RetrogeneDB ID: retro_cjac_1892

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:20321689..20322485(-)
• 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_1892
ACCCCAGAAAGCAGAGGTCTTCCAGAAAAGCCCAACCCTGCCACGATCGCTGCCACTCTGTCCTCCATGGGCACTGTCTT
CATCCTCTTGAAGTCTGCGCTGGGAGCTGGCCTACTCAACTTTCCCTGGGCCTTCTCCAAAGTGGGTGGAGTGGTCCCTG
CCTTGCTGGTGGAGCTGGTCTCCTTGGTCTTCCTGGTCAGCGAGCTGGTCATCCTGGGCTATGCTACCGCTGTCAGTGGC
CAGGCCACCTACCAGGGTGTCGTTAGGGGACTGTGTGGCCCCTGCCATCGGGAAGCTGTGTGAGGCCTGCTTCCTCGTCA
ACCTGCTCATGATCTCTGTGGCCTTCCTCAGGGTGATTGGGGACCAGCTGGAGAAGCTGTGTGACTCCCTCCTGTCTGGC
ACACCGCCTGCTCCATGGCCCTGGTACCCAGACCAGCGCTTTACCCTGCCCCTGCTCTCCACGCTGGTCATCCTGCCCCT
GTCCACCCCACGGGAGATCGCCTTCCAGAAATACACAAACATCCTAGGTACGCTGGCCGCCTGTTACCTGGCCCTGGTCA
TCACAGTGCAGTACTACCTCTGGCCCCAGGGCCTCATGCATGAGCGCGGTCCTTCACTGAGCCCTGCCTCCTGGACCTCT
GTGTTCAGCGTCTTCCCCACCATCTGCTTCAGGTTTCAGTGTCAGGAAGCTGCAGTCTCCATCTACTGCAGCATGCACAA
GCAGAGCCTCTCGCACTGGGCCCTGGTCTCCCTGCTGTCCTTACTGGACTACTACTGCCTCATCTATTCACTGACC

Alignment

ORF - retro_cjac_1892 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.11 %
• Parental protein coverage: 60.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TPESRGLPEKPDPASTAATLSSMGAVFILLKSALGAGLLNFPWAFSKAGGVVPALLVELVSLVFLVSGLV
          TPESRGLPEKP.PA..AATLSSMG.VFILLKSALGAGLLNFPWAFSK.GGVVPALLVELVSLVFLVS.LV
Retrocopy TPESRGLPEKPNPATIAATLSSMGTVFILLKSALGAGLLNFPWAFSKVGGVVPALLVELVSLVFLVSELV

Parental  ILGYAAAVSGQATYQGVVRGLCG-PAIGKLCEACFLVNLLMISVAFLRVIGDQLEKLCDSLLSGTPPTPR
          ILGYA.AVSGQATYQGVVRGLCG.PAIGKLCEACFLVNLLMISVAFLRVIGDQLEKLCDSLLSGTPP.P.
Retrocopy ILGYATAVSGQATYQGVVRGLCG>PAIGKLCEACFLVNLLMISVAFLRVIGDQLEKLCDSLLSGTPPAPW

Parental  PWYADQRFTLPLLSTLVILPLSTPREIAFQKYTSILGTLAACYLALVITVQYYLWPQGLMREPGPSLSPA
          PWY.DQRFTLPLLSTLVILPLSTPREIAFQKYT.ILGTLAACYLALVITVQYYLWPQGLM.E.GPSLSPA
Retrocopy PWYPDQRFTLPLLSTLVILPLSTPREIAFQKYTNILGTLAACYLALVITVQYYLWPQGLMHERGPSLSPA

Parental  SWTSVFSVFPTICFGFQCHEAAVSIYCSMRKRSLSHWALVSLLSLLG-CCLIYSLT
          SWTSVFSVFPTICF.FQC.EAAVSIYCSM.K.SLSHWALVSLLSLL...CLIYSLT
Retrocopy SWTSVFSVFPTICFRFQCQEAAVSIYCSMHKQSLSHWALVSLLSLLDYYCLIYSLT

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

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1892 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1892 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1892 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 ,