RetrogeneDB ID: retro_cjac_4056

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:43620722..43621220(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAP2
• Ensembl ID: ENSCJAG00000015470
• Aliases: None
• Description: post-GPI attachment to proteins 2 [Source:HGNC Symbol;Acc:17893]

Sequence

>retro_cjac_4056
GCGCAGAGACTCGGGCTGCGGGAGCTTGGGCCAATCAGAGGGACAGCCCGAGAATGGCATGGTGATGGAATGCAGCTGAG
AGGTCTGACAAGATGTACCAGGTCCCACTGCCACTGGACCGGGATGGGACCCTGGTACGGCTTCACCTTGGTTGCCCTGG
TCACGATCTGCTGTCCACTTGTCGCCGCTTTCCTCTTCTGCATCCTCTTGTCCCTGATCTTCCACTTCAAGGAGACAATG
GCCACTCACTGTGGGGTGCCCTCAGTGAGCTCGGCCATCAGCGGGGAAGTGCCCCCGCACTACGTGTGGCGTTTCTGCAT
CGGCCTGCACTCAGCGCCTCACTTCTTGGTGGCCTTTGCCTATAGGAACCACTACCTCAGCTGCACCTCCCCATGTTCCT
GCTACCGCCCACTCTGCCCCACCAACTTCGGACTCAATGTCTTGGAGAACCTTGCGTTGCTAGTGCTCACTTACATCTCC
TCCTCTGAGGACTTCACT

Alignment

ORF - retro_cjac_4056 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.31 %
• Parental protein coverage: 55.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ALRLRLRELGPMRGTAPEWHGK-WNAAERSDKMYQVPLPLDRDGTLVRLR-FTLVALVTVCCPLVA-FLF
          A.RL.LRELGP.RGTA.EWHG..WNAAERSDKMYQV..PL..D......R.FTLVALVT.CCPLVA.FLF
Retrocopy AQRLGLRELGPIRGTAREWHGD<WNAAERSDKMYQV--PLPLDRDGTLVR>FTLVALVTICCPLVAAFLF

Parental  CILWSLLFHFKETTATHCGVPNYLPSVSSAIGGEVPQRYVWRFCIGLHSAPRFLVAFAYWNHYLSCASPC
          CIL.SL.FHFKET.ATHCGV....PSVSSAI.GEVP..YVWRFCIGLHSAP.FLVAFAY.NHYLSC.SPC
Retrocopy CILLSLIFHFKETMATHCGV----PSVSSAISGEVPPHYVWRFCIGLHSAPHFLVAFAYRNHYLSCTSPC

Parental  SCYRPLCRINFGLNVVENLALLVLTYVSSSEDFT
          SCYRPLC..NFGLNV.ENLALLVLTY.SSSEDFT
Retrocopy SCYRPLCPTNFGLNVLENLALLVLTYISSSEDFT

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	4.30 RPM
SRP051959_heart	0.00 RPM	5.84 RPM
SRP051959_kidney	0.00 RPM	7.70 RPM
SRP051959_liver	0.00 RPM	4.79 RPM
SRP051959_lung	0.00 RPM	8.25 RPM
SRP051959_lymph_node	0.00 RPM	7.85 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.16 RPM
SRP051959_spleen	0.00 RPM	7.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4056 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4056 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4056 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015470	1 retrocopy	retro_cjac_4056 ,
Macropus eugenii	ENSMEUG00000009912	1 retrocopy	retro_meug_2064,
Rattus norvegicus	ENSRNOG00000020371	1 retrocopy	retro_rnor_2731,