RetrogeneDB ID: retro_cjac_4220

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:123413786..123414633(-)
• Located in intron of: ENSCJAG00000009004

Retrocopy information

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

Parental gene information

• Parental gene symbol: ETS2
• Ensembl ID: ENSCJAG00000008102
• Aliases: None
• Description: None

Sequence

>retro_cjac_4220
ATGAATGATTTTAGAATCAAGAATATGGACCACATAGCCCCTGTGGCTAACAGCTACAGAGGGACCCTCAGGCACCAGCC
AGCCTCTGACACTTTTTATGGGTCTCTGTTTGCAGTTTTTCACCCTCTAAATAAAGAGCAAACACTGTAAGAAATGCCAA
CAGTCTTACATTCAATTTCTCATGACTTGCCAACTGTGTATTGCCCTTGTTAACTCTGTGTAGCAAGACTGTGATGAATT
CAAGCTTTAAAAGCTACCTTCAGTGGCTTCAAAAAGGAGAAAGAGTGCCTTGGCATTCCAAAGAAACCCTGGCTGTGGAG
TGAGCAGCAAGTATGCCAGTGGCTTCTCTGCACTACCAACAAGTTCAGTCTGGTGAACGTGAATCTCCAGAGGCTTAGCA
TGAGTGGCCAGGTGTTGTATAACCTTGGCAAGGAGTACTTCTGGAGCTTGCATTTGACTTTGTGGATGACATTTTCTGGG
AACATCTGGACCAGATGACTGAAGAAAAACACAAAAAGACAAAAGATCAATATAAAGAAAATTCATGCCTCAACTCAGTT
CCTCATTGTATTAAAAGCAATGCATTAGGTTTTGACATACAGCAGGTACCATATTGAATGCAGACACACAATTACCCCAA
AGGCAGCCTCCCGGACAGCATGTGTCCAGCTTCTGCACCCAGCGCACTCAGCTCTGAACAGGAGTTTCAGATGTCCTCGA
AGTCTCAGCTCAGTTCTGTCAGCCTCAACTATGCTCCATTAGTCAGGACTTTCTAGGCAACTTGAATTTGATCACCAACA
ATTATGGGAAGCCTAAAGACCAGAGATCCCCTGATAATGGTGCAGAC

Alignment

ORF - retro_cjac_4220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.57 %
• Parental protein coverage: 60.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MNDFGIKNMDQVAPVANSYRGTLKRQPAFDTFDGSLFAVFPSLNEEQTLQEVPTGLDSISHDS-ANCELP
          MNDF.IKNMD..APVANSYRGTL..QPA.DTF.GSLFAVF..LN.EQTL.E.PT.L.SISHD..ANC.LP
Retrocopy MNDFRIKNMDHIAPVANSYRGTLRHQPASDTFYGSLFAVFHPLNKEQTL*EMPTVLHSISHDL<ANCVLP

Parental  LLTPCSKAVMS-QALKATFSGFKKEQRRLGIPKNPWLWSEQQVCQWLLWATNEFSLVNVNLQRFGMNGQM
          LLT.CSK.VM..QALKATFSGFKKE...LGIPK.PWLWSEQQVCQWLL..TN.FSLVNVNLQR..M.GQ.
Retrocopy LLTLCSKTVMN>QALKATFSGFKKEKECLGIPKKPWLWSEQQVCQWLLCTTNKFSLVNVNLQRLSMSGQV

Parental  LCNLGKERF-LELAPDFVGDILWEHLEQMIKENQEKTEDQYEENSHLTSVPHWINSNTLGFGTEQAPYGM
          L.NLGKE.F.LELA.DFV.DI.WEHL.QM..E...KT.DQY.ENS.L.SVPH.I.SN.LGF...Q.PY.M
Retrocopy LYNLGKEYF<LELAFDFVDDIFWEHLDQMTEEKHKKTKDQYKENSCLNSVPHCIKSNALGFDIQQVPY*M

Parental  QTQNYPKGGLLDSMCPSSTPSVLSSEQEFQMFPKSRLSSVSVAY-CSVSQDFPGSNLSLLTNNSGTPKDH
          QT.NYPKG.L.DSMCP.S.PS.LSSEQEFQM..KS.LSSVS..Y.CS.SQDF.G.NL.L.TNN.G.PKD.
Retrocopy QTHNYPKGSLPDSMCPASAPSALSSEQEFQMSSKSQLSSVSLNY<CSISQDFLG-NLNLITNNYGKPKDQ

Parental  VSTENGAD
          .S..NGAD
Retrocopy RSPDNGAD

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	76.61 RPM
SRP051959_heart	0.04 RPM	19.59 RPM
SRP051959_kidney	0.00 RPM	49.03 RPM
SRP051959_liver	0.00 RPM	24.24 RPM
SRP051959_lung	0.07 RPM	51.34 RPM
SRP051959_lymph_node	0.00 RPM	15.96 RPM
SRP051959_skeletal_muscle	0.00 RPM	51.38 RPM
SRP051959_spleen	0.04 RPM	38.72 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4220 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4220 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4220 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002592	1 retrocopy	retro_cjac_1312,
Callithrix jacchus	ENSCJAG00000008102	1 retrocopy	retro_cjac_4220 ,
Callithrix jacchus	ENSCJAG00000013817	1 retrocopy	retro_cjac_2487,
Gorilla gorilla	ENSGGOG00000015464	1 retrocopy	retro_ggor_3064,