RetrogeneDB ID: retro_cjac_2273

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:126011039..126011717(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFSD3
• Ensembl ID: ENSCJAG00000021402
• Aliases: None
• Description: major facilitator superfamily domain containing 3 [Source:HGNC Symbol;Acc:25157]

Sequence

>retro_cjac_2273
TTGCGGCGGCTCCCAAGGCCGCCCCGCCCCGAGCAGCGTCCCCACACCATGCACCTTCTGCGGGACCTGCTGGCAGTGCC
GGGGACTCTGTGGACTGCAGGCTTTGTGCTCACCTACAAGCTGGGTGAGCAGGGTGCCAGCAGCCTGTTTCCTCTTCTCC
TGCTGGACCGCGGCGTTTCTGCCCCCGAGCTGGGACTGTGGAATGGTGTGGGTGTCATGGTGTGCTCCATCGCTGGCTCC
TTCCTGGATGGGACATTGCTGGCCAAGCACCGGGAGCCGCTGCCTCTGCTGAAGTCAGTGTTGCGGCTCCGCCTTGGGGG
CTTGGCCTGCCAGACTGACTTGCTCTTCCGCCTGGATACCCTGGGTGCCAGGTTGGGCCCTGGCACAATCTTGAGAGGGG
CAGCCTTGCTGAGCCTTTGTCTGCAGCACTTCTTGGGAGGCCTGGTCCCCACAGCCACCTTCACTGGGATGATGCGCTGC
AGCCAGCTGGCCCCCAGGGCCCTGCAGGCCACACATTACAACCTTCTGACCATTCTGCAGCTGCTGGGGAAGCTGCTGCT
GGGTGCTCTGGCTGGAGCCCTGGCCGACGGGTTAGGGCCACATACCTGCTTCTCCCTCCTGCTCATCCTCTCTGCCCTGC
CCCTTCTGTACCTGGGCCTAGCATCCAGCACCTTGCTC

Alignment

ORF - retro_cjac_2273 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.5 %
• Parental protein coverage: 54.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRQLPRPPPSEQRPHTMHLMRDVLAVPGTLWTAGFVLTYKLGEQGASSLFPLLLLDHGISAPELGLWNGV
          LR.LPRPP..EQRPHTMHL.RD.LAVPGTLWTAGFVLTYKLGEQGASSLFPLLLLD.G.SAPELGLWNGV
Retrocopy LRRLPRPPRPEQRPHTMHLLRDLLAVPGTLWTAGFVLTYKLGEQGASSLFPLLLLDRGVSAPELGLWNGV

Parental  GAMVCSIAGSSLGGTLLAKHWELLPLLKSVLWLRLGGLACQTALLFHLDALGASLGPGTILRGAALLSLC
          G.MVCSIAGS.L.GTLLAKH.E.LPLLKSVL.LRLGGLACQT.LLF.LD.LGA.LGPGTILRGAALLSLC
Retrocopy GVMVCSIAGSFLDGTLLAKHREPLPLLKSVLRLRLGGLACQTDLLFRLDTLGARLGPGTILRGAALLSLC

Parental  LQHFLGGLVTTATFTGMMRCSQLAPRALQATHYSLLATLELLGKLLLGALAGALVDGLGPHSCFSLLLIL
          LQHFLGGLV.TATFTGMMRCSQLAPRALQATHY.LL..L.LLGKLLLGALAGAL.DGLGPH.CFSLLLIL
Retrocopy LQHFLGGLVPTATFTGMMRCSQLAPRALQATHYNLLTILQLLGKLLLGALAGALADGLGPHTCFSLLLIL

Parental  SALPLLNLGLAPSTLL
          SALPLL.LGLA.STLL
Retrocopy SALPLLYLGLASSTLL

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	0.80 RPM
SRP051959_heart	0.00 RPM	1.16 RPM
SRP051959_kidney	0.00 RPM	1.95 RPM
SRP051959_liver	0.00 RPM	2.25 RPM
SRP051959_lung	0.00 RPM	1.09 RPM
SRP051959_lymph_node	0.00 RPM	1.44 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.27 RPM
SRP051959_spleen	0.00 RPM	0.80 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2273 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2273 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021402	1 retrocopy	retro_cjac_2273 ,