RetrogeneDB ID: retro_cjac_483

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:172233319..172233865(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRI1
• Ensembl ID: ENSCJAG00000004436
• Aliases: None
• Description: None

Sequence

>retro_cjac_483
ATGAAGCTGGAGGTGATCCACTACTCGAGGGGCTCCCTGCAGATCCTGGACCAGCTGCTGCTGCCCCAGCAAAGCCGCTA
CGAGGCGGTGGGCTCGGTGCGCCAAGCCTGGGAGGCAATCCGTGACATGAAGGTGCAGGGTGCCCCAGCCATCGCCCTAG
TAGGCTGCCTCAGCGTCGCCGTGGAGCTGCATATGGGCGCCGGGGGACCGGGACTTGCCGCACTGGTGGCCTTCGTGCAC
GACAAGGTGAGCTTCCTCGTCACTGCCGGGCCCACCGCTGTCAACATGGCCCACACTGCCTGCGACCTGGCTGATGCTGC
AGCTCGGGAGGCCGAGCAGGAGGGCGCTACAGAGGAGGCAGTCCAGGAGAGAGTGATCCATTGCACCAAGGACATGCTGG
AGAAAGACCTCAGAGACAACTGGAACATCGGGGATCTCGGAGCCCACCATCTCCTGGACTGGGTGGCCCCCAACGGTGGC
AAGGTGACTGTGCTGACCCACTGTAACACCGGTGCTCTGGCCACTGCTGGCTATGGCACAGCCCTA

Alignment

ORF - retro_cjac_483 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.52 %
• Parental protein coverage: 50.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTLKAIRYSRGSLQILNQLLLPQQTHYEAVGSVRQAWEAIRAMKVRGAPAIALVGCLSLAVELQTGAGGP
          M.L..I.YSRGSLQIL.QLLLPQQ..YEAVGSVRQAWEAIR.MKV.GAPAIALVGCLS.AVEL..GAGGP
Retrocopy MKLEVIHYSRGSLQILDQLLLPQQSRYEAVGSVRQAWEAIRDMKVQGAPAIALVGCLSVAVELHMGAGGP

Parental  GLAALVAFVRDKLSFLVTARPTAVNMARAARDMADAAAREAEREGATEEAVRERVIRCAEDMLEKDLRDN
          GLAALVAFV.DK.SFLVTA.PTAVNMA..A.D.ADAAAREAE.EGATEEAV.ERVI.C..DMLEKDLRDN
Retrocopy GLAALVAFVHDKVSFLVTAGPTAVNMAHTACDLADAAAREAEQEGATEEAVQERVIHCTKDMLEKDLRDN

Parental  ESIGDFGALFLLDQVAPNGGKVTVLTHCNTGALATAGYGTAL
          ..IGD.GA..LLD.VAPNGGKVTVLTHCNTGALATAGYGTAL
Retrocopy WNIGDLGAHHLLDWVAPNGGKVTVLTHCNTGALATAGYGTAL

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	0.18 RPM	1.80 RPM
SRP051959_heart	0.23 RPM	1.63 RPM
SRP051959_kidney	0.18 RPM	3.95 RPM
SRP051959_liver	0.30 RPM	3.90 RPM
SRP051959_lung	0.16 RPM	2.91 RPM
SRP051959_lymph_node	0.11 RPM	2.56 RPM
SRP051959_skeletal_muscle	0.11 RPM	2.73 RPM
SRP051959_spleen	0.19 RPM	2.52 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_483 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_483 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_483 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	ENSCJAG00000004436	1 retrocopy	retro_cjac_483 ,