RetrogeneDB ID: retro_cjac_1573

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:70097959..70098291(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFU1
• Ensembl ID: ENSCJAG00000019156
• Aliases: None
• Description: NFU1 iron-sulfur cluster scaffold homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16287]

Sequence

>retro_cjac_1573
ATGGACTTCTTTGCATCTGGTTTACCACAGTTACTGAGCAAGGATCTTCATGAGAAGCGGGTCCGAGGATGGCGAACCTG
TGGCGATGACTGGGGAAGTGTTAGGTACTGGTCTACGGCCAACCGTGCAGGAAGAGGCAGGAACATGATCTACAAAAGCT
GTGAAGATGGCATCGTATGACTGAAAACTCCATGGTTCTTGTACCAGCTTCCCTAGTTCAATCATTACTCTGGAAATGGA
ATTCAGACATGCTGCAGTTTTACATTCCAGAGGTAGAAGGCATAGAACAGGTTATGGATGATGAATCAGATGAAAAGGAA
GCAAACGCACCT

Alignment

ORF - retro_cjac_1573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MDFFASGLP-LVTEETPSGEA-GSEEDDEVVAMIKELLDTRIRPTVQEDGG-DVIYKGFEDGIVQLK-LQ
          MDFFASGLP..VTE...S.EA.GSE.D.E.VAM..E.L.T..RPTVQE..G...IYK..EDGIV.LK.L.
Retrocopy MDFFASGLP<TVTEQGSS*EA<GSE-DGEPVAMTGEVLGTGLRPTVQEEAG<NMIYKSCEDGIV*LK>LH

Parental  GSCTSCPSSIITLK-NGIQ-NMLQFYIPEVEGVEQVMDDESDEKEANSP
          GSCTS.PSSIITL..NGIQ..MLQFYIPEVEG.EQVMDDESDEKEAN.P
Retrocopy GSCTSFPSSIITLE<NGIQ<DMLQFYIPEVEGIEQVMDDESDEKEANAP

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	0.02 RPM	3.15 RPM
SRP051959_heart	0.05 RPM	6.44 RPM
SRP051959_kidney	0.00 RPM	5.52 RPM
SRP051959_liver	0.00 RPM	4.87 RPM
SRP051959_lung	0.02 RPM	3.46 RPM
SRP051959_lymph_node	0.09 RPM	4.02 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.70 RPM
SRP051959_spleen	0.02 RPM	3.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1573 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1573 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1573 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005978	1 retrocopy	retro_chof_456,
Callithrix jacchus	ENSCJAG00000019156	1 retrocopy	retro_cjac_1573 ,
Echinops telfairi	ENSETEG00000019002	1 retrocopy	retro_etel_1371,
Homo sapiens	ENSG00000169599	1 retrocopy	retro_hsap_2638,
Macaca mulatta	ENSMMUG00000000435	1 retrocopy	retro_mmul_1524,
Monodelphis domestica	ENSMODG00000011805	1 retrocopy	retro_mdom_1395,
Mustela putorius furo	ENSMPUG00000006663	1 retrocopy	retro_mputfur_67,
Mus musculus	ENSMUSG00000029993	1 retrocopy	retro_mmus_1401,
Nomascus leucogenys	ENSNLEG00000010101	1 retrocopy	retro_nleu_646,
Ochotona princeps	ENSOPRG00000016760	2 retrocopies	retro_opri_380, retro_opri_48,
Pongo abelii	ENSPPYG00000012339	1 retrocopy	retro_pabe_2329,
Pan troglodytes	ENSPTRG00000012016	1 retrocopy	retro_ptro_1778,
Tupaia belangeri	ENSTBEG00000008616	1 retrocopy	retro_tbel_525,
Tarsius syrichta	ENSTSYG00000013765	1 retrocopy	retro_tsyr_108,