RetrogeneDB ID: retro_cjac_3361

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01174897.1:4395..5383(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TES
• Ensembl ID: ENSCJAG00000005193
• Aliases: LOC100407335, TES, Testin
• Description: Testin [Source:UniProtKB/Swiss-Prot;Acc:Q2QLG8]

Sequence

>retro_cjac_3361
ATGGACCTGGAAAACAAAGTGAAGACGACGGGCTTAGGTCACAAGCAAGGATTTGGAGCCCCTTGTTTAAAATGCAAAGA
AAAATGTGAAGGATTCGAACTGCACTTCTGGAGAAAAATATGTTGTAACTGCAAGTGTGGCCAAGAAGAGCATGATGTCC
TCTTGAGCAATGAAGAGGATCGAAAACTGGGAAAATTTTTTGAAGACACCAAGTATACCACTCTGATTGCAAAACTAAAG
TCAGGTGGAATTCCCATGTATAAACGCAATGTTATGATATTGACCAATCCAGTTGCTGCCAAGAAGAATGTCTCCATCAA
TACAGTTACCTATGAGTGGGCTCCTCCTGTCCACAGTCAGGCATTGGCCACGTAGTACGTGCAGATGCTACCCAAGGAAA
AGCAGCCAGTGGCAGGCTCAGAGGGGGCACAGTACCGGAAGCAGCAGCTGGCAAAGAGCTCCCTGCACATGATCAGGACC
CTTCAAAGTGCCATGAATTGTCTCCCAGAGAGGTGAAGGAGATGGAACAGTTTGTGAAGTAATTTAAGAGTGAGGATCTG
GGAGTAGGAGATGTCAAACTTCCCTGTGAGATGGATGCCTGAGGCCCCAAACAAATGTGCATTCCTGGAGGGGATGGAAG
CACCCCACCAGCAGCGGGGGCCATGGAGGACAGATCTGCTGAGCACAAAAGTATTCAACATTCCTGCTATTGTTGCAAAC
TGAGTATGAAGGCAGGCAACCCACCATCTATGCCGAAAGGGCCGGCTGTGATAAACTGTGGCACCCAGCCTCTTTTGTCT
GCAGCATCTGCCATGAACTCCTGGTTGACATGATTTATTTCTGGAAGAATGAGAAGCTATACTGTGGCAGACATTACTGT
TTCAGTGAGAAACCCCGACGTGCTGGCTGTGATGAGCTGATATTCAGCAGTGAGTCTACCCAGGCAGAAAACCAGAATTG
GCACCTGACACACCTCTGCTGCTTTAGC

Alignment

ORF - retro_cjac_3361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.55 %
• Parental protein coverage: 78.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDLENKVKKMGLGHEQGFGAPCLKCKEKCEGFELHFWRKICRNCKCGQEEHDVLLSNEEDRKVGKLFEDT
          MDLENKVK..GLGH.QGFGAPCLKCKEKCEGFELHFWRKIC.NCKCGQEEHDVLLSNEEDRK.GK.FEDT
Retrocopy MDLENKVKTTGLGHKQGFGAPCLKCKEKCEGFELHFWRKICCNCKCGQEEHDVLLSNEEDRKLGKFFEDT

Parental  KYTTLIAKLKSDGIPMYKRNVMILTNPVAAKKNVSINTVTYEWAPPVHNQALARQYMQMLPKEKQPVAGS
          KYTTLIAKLKS.GIPMYKRNVMILTNPVAAKKNVSINTVTYEWAPPVH.QALA..Y.QMLPKEKQPVAGS
Retrocopy KYTTLIAKLKSGGIPMYKRNVMILTNPVAAKKNVSINTVTYEWAPPVHSQALAT*YVQMLPKEKQPVAGS

Parental  EGAQYRKKQLA-KQLPAHDQDPSKCHELSPREVKEMEQFVKKYKSEALGVGDVKLPCEMDAQGPKQMYIP
          EGAQYRK.QLA.K.LPAHDQDPSKCHELSPREVKEMEQFVK..KSE.LGVGDVKLPCEMDA.GPKQM.IP
Retrocopy EGAQYRKQQLA<KELPAHDQDPSKCHELSPREVKEMEQFVK*FKSEDLGVGDVKLPCEMDA*GPKQMCIP

Parental  GGDRSTPPAAGAMEDKSAEHKSTQYSCYCCKLSMKEGD-PAIYAERAGYDKLWHPACFVCSICHELLVDM
          GGD.STPPAAGAMED.SAEHKS.Q.SCYCCKLSMK.G..P.IYAERAG.DKLWHPA.FVCSICHELLVDM
Retrocopy GGDGSTPPAAGAMEDRSAEHKSIQHSCYCCKLSMKAGN<PTIYAERAGCDKLWHPASFVCSICHELLVDM

Parental  IYFWKNEKLYCGRHYCDSEKPRCAGCDELIFSNEYTQAEKQSWHLKHFCCFA
          IYFWKNEKLYCGRHYC.SEKPR.AGCDELIFS.E.TQAE.Q.WHL.H.CCF.
Retrocopy IYFWKNEKLYCGRHYCFSEKPRRAGCDELIFSSESTQAENQNWHLTHLCCFS

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	40.40 RPM
SRP051959_heart	0.02 RPM	9.10 RPM
SRP051959_kidney	0.00 RPM	3.75 RPM
SRP051959_liver	0.00 RPM	1.02 RPM
SRP051959_lung	0.02 RPM	13.08 RPM
SRP051959_lymph_node	0.00 RPM	11.67 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.55 RPM
SRP051959_spleen	0.02 RPM	5.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3361 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3361 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3361 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005193	2 retrocopies	retro_cjac_3361 , retro_cjac_3870,
Mus musculus	ENSMUSG00000029552	3 retrocopies	retro_mmus_253, retro_mmus_3438, retro_mmus_3586,
Rattus norvegicus	ENSRNOG00000032978	3 retrocopies	retro_rnor_2974, retro_rnor_2975, retro_rnor_9,