIYECGFNGDYVHLFVATLHFPHASNIT*YKDQLQLWI*GNVSACVRSIFVFDEMDKMHAGLIHAI

Parental  KPFLDYYDLVDGVSYQKAIFIFLSNAGAERITDVALDFWRSGKQREDIKLKDIEHALSVSVFNNKNSGFW
          KPFLDY.DLVDGVSYQKAIFI.LSNAGAE.ITDVALDFWRSGKQREDIKLKDIEHALS.SVFNNKNSGFW
Retrocopy KPFLDY*DLVDGVSYQKAIFIYLSNAGAEMITDVALDFWRSGKQREDIKLKDIEHALSASVFNNKNSGFW

Parental  HSSLIDRNLIDYFVPFLPLEYKHLKMCIRVEMQSRGYDIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVF
          H.SLIDRNLIDYFVPFLPLEYKHLKMCIRV.MQSRGYDIDEDIVSRVAEEMTFFPKEER.F.DKGCKTVF
Retrocopy HRSLIDRNLIDYFVPFLPLEYKHLKMCIRVKMQSRGYDIDEDIVSRVAEEMTFFPKEERIF*DKGCKTVF

Parental  TKLDYYYDD
          TKLDYYYDD
Retrocopy TKLDYYYDD

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	5.24 RPM
SRP051959_heart	0.00 RPM	4.84 RPM
SRP051959_kidney	0.00 RPM	6.12 RPM
SRP051959_liver	0.00 RPM	6.78 RPM
SRP051959_lung	0.00 RPM	6.88 RPM
SRP051959_lymph_node	0.00 RPM	8.52 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.78 RPM
SRP051959_spleen	0.00 RPM	7.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2243 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2243 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2243 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020343	1 retrocopy	retro_cjac_1349,
Callithrix jacchus	ENSCJAG00000020346	2 retrocopies	retro_cjac_2243 , retro_cjac_2758,