RetrogeneDB ID: retro_cjac_1810

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:69065067..69066046(+)
• Located in intron of: ENSCJAG00000019368

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSFM
• Ensembl ID: ENSCJAG00000006600
• Aliases: None
• Description: Ts translation elongation factor, mitochondrial [Source:HGNC Symbol;Acc:12367]

Sequence

>retro_cjac_1810
ATGTGGATGCTGCGGTAACTGTGCGTGTTCCTCCTGGTCACGCGGACCAGGAGCCACCCGGCCGGGTCCCTTCTGCGTCA
GTCGCCCCAGCCACCACACACATTTCATGCTGGGCCATGTCTGTCTGCCTCGGCCTCCAGCAAGGAGCTCCTCATGAAAC
TGCGGCGGAAAACAGGCTACTCTTTTGTAAATTGCAAGAAAGCTCTGGAGACTTGTGGCGAGGACCTCAAACAGGCAGAG
ATCTGGCTCCACAAGCAGGCCCAGAAGGAAGGCTGGAGCAAAGCTCCCAAGCTCCAAGGGAGGAAGACCAAAGAAGGCCT
GATTGGACTGTTGCAGGAAGGAAACGTAACTGTATTAGTAGAGGTAAACTGTGAGACGGATTTTGTTTCTAGAAATTTAA
AATTTCAACAGTTGGTCCAGCAAGTAGCCCTTGGAACCATGATGCATTGTCAGAACTTAAAGGATCAACTGTCTACATAC
AGTAAAGGTCTCTTGAATTCCTCTGAGCTTTCTAGAATTCCAGCGGGGCCTGACAGAGAAGGCTCACTCAAGGATCACTT
GGCTTTAGCAATTGGAAAACTGGGAGAAAACATGACTCTTAAATGAGCTGCGTGGGTGACGGTGCCATCTAGGTTCTACG
TTGGCTCTTATGTCCACGGAGTAATGCAGAGACCCTCCCTTCACAACCTGGTGCTGGGGAAGTATGGGGCCCTGGTCATC
TGCGAGACATCTGAACAGAATGCAAACCTTGAAGACATTGGCCACCACCTTGGGCAGCATGTGGTGGGCATGGCCCCTCT
CTCTGTTGGCTCCCTGGATGATGAGCCTGGGGGAGAGGCAGAGACCAAGATGCTGTTCCAGCCGTACTTGCCGGATCCCT
CCATTACCTTGGGGCAGTTATGTGTAGCCTCAGGGAGTGTCAGTAGTAGACTTTGTGCGGTTTGAATGTGGAGAAGGTGA
AGAGGCAGCAGAAACTGAA

Alignment

ORF - retro_cjac_1810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MWMLRSLRVFLLVARTGSHPAGSLLRQSPQPPHTFHAGPCLSASASSKELLMKLRRKTGYSFVNCKKALE
          MWMLR.L.VFLLV.RT.SHPAGSLLRQSPQPPHTFHAGPCLSASASSKELLMKLRRKTGYSFVNCKKALE
Retrocopy MWMLR*LCVFLLVTRTRSHPAGSLLRQSPQPPHTFHAGPCLSASASSKELLMKLRRKTGYSFVNCKKALE

Parental  TCGEDLKQAEIWLHKQAQKEGWSKAAKLQGRKTKEGLIGLLQEGNITVLVEVNCETDFVSRNLKFQQLVQ
          TCGEDLKQAEIWLHKQAQKEGWSKA.KLQGRKTKEGLIGLLQEGN.TVLVEVNCETDFVSRNLKFQQLVQ
Retrocopy TCGEDLKQAEIWLHKQAQKEGWSKAPKLQGRKTKEGLIGLLQEGNVTVLVEVNCETDFVSRNLKFQQLVQ

Parental  QVALGTMMHCQNLKDQLSTYSKGFLNSSELSRLPAGPDREGSLKDHLALAIGKLGENMTLKRAAWVKVPS
          QVALGTMMHCQNLKDQLSTYSKG.LNSSELSR.PAGPDREGSLKDHLALAIGKLGENMTLK.AAWV.VPS
Retrocopy QVALGTMMHCQNLKDQLSTYSKGLLNSSELSRIPAGPDREGSLKDHLALAIGKLGENMTLK*AAWVTVPS

Parental  GFYVGSYVHGVMQSPSLHNLVLGKYGALVICETSEQNANLEDIGRRLGQHVVGMAPLSVGSLDDEPGGEA
          .FYVGSYVHGVMQ.PSLHNLVLGKYGALVICETSEQNANLEDIG..LGQHVVGMAPLSVGSLDDEPGGEA
Retrocopy RFYVGSYVHGVMQRPSLHNLVLGKYGALVICETSEQNANLEDIGHHLGQHVVGMAPLSVGSLDDEPGGEA

Parental  ETKMLSQPYLLDPSITLGQ-YVQPQGVSVVDFVRFECGEGEEAAETE
          ETKML.QPYL.DPSITLGQ.YV.PQGVSVVDFVRFECGEGEEAAETE
Retrocopy ETKMLFQPYLPDPSITLGQ>YV*PQGVSVVDFVRFECGEGEEAAETE

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	0.22 RPM	5.97 RPM
SRP051959_heart	0.07 RPM	6.61 RPM
SRP051959_kidney	0.53 RPM	9.54 RPM
SRP051959_liver	0.11 RPM	8.58 RPM
SRP051959_lung	0.00 RPM	4.80 RPM
SRP051959_lymph_node	0.05 RPM	5.37 RPM
SRP051959_skeletal_muscle	0.02 RPM	7.32 RPM
SRP051959_spleen	0.00 RPM	3.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1810 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1810 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1810 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006600	1 retrocopy	retro_cjac_1810 ,