RetrogeneDB ID: retro_cjac_3272

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:19339687..19340157(-)
• Located in intron of: ENSCJAG00000005091

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBL4A
• Ensembl ID: ENSCJAG00000016805
• Aliases: None
• Description: Ubiquitin-like protein 4A [Source:UniProtKB/Swiss-Prot;Acc:B0KWT6]

Sequence

>retro_cjac_3272
ATGCAGCTGACGGTGAAGGCCTGCAGGGCCGCCAGTGCAGCCTGCAGGTGCCGGAGGATGAGCTGGTGTCCACGCTGAAG
CAGCTGGTGTCAGAGAAGCTGAACGTCCCCCTGCGCCAGCAGCAGCTGCTCTTCAAGGGCAAGGCCCTGGCAGATGGGAA
ACAACTCTCGGATTATTGCATCGAGCCCAACTCCAAGCTCAACCTAGTGGTCAAACCCCTGGAGAAGGTGCCACTAGCAG
AAGGCTCTGGCCGGAGACTGGCCGACTCCCCACCCCCTCAGGTCTGGCAGCTGATCTCCAAAGTCTTGGCCCACCACTTC
AGCGCAGCAGATGCCAGCATGGTCCTGGAACAGCTACAGAGGGATTACGAGAGGTCCCTGAGCCGCCTGACGCTGGACGA
CATCGAACCATTGGCTAGCCGCTTCTTGCACCCAGAAGCGACTGAGATGATGGAGAAGGGCTTCTCCAAA

Alignment

ORF - retro_cjac_3272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQLTVKA-LQGRDCSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNL
          MQLTVKA.LQGR.CSLQVPEDELVSTLKQLVSEKLNVP.RQQ.LLFKGKALADGK.LSDY.I.PNSKLNL
Retrocopy MQLTVKA<LQGRQCSLQVPEDELVSTLKQLVSEKLNVPLRQQQLLFKGKALADGKQLSDYCIEPNSKLNL

Parental  VVKPLEKVLLEEGTGRRLADSPPPQVWQLISKVLARHFSAADASRVLEQLQRDYERSLSRLTLDDIERLA
          VVKPLEKV.L.EG.GRRLADSPPPQVWQLISKVLA.HFSAADAS.VLEQLQRDYERSLSRLTLDDIE.LA
Retrocopy VVKPLEKVPLAEGSGRRLADSPPPQVWQLISKVLAHHFSAADASMVLEQLQRDYERSLSRLTLDDIEPLA

Parental  GRFLHPEVTETMEKGFSK
          .RFLHPE.TE.MEKGFSK
Retrocopy SRFLHPEATEMMEKGFSK

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	0.40 RPM	3.68 RPM
SRP051959_heart	0.00 RPM	4.33 RPM
SRP051959_kidney	0.00 RPM	3.17 RPM
SRP051959_liver	0.04 RPM	1.78 RPM
SRP051959_lung	0.02 RPM	4.93 RPM
SRP051959_lymph_node	0.05 RPM	4.86 RPM
SRP051959_skeletal_muscle	0.02 RPM	3.17 RPM
SRP051959_spleen	0.00 RPM	3.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3272 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3272 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3272 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005040	1 retrocopy	retro_acar_123,
Bos taurus	ENSBTAG00000014331	1 retrocopy	retro_btau_195,
Callithrix jacchus	ENSCJAG00000016805	1 retrocopy	retro_cjac_3272 ,
Ochotona princeps	ENSOPRG00000012645	1 retrocopy	retro_opri_714,
Rattus norvegicus	ENSRNOG00000037250	1 retrocopy	retro_rnor_2789,