RetrogeneDB ID: retro_cjac_2028

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:29646588..29646915(+)
• Located in intron of: ENSCJAG00000013778

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDX1
• Ensembl ID: ENSCJAG00000010395
• Aliases: None
• Description: ferredoxin 1 [Source:HGNC Symbol;Acc:3638]

Sequence

>retro_cjac_2028
AACAGTGAAACATTAACAAACAAAGGAAAAGTTGATGATGCTCTGTTAGATGTTGTGGTTGAAAATAATCTAGATATTAA
TAGGTTTGTTGCAGGGGAGGGAACCTTGGCTTGCTCTGTCTGTCACCTCGTCTTTGAAAAACACATATTTGAGAAGTTAG
ACACAATCACTGACAAGGAGATTGATATGCTTGATCTGGCATATGGACTGACGGACAGATCAGAGTTGCATTGCCAAATC
TGTTTGACAAAATCTATGGACCATATGACTATGAGTACCTGAGGAGTGGCCAGTGCCAGACCATCCATTGATATGGGCAA
GACCACC

Alignment

ORF - retro_cjac_2028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.64 %
• Parental protein coverage: 63.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DGETLTTKGKVGDSLLDVVVENNLDIDGFGACEGTLACSTCHLIFEDHIFEKLDAITDEENDMLDLAYGL
          ..ETLT.KGKV.D.LLDVVVENNLDI..F.A.EGTLACS.CHL.FE.HIFEKLD.ITD.E.DMLDLAYGL
Retrocopy NSETLTNKGKVDDALLDVVVENNLDINRFVAGEGTLACSVCHLVFEKHIFEKLDTITDKEIDMLDLAYGL

Parental  TDRSRLGCQICLTKSMDNMTVRVPETVADARQSVDVGKTS
          TDRS.L.CQICLTKSMD.MT......VA.AR.S.D.GKT.
Retrocopy TDRSELHCQICLTKSMDHMTMST-*GVASARPSIDMGKTT

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	0.09 RPM	6.48 RPM
SRP051959_heart	0.25 RPM	6.30 RPM
SRP051959_kidney	0.04 RPM	9.72 RPM
SRP051959_liver	0.06 RPM	30.71 RPM
SRP051959_lung	0.42 RPM	5.99 RPM
SRP051959_lymph_node	0.05 RPM	3.47 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.26 RPM
SRP051959_spleen	0.06 RPM	4.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2028 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2028 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2028 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2501
Gorilla gorilla	retro_ggor_1560
Pan troglodytes	retro_ptro_1452
Pongo abelii	retro_pabe_1841

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010395	1 retrocopy	retro_cjac_2028 ,
Callithrix jacchus	ENSCJAG00000037004	1 retrocopy	retro_cjac_1753,
Homo sapiens	ENSG00000137714	2 retrocopies	retro_hsap_2472, retro_hsap_2501,
Gorilla gorilla	ENSGGOG00000022443	1 retrocopy	retro_ggor_1560,
Nomascus leucogenys	ENSNLEG00000007249	1 retrocopy	retro_nleu_1432,
Oryctolagus cuniculus	ENSOCUG00000017826	1 retrocopy	retro_ocun_1907,
Pongo abelii	ENSPPYG00000003853	2 retrocopies	retro_pabe_1822, retro_pabe_1841,
Pan troglodytes	ENSPTRG00000004260	2 retrocopies	retro_ptro_1428, retro_ptro_1452,