RetrogeneDB ID: retro_ocun_1902

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:78067296..78067958(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EGLN3
• Ensembl ID: ENSOCUG00000008560
• Aliases: None
• Description: egl nine homolog 3 (C. elegans) [Source:HGNC Symbol;Acc:14661]

Sequence

>retro_ocun_1902
GTGGGTCCCTGCCTCCTTGGGGGCACACTGAGCGTCCCTGACTTCAGTCTTGTGGGCAACATGACCCTGGGACATATTTT
GAGCCTGGATCTGGAGAAAATTGCCCTTAAGTACGTTGTGCCCTGCCTGTATACCAGGTGAGCTTCTGATACCTGGACAA
CTTCCTGGGGGCGGTGGTAGGTGCCTCCATGCTTGAGGGAGTCAAGCCCTGCATTACTATGCACCTTGCAGGATAGCCAG
CTGGCCCGGCTGCGCTGGCACTTCCTAGTGGCACCTGCAGAGCAACCAGGCCATGTGGATTCCAGACACCAAGGAGGGCT
ACAATCCATCAGCTTCCTCTTGGTTCATCATGGACAAACTGGTCCTGTACTGCAGAAGCCAACTTGGAAAATGTAACGTC
AAGGAGAGGTCTAAGGCAATGGTGACTTGCTGTACAGGAAATGGAACAGATGGTATTCGCCATGTAGACAGCCCCAAACT
ATGATGGCTGCTGTATCACCTACACCTATTATCTAAACAGGAACTGGAATGCCAAGCTAGCCAGTGGGATCTTGCGAATA
TTTGCATAAGGTAAATCATTCATAGCAGATGTGAATGCCATTTTTGGCAGTCTCCTGTTCTGGTCAGATCGCAGGAACTC
ACATGAAGTCCAATCTTCCTAC

Alignment

ORF - retro_ocun_1902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.07 %
• Parental protein coverage: 57.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VAPLVPVRTWGVPALRPAGEMPLSHIMSQDLE-KIAVDYIVPC-LHEVGFCYLDNFLGEVVGNCVLERV-
          V.P.....T..VP.....G.M.L.HI.S.DLE.K.......P.....V.F.YLDNFLG.VVG...LE.V.
Retrocopy VGPCLLGGTLSVPDFSLVGNMTLGHILSLDLE>KLPLSTLCPA>VYQVSF*YLDNFLGAVVGASMLEGV<

Parental  KQLHREGALRDGQLAGPRSGVSKRHLRGDQITWIGGNEKG-CEAISFLLS-LIDRLVLYCGSRLGKYYVK
          ..LH.....R.....G...G.S..HL...Q..WI.....G....ISFLL....D.LVLYC.S.LGK..VK
Retrocopy QALHYYAPCRIASWPGC-AGTS*WHLQSNQAMWIPDTKEG<LQSISFLLV>IMDKLVLYCRSQLGKCNVK

Parental  ERSKAMVACYPGNGAGYVRHVDN-PNGDGRCITCIYYLNKNWDAKLHGGILRIFPEGKSFVADVEPIFDR
          ERSKAMV.C..GNG....RHVD..PN.DG.CIT..YYLN.NW.AKL..GILRIF..GKSF.ADV..IF..
Retrocopy ERSKAMVTCCTGNGTDGIRHVDS>PNYDGCCITYTYYLNRNWNAKLASGILRIFA*GKSFIADVNAIFGS

Parental  LLFFWSDRRNPHEVQPSY
          LL.FWSDRRN.HEVQ.SY
Retrocopy LL-FWSDRRNSHEVQSSY

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	25.28 RPM
SRP017611_kidney	0.00 RPM	62.84 RPM
SRP017611_liver	0.00 RPM	1.93 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1902 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1902 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1902 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000129521	1 retrocopy	retro_hsap_1088,
Macaca mulatta	ENSMMUG00000000040	1 retrocopy	retro_mmul_845,
Nomascus leucogenys	ENSNLEG00000003247	1 retrocopy	retro_nleu_1623,
Oryctolagus cuniculus	ENSOCUG00000008560	1 retrocopy	retro_ocun_1902 ,
Pongo abelii	ENSPPYG00000005732	1 retrocopy	retro_pabe_906,
Pan troglodytes	ENSPTRG00000006250	1 retrocopy	retro_ptro_740,