RetrogeneDB ID: retro_cjac_455

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:112345917..112346514(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000012916
• Aliases: None
• Description: None

Sequence

>retro_cjac_455
ACAAATCCTGGGACCAATACGGGCTGGGCAGATGCCATGGCTAAAGTTCTCAACAAGAAAACTCCTGAAAGTAAACCTAC
TATTCTGGTCAAAAATAAGAAGCTGGAAAAGGAAAAAGAAAAGTTAAAGCAAGAAAGACAAGAGAAAATAAAACAGCGTG
ATAAGAGGATGGAGTGGGAAATGATGTGCAGAGTAAAGCCAGATGTTGTCCAAGACAAGGAGACAGAGAGAAATCTTCAG
AGAATTGCAACGAGGGGTGTGGTGCAGTTATTTAATGCTGTTCAGAAACATCAAAAGAACGTTGATGAGAAGGTTAAAGA
AGCTGGAAGCTCTATTAGAAAGCGAACTAAGTTGATATCAACTGTTTCCAAGAAAGATTTTATCAGTGTTTTGAGAGGAA
TGGATGAAAGTACAAATGAGACTACCTCAAGCAAGAAGAAACCAAAAGCCAAACAGACTGAAGTGAAATCAGAAGAGGGC
CCAGGTTGGACGATCCTACGTGACAATTTCATGATGGGAGCATCTATGAAAGACTGGGACAAGGAAAGTGATGGGCCAGA
TGACAGCAGGCCAGAATCTGCAAGTGACTCTGATACA

Alignment

ORF - retro_cjac_455 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.99 %
• Parental protein coverage: 70.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SNPGTNMGWADAMAKVLNKKTPESKPTILVKNKKLEKEKEKLKQERQEKIKQRDKRMEWEMMCRVKPDVV
          .NPGTN.GWADAMAKVLNKKTPESKPTILVKNKKLEKEKEKLKQERQEKIKQRDKRMEWEMMCRVKPDVV
Retrocopy TNPGTNTGWADAMAKVLNKKTPESKPTILVKNKKLEKEKEKLKQERQEKIKQRDKRMEWEMMCRVKPDVV

Parental  QDKETERNLQRIATRGVVQLFNAVQKHQKNVDEKVKEAGSSIRKRTKLISTVSKKDFISVLRGMDESTNE
          QDKETERNLQRIATRGVVQLFNAVQKHQKNVDEKVKEAGSSIRKRTKLISTVSKKDFISVLRGMDESTNE
Retrocopy QDKETERNLQRIATRGVVQLFNAVQKHQKNVDEKVKEAGSSIRKRTKLISTVSKKDFISVLRGMDESTNE

Parental  TTSGKKKPKAKQTEVKSEEGPGWTILRDDFMMGASMKDWDKESDGPDDSRPESASDSDT
          TTS.KKKPKAKQTEVKSEEGPGWTILRD.FMMGASMKDWDKESDGPDDSRPESASDSDT
Retrocopy TTSSKKKPKAKQTEVKSEEGPGWTILRDNFMMGASMKDWDKESDGPDDSRPESASDSDT

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	0.04 RPM	4.33 RPM
SRP051959_heart	0.04 RPM	7.12 RPM
SRP051959_kidney	0.00 RPM	6.79 RPM
SRP051959_liver	0.02 RPM	6.91 RPM
SRP051959_lung	0.07 RPM	6.75 RPM
SRP051959_lymph_node	0.05 RPM	5.91 RPM
SRP051959_skeletal_muscle	0.04 RPM	7.64 RPM
SRP051959_spleen	0.17 RPM	5.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_455 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_455 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_455 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000174	1 retrocopy	retro_chof_1961,
Callithrix jacchus	ENSCJAG00000012916	2 retrocopies	retro_cjac_3789, retro_cjac_455 ,
Mus musculus	ENSMUSG00000001305	1 retrocopy	retro_mmus_3531,
Oryctolagus cuniculus	ENSOCUG00000017863	4 retrocopies	retro_ocun_1738, retro_ocun_820, retro_ocun_962, retro_ocun_992,
Ictidomys tridecemlineatus	ENSSTOG00000001244	1 retrocopy	retro_itri_1554,
Tarsius syrichta	ENSTSYG00000012715	1 retrocopy	retro_tsyr_2006,