RetrogeneDB ID: retro_cjac_2241

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:71686056..71686686(-)
• Located in intron of: ENSCJAG00000002804

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPST1
• Ensembl ID: ENSCJAG00000004198
• Aliases: None
• Description: None

Sequence

>retro_cjac_2241
CCTTATGTATGTAATAAATATCCTTTTGCCCTAAAATTCTTAACTTACCTTGCTAGGTTATTGCTCAATGCCAAATTTCT
CCTGATGGTCCCAGATGGCTGGGCATCAGTACATTCGATGATTTCTCGAAAAGTTACTATAGCTGGATTTGACCTGAACA
GCTACAGGGACTGCTTGACCAAGTGGAATCGTGCCATAGAGACCACGTATAACCAGTGTATGGAGGTTGGTTATAAAAAG
TGCATGTTGGTTCATGACAAATAGCTTGTCTTACATCCTGAATGGTGGATGAGATCACTCTTAAAGTTCTTCCATATTCC
CTGGAACCACTCGGTACTGCACCATGAAGAGATGATTGGGAAAGCTAGGGGAGTGTTTCTGTCAATAGTGGAGAGATCTA
CAGACCAAGTCATCAAGCCAGTCAGTGTAGGAGCTCTATCAAAATGGGTTGGGAAGATAGCACCAGATGTTTTGCAAGAC
ATGGCAGTGATTGCTCCTATGCTTGCCAAACTTGGATATGACCCATATGCCAACCTACCTAACTACGGAAAACCTGATCC
CCAAATTCTTGAAAACACTCGAAGCATCTGTAAGGGAAAATTCCAGCTACCTGACTTTCTTAAAGAAAAA

Alignment

ORF - retro_cjac_2241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 56.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PYLCNKDPFALKSLTYLARLFPNARFLLMVRDGRASVHSMISRKVTIAGFDLNSYRDCLTKWNRAIETMY
          PY.CNK.PFALK.LTYLARL..NA.FLLMV.DG.ASVHSMISRKVTIAGFDLNSYRDCLTKWNRAIET.Y
Retrocopy PYVCNKYPFALKFLTYLARLLLNAKFLLMVPDGWASVHSMISRKVTIAGFDLNSYRDCLTKWNRAIETTY

Parental  NQCMEVGYKKCMLVHYEQLVLHPERWMRTLLKFLQIPWNHSVLHHEEMIGKAGGVSLSKVERSTDQVIKP
          NQCMEVGYKKCMLVH...LVLHPE.WMR.LLKF..IPWNHSVLHHEEMIGKA.GV.LS.VERSTDQVIKP
Retrocopy NQCMEVGYKKCMLVHDK*LVLHPEWWMRSLLKFFHIPWNHSVLHHEEMIGKARGVFLSIVERSTDQVIKP

Parental  VNIGALSKWVGKIPPDVLQDMAVIAPMLAKLGYDPYANPPNYGKPDPKILENTRRVYKGEFQLPDFLKEK
          V..GALSKWVGKI.PDVLQDMAVIAPMLAKLGYDPYAN.PNYGKPDP.ILENTR...KG.FQLPDFLKEK
Retrocopy VSVGALSKWVGKIAPDVLQDMAVIAPMLAKLGYDPYANLPNYGKPDPQILENTRSICKGKFQLPDFLKEK

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	1.93 RPM	5.19 RPM
SRP051959_heart	1.09 RPM	5.31 RPM
SRP051959_kidney	1.58 RPM	18.75 RPM
SRP051959_liver	0.37 RPM	42.24 RPM
SRP051959_lung	1.46 RPM	4.57 RPM
SRP051959_lymph_node	2.08 RPM	6.76 RPM
SRP051959_skeletal_muscle	0.37 RPM	2.34 RPM
SRP051959_spleen	2.06 RPM	4.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2241 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2241 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2241 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004198	1 retrocopy	retro_cjac_2241 ,
Xiphophorus maculatus	ENSXMAG00000007886	1 retrocopy	retro_xmac_17,