RetrogeneDB ID: retro_cjac_3870

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285462.1:6764..7427(-)
• 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_3870
GTTATCTATGAGTGGGCTCCTCCTGTCCACAGTCAGGCATTGGCCACACAGTACATGCAGAGGCTACCCAAGGAAAAGCA
GCCAGTGGCAGGCTCAGAGGGGGCACAGTACTGGAAGCAGCAGCTGGCAAAGAGCTCCCTGCACATGATCAGGACCCTTC
AAAGTGCCATGAATTGTCTCCCAGAGAGGTGAAGGAGATTGAGCAGTTTGTGAAGTAATTTAAGAGTGAGGATCTGGGAG
TAGGAGATGTCAAACTTCCCTGTGAGATGGATGCCTGAGGCCCCAAACAAATGTGCATTCCTGGAGGGGATGGAAGCACC
CCACCAGCAGCGGGGGCCATGGAGGACAGATCTGCTGAGCACAAAAGTACTCAACATTCCTGCTATTGTTGCAAACTAGT
ATGAAGGCAGGCAACCCGCCATCTACACCGAAAGGGCCAGCTGTGATAAACTGTGGCACACAGCCTCTTTTGTCTGCAGC
ATCTGCCATGAACTCCTGGTTGACATGATTTATTTCTGGAAGAATGAGAAGCTATACTGTGGCAGACATTACTGTTTCAG
TGAGAAACCCCGATGTGCTGGCTGTGATGAGCTGATATTCAGCAGTGAGTCTACCCAGGCAGAAAACCAGAATTGGCACC
TGAAACACCTCTGCTGCTTTAGC

Alignment

ORF - retro_cjac_3870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.33 %
• Parental protein coverage: 52.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VTYEWAPPVHNQALARQYMQMLPKEKQPVAGSEGAQYRKKQLAK-QLPAHDQDPSKCHELSPREVKEMEQ
          V.YEWAPPVH.QALA.QYMQ.LPKEKQPVAGSEGAQY.K.QLAK..LPAHDQDPSKCHELSPREVKE.EQ
Retrocopy VIYEWAPPVHSQALATQYMQRLPKEKQPVAGSEGAQYWKQQLAK<ELPAHDQDPSKCHELSPREVKEIEQ

Parental  FVKKYKSEALGVGDVKLPCEMDAQGPKQMYIPGGDRSTPPAAGAMEDKSAEHKSTQYSCYCCKL-SMKEG
          FVK..KSE.LGVGDVKLPCEMDA.GPKQM.IPGGD.STPPAAGAMED.SAEHKSTQ.SCYCCKL.SMK.G
Retrocopy FVK*FKSEDLGVGDVKLPCEMDA*GPKQMCIPGGDGSTPPAAGAMEDRSAEHKSTQHSCYCCKL<SMKAG

Parental  D-PAIYAERAGYDKLWHPACFVCSICHELLVDMIYFWKNEKLYCGRHYCDSEKPRCAGCDELIFSNEYTQ
          ..PAIY.ERA..DKLWH.A.FVCSICHELLVDMIYFWKNEKLYCGRHYC.SEKPRCAGCDELIFS.E.TQ
Retrocopy N<PAIYTERASCDKLWHTASFVCSICHELLVDMIYFWKNEKLYCGRHYCFSEKPRCAGCDELIFSSESTQ

Parental  AEKQSWHLKHFCCFA
          AE.Q.WHLKH.CCF.
Retrocopy AENQNWHLKHLCCFS

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

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3870 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3870 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3870 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,