RetrogeneDB ID: retro_cjac_3945

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286373.1:220978..222459(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALDH9A1
• Ensembl ID: ENSCJAG00000004575
• Aliases: None
• Description: None

Sequence

>retro_cjac_3945
ATGAGCACTGGCACCTTCGTTGTGTCGCAGCCGCTCAATTATCATGGCAGGACCCACGTGGAGCCGGCGGATGCTTCTGG
CACGGAGAAGGCTTTCGAGCCGGCAACCGGCTGAGGGATAGCTACTTTCCCATGTTCAGGAGAAAAGGAAGTAAATTTGA
CTGTTCAGAGTGCAAAGGCTGCTTTTAAAATATGGAGTCTAAAATCTGGTATGGAGCATTGCTGAATCCTTTTGGAGGCT
GCCAGAATAGTAAGGGAACGGAAGGATGAAATTGCCACTGTGGAATGCATCAACAACAGCAAGTCCATCTTTGAGGCCTG
CTTGGACATCAACACTGCCTGACAGTGCCTGGAGTATTTTGCAGGATTGGCTGCGTCCATGGCTGGTGAACACATCCAGC
TCCCAGGCGGATCCTTTGGTTATACCACAAGAGAACCACTTGGGGTATGTGTGGGAATAGGAGTGTGGAACTACCCCTTT
CAGATCACCTCTTGGAAGTCAGCTCCTGTGTTAGCCTGTGGTAATGCCATGGTCTTCAAACCTTCTCCCTTTACACCTGT
TTCTGCATTGCTACTGGCTGAAATCTACACTGAGGCTGCTGTGCCTCCTGGGCTCTTCAATGTGGTGCAGGGCGGGGCTG
CCACTGGCCAGTTTCTGTGTCAGCATCATGATGTGGCCCAAGTCTCCTTCACTGGAAGTGTGCCCACTGGCATGAAGATC
ATGGAGATGGCATCTAAAGGAGTCAAACCTGTTACCTAGGAACTTGGAGGCAAATCTCCACTCATCATCTTCTCAGACTG
TGATATTAACAATGCTGTGAAGGGGGCGCTGATGGCCAACTTCCTCACACAAGGCCAGGTTTGCTGTAATGGCACAAGAT
ATTTGTGCAGAAAGAAATTCTTGATAAATTTACAGAGGAAGTGGTGAAACAGACCCAAAGGATTAAAACTGGAGATCCCC
TTCTGGAAGACACAAGGATGGGTCCACTCATCAACCGACCACACCTGGAGCGAGTCCTTGGGTTTGTTAAAGTGGCAAAG
GAGCAGGGTGCTAAAGTGTTATGTGTTGGAGATATATATGCACCTCAAGATCCCAAATTAAAGGATGGATACTACATGAG
ACCTTGTGTATTAACTAATTGCAGAGATGACATGACCTGTGTGAAAGAAGAGATCTTTCGGCCTGTTATGTCTATTTTAC
CATTTGAGACTAAAGCTGAGGTTCTAGAAAGAGCCAATGATACCACTTTTGGACTAGCAGCTGGCGTCTTTACCAGGGAC
ATCCAGCGGGCTCATAGAGCGGTAGCTGAGCTTCAGGCTGGAACCTGCTTCATTAACAACTATAACGTCAGTCCAGTGAA
GTTGCCCTTTGGTGGATATAAGAAGTCAGGATTTGGCAGAGAGAACGGCTGTGTGACAATTGAATATTATTCACAACTGA
AGACTGTGTGTATGGAGATGGGTGATGTGGAATCTGCTTTT

Alignment

ORF - retro_cjac_3945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTGTFVVSQPLNYRGGTR-GAGGRSGTEKAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSG
          MSTGTFVVSQPLNY.G.T.......SGTEKAFEPATG..IATF.CSGEKEVNL.VQ.AKAAFKIWS.KSG
Retrocopy MSTGTFVVSQPLNYHGRTHVEPADASGTEKAFEPATG*GIATFPCSGEKEVNLTVQSAKAAFKIWSLKSG

Parental  MERCRILLEAARIIRERKDEIATVECINNGKSIFEARLDIDTSWQCLEYFAGLAASMAGEHIQLPGGSFG
          ME.C.ILLEAARI.RERKDEIATVECINN.KSIFEA.LDI.T..QCLEYFAGLAASMAGEHIQLPGGSFG
Retrocopy MEHC*ILLEAARIVRERKDEIATVECINNSKSIFEACLDINTA*QCLEYFAGLAASMAGEHIQLPGGSFG

Parental  YTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYTEAGVPPGLFNVVQ
          YT.REPLGVCVGIG.WNYPFQI.SWKSAP.LACGNAMVFKPSPFTPVSALLLAEIYTEA.VPPGLFNVVQ
Retrocopy YTTREPLGVCVGIGVWNYPFQITSWKSAPVLACGNAMVFKPSPFTPVSALLLAEIYTEAAVPPGLFNVVQ

Parental  GGVATGQFLCQHHDVAKVSFTGSVPTGMKIMEMASKGVKPVTLELGGKSPLIIFSDCDMNNAVKGALMAN
          GG.ATGQFLCQHHDVA.VSFTGSVPTGMKIMEMASKGVKPVT.ELGGKSPLIIFSDCD.NNAVKGALMAN
Retrocopy GGAATGQFLCQHHDVAQVSFTGSVPTGMKIMEMASKGVKPVT*ELGGKSPLIIFSDCDINNAVKGALMAN

Parental  FLTQGQVCCNGTR-VFVQKEILDKFTEEVVKQTQRIKIGDPLLEDTRMGPLINRPHLERVLGFVKVAKEQ
          FLTQGQVCCNGTR..FVQKEILDKFTEEVVKQTQRIK.GDPLLEDTRMGPLINRPHLERVLGFVKVAKEQ
Retrocopy FLTQGQVCCNGTR<IFVQKEILDKFTEEVVKQTQRIKTGDPLLEDTRMGPLINRPHLERVLGFVKVAKEQ

Parental  GAKVLCGGDTYVPEDPKLKDGYYMRPCVLTNCRDDMTCVKEEIFGPVMSILPFDTEAEVLERANDTTFGL
          GAKVLC.GD.Y.P.DPKLKDGYYMRPCVLTNCRDDMTCVKEEIF.PVMSILPF.T.AEVLERANDTTFGL
Retrocopy GAKVLCVGDIYAPQDPKLKDGYYMRPCVLTNCRDDMTCVKEEIFRPVMSILPFETKAEVLERANDTTFGL

Parental  AAGVFTRDIQRAHRVVAELQAGTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGD
          AAGVFTRDIQRAHR.VAELQAGTCFINNYNVSPV.LPFGGYKKSGFGRENG.VTIEYYSQLKTVC.EMGD
Retrocopy AAGVFTRDIQRAHRAVAELQAGTCFINNYNVSPVKLPFGGYKKSGFGRENGCVTIEYYSQLKTVCMEMGD

Parental  VESAF
          VESAF
Retrocopy VESAF

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	2.02 RPM	17.84 RPM
SRP051959_heart	1.98 RPM	10.77 RPM
SRP051959_kidney	3.71 RPM	23.12 RPM
SRP051959_liver	2.21 RPM	34.25 RPM
SRP051959_lung	2.68 RPM	16.22 RPM
SRP051959_lymph_node	3.54 RPM	25.48 RPM
SRP051959_skeletal_muscle	2.40 RPM	13.06 RPM
SRP051959_spleen	2.96 RPM	36.39 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3945 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3945 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3945 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	ENSCJAG00000004575	1 retrocopy	retro_cjac_3945 ,