RetrogeneDB ID: retro_cjac_1300

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:77847373..77847850(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDPN
• Ensembl ID: ENSCJAG00000013772
• Aliases: None
• Description: None

Sequence

>retro_cjac_1300
ATGTGGAAGGTGTCAGCTCTACTCTTCATTTTGGGGAGCCGATGCTCTGGGTCCCGGCAGAGAGGAGCCAGCATGGGCCA
GCCAGAAGATGACATTGAGACTCCAGGTACAGAAGGCAGCATTGTGATGCCAGGTGCCGAAGATGATGTGGTGACCCCAG
GAGCTGGTGAAGACCTCTCTACGGCTGGCTTGACAACTCTGGTGGCAATGAGTGTCAAGAGTGTGACCGACACTGGCCCC
GAGGATCTGCCAACTCCAGAAAGCACAGCACACACCAAAGAAGGAAGTCCGAGCACCACAACCTCAAACGTGGCAACCAG
TCCCTCCAGGGAGAAAGTGGATGGAGAGACACAGATAACAGTTGACAAGGATGGTTTGGCAACAGTGACCCTGGTCGGAA
TTATAGTTGGGGTCTTACTAGCCATTGGCTTCATTGGCGGAATCACCGTGGTGGTTATGCGAAAAATGTCTGGAAGG

Alignment

ORF - retro_cjac_1300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.68 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MWKVSALLFVLGSAS-LWVLAE-GASTGQPEDDIETPGTEGSIVMPGAEDDVLTPGAGEDLSTAGLTTLV
          MWKVSALLF.LGS...LWV.AE.GAS.GQPEDDIETPGTEGSIVMPGAEDDV.TPGAGEDLSTAGLTTLV
Retrocopy MWKVSALLFILGSRC<LWVPAE>GASMGQPEDDIETPGTEGSIVMPGAEDDVVTPGAGEDLSTAGLTTLV

Parental  ATSVKSVTDIGPEDLPTPESTAHPEEGSPSTTTSNMATSHSREKVDGETQITVDKDGLATVTLVGIIVGV
          A.SVKSVTD.GPEDLPTPESTAH..EGSPSTTTSN.ATS.SREKVDGETQITVDKDGLATVTLVGIIVGV
Retrocopy AMSVKSVTDTGPEDLPTPESTAHTKEGSPSTTTSNVATSPSREKVDGETQITVDKDGLATVTLVGIIVGV

Parental  LLAIGFIGGIIVVVMRKMSGR
          LLAIGFIGGI.VVVMRKMSGR
Retrocopy LLAIGFIGGITVVVMRKMSGR

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	7.99 RPM
SRP051959_heart	0.00 RPM	1.40 RPM
SRP051959_kidney	0.02 RPM	0.73 RPM
SRP051959_liver	0.00 RPM	0.06 RPM
SRP051959_lung	0.00 RPM	17.05 RPM
SRP051959_lymph_node	0.00 RPM	1.05 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.50 RPM
SRP051959_spleen	0.00 RPM	0.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1300 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1300 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007003	3 retrocopies	retro_chof_1612, retro_chof_2419, retro_chof_583,
Callithrix jacchus	ENSCJAG00000013772	1 retrocopy	retro_cjac_1300 ,
Mus musculus	ENSMUSG00000028583	1 retrocopy	retro_mmus_774,
Pteropus vampyrus	ENSPVAG00000011180	1 retrocopy	retro_pvam_1402,
Tarsius syrichta	ENSTSYG00000005667	1 retrocopy	retro_tsyr_1571,