RetrogeneDB ID: retro_cjac_1754

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:40739058..40739866(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGCS1
• Ensembl ID: ENSCJAG00000001303
• Aliases: None
• Description: None

Sequence

>retro_cjac_1754
AGTCAGTCGGTGAAGACTAATTTGATGCAGCTGTTGAGGAGTCTGGGAATATAGATAGAGAAGGAACTGACACACTCAGG
CATGGTGTGGAGTCCCAGCTGCTGTCTTCAGTGCTGTGAACTGGACTGAGTCCAGCTCTTGGGATGGACGGAATGTGCTG
GGAGTTTCAAGAGATATTGCTGGATATGCCACAGGAAGTGCTCGACCTACAGGTGGACCTGGAGCGGTAGCTCTGCTGAT
TGGGCCACAGGCAACTTTAATTTTTGAACGAGGGCTTCGTGGGACACATATGCAACGTGCCTGTGACTTTTACGAGCCTG
ATACGCTCTCTGAATGTCCTATAGTAGATGGAAAACTCTCCACACAGCACTGCTTCAGTGCATGAGACCACTGCTATTCT
ATCAACCACAAAAACATCAGTGCCCAGTTGCAGAAAGAGGGAAATGATAAAAGGTTTTACCTTGAATAATTTTGGCATCA
CTCACCATCTTGTAAACTGCTGAGTTTATCTCCAGCTCAGATGTTGCAGAATGACTTTCCTAATGATCAGAATAGAGATA
AAAACAGTATTTAGAGTGGTCTGGAAGCCTTTGGGGATGTTAAATTAGAAGACATCGATTTTGATACAGATGTGGAGATG
GCGTTTATGGAGGCTAGTTCTGAACCCTTCTATCAGAAAACAAAGACATCTTTGCTGTATCCATTCAAAATGGAAATACA
TACACATTGCCAGTATGTGGCTCCCTGAAACTGTCACATAGCACAGGACTCACCTCAGCAATAATCAGGGAAGAGACCTG
GAGTGTTC

Alignment

ORF - retro_cjac_1754 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.04 %
• Parental protein coverage: 52.5 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SKSVKTNLMQLF-EESGNTDIEGIDT-TNACYGGTAAVFNAVNWIESSSWDGRYALVVAGDIAVYATGNA
          S.SVKTNLMQL..EESGN.D.EG.DT.T.A..G..AAVF.AVNW.ESSSWDGR..L.V..DIA.YATG.A
Retrocopy SQSVKTNLMQLL<EESGNIDREGTDT<TQAWCGVPAAVFSAVNWTESSSWDGRNVLGVSRDIAGYATGSA

Parental  RPTGGVGAVALLIGPNAPLIFERGLRGTHMQHAYDFYKPDMLSEYPIVDGKLSIQCYLSALDRCYSVYCK
          RPTGG.GAVALLIGP.A.LIFERGLRGTHMQ.A.DFY.PD.LSE.PIVDGKLS.Q...SA.D.CYS...K
Retrocopy RPTGGPGAVALLIGPQATLIFERGLRGTHMQRACDFYEPDTLSECPIVDGKLSTQHCFSA*DHCYSINHK

Parental  KIRAQWQKEGNDKDFTLNDFGFMIFHSPYCKLVQKSLARMLLNDFLNDQNRDKNTIYSGLEAFGDVKLED
          .I.AQ.QKEGNDK.F.L..F.....HSP.CKL...S.A.ML.NDF.NDQNRDKN.I.SGLEAFGDVKLED
Retrocopy NISAQLQKEGNDKRFYLE*FWH---HSPSCKLLSLSPAQMLQNDFPNDQNRDKNSI*SGLEAFGDVKLED

Parental  TYFDRDVEKAFMKASSELFNQKTKASLL-VSNQNGNMYTSSVYGSLA-SVLAQYSPQQLAGKRIGVF
          ..FD.DVE.AFM.ASSE.F.QKTK.SLL.VS.QNGN.YT..V.GSL.....AQ.SPQQ..GKR.GVF
Retrocopy IDFDTDVEMAFMEASSEPFYQKTKTSLL<VSIQNGNTYTLPVCGSLK>CHIAQDSPQQ*SGKRPGVF

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	47.46 RPM
SRP051959_heart	0.00 RPM	7.68 RPM
SRP051959_kidney	0.00 RPM	9.90 RPM
SRP051959_liver	0.00 RPM	244.68 RPM
SRP051959_lung	0.00 RPM	7.19 RPM
SRP051959_lymph_node	0.00 RPM	8.74 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.35 RPM
SRP051959_spleen	0.00 RPM	5.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1754 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1754 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1754 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001303	1 retrocopy	retro_cjac_1754 ,
Echinops telfairi	ENSETEG00000003583	1 retrocopy	retro_etel_526,
Homo sapiens	ENSG00000112972	1 retrocopy	retro_hsap_328,
Pongo abelii	ENSPPYG00000015439	1 retrocopy	retro_pabe_361,
Pan troglodytes	ENSPTRG00000016845	1 retrocopy	retro_ptro_265,