RetrogeneDB ID: retro_cjac_3948

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286373.1:198356..198669(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNPH1
• Ensembl ID: ENSCJAG00000005337
• Aliases: None
• Description: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 [Source:HGNC Symbol;Acc:21218]

Sequence

>retro_cjac_3948
GATAAGGCTGCTGGGGGTGACAGGCTTATCCATGAACAGTACTTGGCGTGGCTGCTGCAGGCTAATGTGGTCGTGGCAGA
AGTGAAACAGCCATCCTTGGGTGCAGGCTATGAGCTGGGCCAGGCCATGGCCCTCCACAGCTAATCCTGTTCGTGCTCCA
GCCGCAGTCTGGCAGAGTGCTGTTGGCCATGATCTGGGCAACAGCAGATGGCTCTGGGTTCCAGGTGTGGTCCTATGGAC
AGGGAGGGTGGAGGTCCTGTTGGATGGAAAGGCTGAGGCAGAACCTCCTGAGCAGGTTGCCTCCCCCAACCCA

Alignment

ORF - retro_cjac_3948 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.81 %
• Parental protein coverage: 60.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEAAGDDRLIHEQDLAWLQQADRVVAEVTQPSLGVGYELGRAVALN-KRILCLFRPQSGRVLSAMIRGAA
          ..AAG.DRLIHEQ.LAWL.QA..VVAEV.QPSLG.GYELG.A.AL....IL....PQSGRVL.AMI...A
Retrocopy DKAAGGDRLIHEQYLAWLLQANVVVAEVKQPSLGAGYELGQAMALH<QLILFVLQPQSGRVLLAMIWATA

Parental  DGSRIQVWDYEE-GEVEALLDRYFEADPPGQVAASPDP
          DGS..QVW.Y...G.VE.LLD...EA.PP.QV.ASP.P
Retrocopy DGSGFQVWSYGQ<GRVEVLLDGKAEAEPPEQV-ASPNP

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	1.00 RPM
SRP051959_heart	0.00 RPM	0.33 RPM
SRP051959_kidney	0.04 RPM	0.42 RPM
SRP051959_liver	0.35 RPM	0.80 RPM
SRP051959_lung	0.00 RPM	0.13 RPM
SRP051959_lymph_node	0.02 RPM	0.41 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.09 RPM
SRP051959_spleen	0.00 RPM	0.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3948 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3948 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3948 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012390	1 retrocopy	retro_amel_1012,
Bos taurus	ENSBTAG00000019913	1 retrocopy	retro_btau_518,
Canis familiaris	ENSCAFG00000001837	1 retrocopy	retro_cfam_1148,
Callithrix jacchus	ENSCJAG00000005337	1 retrocopy	retro_cjac_3948 ,
Equus caballus	ENSECAG00000006660	1 retrocopy	retro_ecab_595,
Felis catus	ENSFCAG00000009722	1 retrocopy	retro_fcat_365,
Homo sapiens	ENSG00000112667	1 retrocopy	retro_hsap_2562,
Nomascus leucogenys	ENSNLEG00000000516	1 retrocopy	retro_nleu_1515,
Pongo abelii	ENSPPYG00000016635	1 retrocopy	retro_pabe_1888,
Pan troglodytes	ENSPTRG00000029662	1 retrocopy	retro_ptro_1493,
Pteropus vampyrus	ENSPVAG00000008743	1 retrocopy	retro_pvam_1400,
Rattus norvegicus	ENSRNOG00000018397	1 retrocopy	retro_rnor_580,
Tursiops truncatus	ENSTTRG00000007022	1 retrocopy	retro_ttru_1520,