RetrogeneDB ID: retro_ocun_1907

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:100822150..100822448(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDX1
• Ensembl ID: ENSOCUG00000017826
• Aliases: None
• Description: ferredoxin 1 [Source:HGNC Symbol;Acc:3638]

Sequence

>retro_ocun_1907
TCAGAAGAAAAAGGTACAATACACTTTATAAACCGTGAGGGTGCAACATTAACAACCAAAAGCAAAGTTGGTGACTCTCT
GCTAGATGTTGTGGTTCAAAAGAATCTAGATATTGATGGTTTGGGTGCTTGTGAGGGAACCCAGGGCCTGCTCTACCTGC
CAACTCATCTTTGAAGAGCACATATACGACAAGTTACAGCCAGTCACTAATGACAATGACATGCTTGATCTGGTGCATGG
ACGTACAGACGAATCACTGTTGGGCTGCCAAATCTGTTTGACAAAATCTATGGACAAT

Alignment

ORF - retro_ocun_1907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.21 %
• Parental protein coverage: 69.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SEDKVTVHFINRDGETLTAKGKVGDSLLDVVVENNLDIDGFGACEGT-LACSTCHLIFEEHIYDKLQPVT
          SE.K.T.HFINR.G.TLT.K.KVGDSLLDVVV..NLDIDG.GACEGT..ACSTC.LIFEEHIYDKLQPVT
Retrocopy SEEKGTIHFINREGATLTTKSKVGDSLLDVVVQKNLDIDGLGACEGT>RACSTCQLIFEEHIYDKLQPVT

Parental  DEENDMLDLAYGLTDRSRLGCQICLTKSMDN
          ...NDMLDL..G.TD.S.LGCQICLTKSMDN
Retrocopy N-DNDMLDLVHGRTDESLLGCQICLTKSMDN

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
SRP017611_brain	0.00 RPM	6.40 RPM
SRP017611_kidney	0.00 RPM	32.03 RPM
SRP017611_liver	0.00 RPM	36.53 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1907 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1907 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1907 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010395	1 retrocopy	retro_cjac_2028,
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,