RetrogeneDB ID: retro_cjac_2588

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:4559982..4560410(-)
• Located in intron of: ENSCJAG00000015717

Retrocopy information

• Ensembl ID: ENSCJAG00000032009
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000003896
• Aliases: None
• Description: Glutathione peroxidase [Source:UniProtKB/TrEMBL;Acc:F6T6G6]

Sequence

>retro_cjac_2588
ATGAACAAGCTGCAGTGGCGCCTTGGGCCCAGTGACCTGGTGGTTCTCGGCTTCCCGTGCAACCAGTTTGGGCATCAGGA
GAACACCAAGAAAGAAGAGATTCTGAATTCCCTAAAGTACGTCCAACCTCGTGGTGGGTTCCAGCCCAACTTCTCGTTCT
TTGAAAAGTGCGAGGTCAACGGTGTAAGGTCGCACCCTCTCTTAGCCTTCCTGTGGAGGCCCTGCCAGTGCCCAGCAATG
ACGCCACGGCACTCATGACCGACCCGGTCTTCAGTGTCTCTAATGTGTGGCAACGATGTTGCCTGGAACTTCAAGAAGTT
CCTGGATGGCCCTGCCGGTGCCCCCGTGCACAGGTACAGCCGCGCTTCCAGACCATTGACATTGAGGCTGACATCCAAGC
CCTGTTGTCCCAACGGTCCAGCCATGCC

Alignment

ORF - retro_cjac_2588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNELQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNSAGSHPLFAF
          MN.LQ.RLGP..LVVLGFPCNQFGHQEN.K.EEILNSLKYV.P.GGF.PNF..FEKCEVN...SHPL.AF
Retrocopy MNKLQWRLGPSDLVVLGFPCNQFGHQENTKKEEILNSLKYVQPRGGFQPNFSFFEKCEVNGVRSHPLLAF

Parental  LREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVGPDGIPVRRYSR-RFQTIDIEPDIEALLS
          L......P....T.....P.....S..C.NDVAWNF.KFL.GP.G.PV.RYSR.RFQTIDIE.DI.ALLS
Retrocopy LWRPCQCPA--MTPRHS*PTRSSVSLMCGNDVAWNFKKFLDGPAGAPVHRYSR<RFQTIDIEADIQALLS

Parental  QGPSCA
          Q..S.A
Retrocopy QRSSHA

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	0.35 RPM	18.88 RPM
SRP051959_heart	0.61 RPM	18.19 RPM
SRP051959_kidney	0.44 RPM	27.11 RPM
SRP051959_liver	0.19 RPM	33.79 RPM
SRP051959_lung	0.44 RPM	11.63 RPM
SRP051959_lymph_node	0.82 RPM	11.67 RPM
SRP051959_skeletal_muscle	0.33 RPM	14.00 RPM
SRP051959_spleen	0.50 RPM	16.30 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2588 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2588 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2588 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003896	6 retrocopies	retro_cjac_217, retro_cjac_2588 , retro_cjac_2764, retro_cjac_3464, retro_cjac_447, retro_cjac_448,