RetrogeneDB ID: retro_cjac_2758

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:118911906..118912899(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022886
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_2758
AAGCTGAGCCGGGCTGCGCTGGGCCTGCTGCTGCTGGCGCCGTCCGTGGTGCAGGCGGTAGAGCCCATCAGCCTGGGACT
GGCCCTGGCCGGCGTCCTCACCGGCTACATCTACCCGCGTCTCTACTGCCTCTTCGCCGAGTGCTGCGGCCAGAAGCGGA
GCCTCAGCCGGGAGGCGCTGCAGAAGGATCTGGACAACAAGCTCTTTGGACAGCATCTTGCAAAGAAAATCATCTTAAAT
GCTGTGTTTGGTTTCATAAACAACCCAAAGCCCAAGAAACCTCTCACCCTCTCCCTGCGTGGGTGGACGGGCACCGGCAA
AAATTTCGTCAGCAAGATCATCGCGGAGAATATTTACGAGGGTGGTCTCAACAGTGACTATGTCCACCTGTTTGTGGCCA
CACTGCACTTTCCACATGCCTCAAACATCACCTTGTACAAGGACCAGTTACAGTTGTGGATTCGAGGCAACGTGAGCGCC
TGTGCGAGGTCCATCTTCATATTCGATGAAATGGATAAGATGCATGCAGGTCTCATAGATGCCATCAAGCCTTTCCTTGA
CTACTACGACCTGGTGGATGGGGTCTCCTACCAGAAAGCCATCTTCATATTTCTCAGCAATGCTGGAGCAGAAAGGATCA
CAGATGTGGCTTTAGATTTCTGGAGGAGTGGAAAGCAGAGGGAAGACATCAAGCTCAAAGACATTGAACACGCCTTATCT
GTGTCGGTTTTCAATAACAAAAACAGTGGCTTCTGGCACAGCAGCTTAATTGACCGGAACCTCATTGATTATTTTGTTCC
CTTCCTCCCCCTGGAATACAAACACCTAAAAATGTGTATCAGAGTCGAAATGCAGTCCCGAGGCTATGACATTGATGAAG
ACATTGTAAGCAGAGTGGCTGAGGAGATGACATTTTTCCCCAAAGAGGAGAGAGTTTTCTCAGATAAAGGCTGCAAAACC
GTGTTTACCAAGTTAGATTATTACTACGATGAT

Alignment

ORF - retro_cjac_2758 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.7 %
• Parental protein coverage: 90.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLSRAALGLLLLAPSVVQAVEPISLGLALAGVLTGYIYPRLYCLFAECCGQKRSLSREALQKDLDNKLFG
          KLSRAALGLLLLAPSVVQAVEPISLGLALAGVLTGYIYPRLYCLFAECCGQKRSLSREALQKDLDNKLFG
Retrocopy KLSRAALGLLLLAPSVVQAVEPISLGLALAGVLTGYIYPRLYCLFAECCGQKRSLSREALQKDLDNKLFG

Parental  QHLAKKIILNAVFGFINNPKPKKPLTLSLHGWTGTGKNFVSKIIAENIYEGGLNSDYVHLFVATLHFPHA
          QHLAKKIILNAVFGFINNPKPKKPLTLSL.GWTGTGKNFVSKIIAENIYEGGLNSDYVHLFVATLHFPHA
Retrocopy QHLAKKIILNAVFGFINNPKPKKPLTLSLRGWTGTGKNFVSKIIAENIYEGGLNSDYVHLFVATLHFPHA

Parental  SNITLYKDQLQLWIRGNVSACARSIFIFDEMDKMHAGLIDAIKPFLDYYDLVDGVSYQKAIFIFLSNAGA
          SNITLYKDQLQLWIRGNVSACARSIFIFDEMDKMHAGLIDAIKPFLDYYDLVDGVSYQKAIFIFLSNAGA
Retrocopy SNITLYKDQLQLWIRGNVSACARSIFIFDEMDKMHAGLIDAIKPFLDYYDLVDGVSYQKAIFIFLSNAGA

Parental  ERITDVALDFWRSGKQREDIKLKDIEHALSVSVFNNKNSGFWHSSLIDRNLIDYFVPFLPLEYKHLKMCI
          ERITDVALDFWRSGKQREDIKLKDIEHALSVSVFNNKNSGFWHSSLIDRNLIDYFVPFLPLEYKHLKMCI
Retrocopy ERITDVALDFWRSGKQREDIKLKDIEHALSVSVFNNKNSGFWHSSLIDRNLIDYFVPFLPLEYKHLKMCI

Parental  RVEMQSRGYDIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYYYDD
          RVEMQSRGYDIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYYYDD
Retrocopy RVEMQSRGYDIDEDIVSRVAEEMTFFPKEERVFSDKGCKTVFTKLDYYYDD

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	0.93 RPM	5.24 RPM
SRP051959_heart	0.56 RPM	4.84 RPM
SRP051959_kidney	0.82 RPM	6.12 RPM
SRP051959_liver	0.65 RPM	6.78 RPM
SRP051959_lung	0.65 RPM	6.88 RPM
SRP051959_lymph_node	0.71 RPM	8.52 RPM
SRP051959_skeletal_muscle	0.66 RPM	4.78 RPM
SRP051959_spleen	0.82 RPM	7.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2758 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2758 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2758 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 ,