RetrogeneDB ID: retro_cjac_1399

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:48741377..48742268(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC38A8
• Ensembl ID: ENSCJAG00000003812
• Aliases: None
• Description: None

Sequence

>retro_cjac_1399
ATGGCAGGACAGACCCCAGAAAGCAGAGGTCTTCCAGAAAAGCCGGACCCTGCCTCGACCGCTGCCACTCTGTCCTCCAT
GGGTGCTGTCTTCATCCTCTTGAAGTCTGCGCTGGGAGCTGGCCTGCTCAACTTTCCCTGGGCCTTCTCCAAAGCTGGTG
GAGTGGTCCCTGCCTTGCTGGTGGAGCTGGTGTCCTTGGTCTTCCTGGTCAGTGGGCTGGTCATCCTGGGCTATGCTGCT
GCTGTCAGTGGCCAGGCCACCTACCAGGGTGTGGTTAGGGGACTGTGTGGCCCCGCCATTGGGAAGCTGTGTGAGGCCTG
CTTCCTCATCAACCTGCTCGTGATCTCTGTGGCCTTCCTCAGGGTGATCGGGGACCAGCTGGAGAAGCTGTGTGACTCCC
TCCTGTCTGGCACACCTCCTGCTCCACGGCCCTGGTACGCAGACCAGCGCTTTACCCTGCCCCTGCTCTCCACGCTGGTC
ATCCTGCCCCTGTCCACCCCACGGGAGATCGCCTTCCAGAAATACACAAGCATCCTAGGTACGCTGGCCGCCTGTTACCT
GGCCCTCGTCATCACAGTGCAGTACTACCTCTGGCCCCAGGGCCTCATGCGTGAGCCCGGTCCTTCACTGAGCCCTGCCT
CCTGGACCTCTGTGTTCAGCGTCTTCCCCACCATCTGCTTCGGGTTTCAGTGTCACGAAGCCGCGGTCTCCATCTACTGT
AGCATGCGTAAGCGGAGCCTCTCGCACTGGGCCCTGGTCTCCCTGCTGTCCTTGCTGGGCTGCTGCCTCATCTATTCACT
GACCGGTCATATAGTGCATTGGAGGCACAGAACCCGGGTCCCAGGCACGGCTGGCTCTGGCTGGCCACTTGACTCCAGTC
TTTTTTTCATT

Alignment

ORF - retro_cjac_1399 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.91 %
• Parental protein coverage: 68.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGQTPESRGLPEKPDPASTAATLSSMGAVFILLKSALGAGLLNFPWAFSKAGGVVPALLVELVSLVFLV
          MAGQTPESRGLPEKPDPASTAATLSSMGAVFILLKSALGAGLLNFPWAFSKAGGVVPALLVELVSLVFLV
Retrocopy MAGQTPESRGLPEKPDPASTAATLSSMGAVFILLKSALGAGLLNFPWAFSKAGGVVPALLVELVSLVFLV

Parental  SGLVILGYAAAVSGQATYQGVVRGLCGPAIGKLCEACFLVNLLMISVAFLRVIGDQLEKLCDSLLSGTPP
          SGLVILGYAAAVSGQATYQGVVRGLCGPAIGKLCEACFL.NLL.ISVAFLRVIGDQLEKLCDSLLSGTPP
Retrocopy SGLVILGYAAAVSGQATYQGVVRGLCGPAIGKLCEACFLINLLVISVAFLRVIGDQLEKLCDSLLSGTPP

Parental  TPRPWYADQRFTLPLLSTLVILPLSTPREIAFQKYTSILGTLAACYLALVITVQYYLWPQGLMREPGPSL
          .PRPWYADQRFTLPLLSTLVILPLSTPREIAFQKYTSILGTLAACYLALVITVQYYLWPQGLMREPGPSL
Retrocopy APRPWYADQRFTLPLLSTLVILPLSTPREIAFQKYTSILGTLAACYLALVITVQYYLWPQGLMREPGPSL

Parental  SPASWTSVFSVFPTICFGFQCHEAAVSIYCSMRKRSLSHWALVSLLSLLGCCLIYSLTGVYGFLTFRTEV
          SPASWTSVFSVFPTICFGFQCHEAAVSIYCSMRKRSLSHWALVSLLSLLGCCLIYSLTG.......RT.V
Retrocopy SPASWTSVFSVFPTICFGFQCHEAAVSIYCSMRKRSLSHWALVSLLSLLGCCLIYSLTGHIVHWRHRTRV

Parental  SADVLMSYPGNNTVIIV
          ........P........
Retrocopy PGTAGSGWPLDSSLFFI

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	0.09 RPM
SRP051959_heart	0.00 RPM	0.04 RPM
SRP051959_kidney	0.04 RPM	0.60 RPM
SRP051959_liver	0.00 RPM	0.02 RPM
SRP051959_lung	0.05 RPM	0.03 RPM
SRP051959_lymph_node	0.14 RPM	0.09 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.09 RPM
SRP051959_spleen	0.06 RPM	0.04 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1399 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1399 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003812	2 retrocopies	retro_cjac_1399 , retro_cjac_1892,