RetrogeneDB ID: retro_ocun_1874

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:10643287..10643585(+)
• Located in intron of: ENSOCUG00000015209

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP7
• Ensembl ID: ENSOCUG00000001497
• Aliases: None
• Description: fatty acid binding protein 7, brain [Source:HGNC Symbol;Acc:3562]

Sequence

>retro_ocun_1874
GCTGCCTGGGAGCCGACGGACAGGCAGAACTTTGAGTCCACAGAGGCTCTCCTTATGGATTTTGCCATGAGACAGGTGGG
AAATGTGACCCAACCATCAGTGATTATCAGTTGGAAAGGGGTCACAGTGGTGATTGGGGAGTATTGCACAAGAGAAGACG
GAGCTGAATTTCGACCTGGGAGAGGAGCTAGATGAAATCAGTACCAGTGGCAGAACCTCTGAGACTGTCGTTAGCTGGAG
TGGAGGCAAACTTGGTCACACACAGAAATGGGATGGCAAAGGAAAATGTTTTGTAAGA

Alignment

ORF - retro_ocun_1874 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.92 %
• Parental protein coverage: 76.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ATWKLTDSQNFDEYMKALGVGFATRQVGNVTKPTVIISQEGDKVVIRTQSTFKNTEISFR-LGEEFDEIS
          A.W..TD.QNF.E...AL...FA.RQVGNVT.P.VIIS..G..VVI....T.......FR.LGEE.DEIS
Retrocopy AAWEPTDRQNF-ESTEALLMDFAMRQVGNVTQPSVIISWKGVTVVIGEYCT-REDGAEFR>LGEELDEIS

Parental  VDDRNCKSVISLDGDKLVHVQKWDGKQTNFVR
          ...R....V.S..G.KL.H.QKWDGK...FVR
Retrocopy TSGRTSETVVSWSGGKLGHTQKWDGKGKCFVR

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	168.43 RPM
SRP017611_kidney	0.00 RPM	14.80 RPM
SRP017611_liver	0.00 RPM	33.91 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1874 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1874 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1874 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014056	1 retrocopy	retro_cpor_34,
Homo sapiens	ENSG00000164434	1 retrocopy	retro_hsap_536,
Gorilla gorilla	ENSGGOG00000025475	1 retrocopy	retro_ggor_489,
Macaca mulatta	ENSMMUG00000021907	1 retrocopy	retro_mmul_458,
Oryctolagus cuniculus	ENSOCUG00000001497	1 retrocopy	retro_ocun_1874 ,
Oryctolagus cuniculus	ENSOCUG00000008146	1 retrocopy	retro_ocun_985,
Otolemur garnettii	ENSOGAG00000031110	1 retrocopy	retro_ogar_2821,
Ochotona princeps	ENSOPRG00000000992	1 retrocopy	retro_opri_840,
Pongo abelii	ENSPPYG00000016979	1 retrocopy	retro_pabe_213,
Pan troglodytes	ENSPTRG00000018564	1 retrocopy	retro_ptro_402,
Sarcophilus harrisii	ENSSHAG00000003313	1 retrocopy	retro_shar_521,