RetrogeneDB ID: retro_ocun_277

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:23795540..23796080(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARG2
• Ensembl ID: ENSOCUG00000000584
• Aliases: None
• Description: arginase, type II (ARG2), nuclear gene encoding mitochondrial protein, mRNA [Source:RefSeq mRNA;Acc:NM_001082181]

Sequence

>retro_ocun_277
GATCTTTTTGTTGTCTGGGTTGATGCTCATGGTGACATAAATACATCCCTCACTACTTCGCCAAGAATTCTTTGTGGACA
GCCAGTGTCATTTCTTCTCAGACAACTACTGGACAAGTTACCACAAATCTCAAGATTTTCCTGAATCAAACTTTGTATCT
CTTCCTCAGGTATTGTGTATATTGGTCTAAGAGACATGGTCCCTCCTGAACATTTTATTTTAAAGAACTATGATATCCAG
TATTTTTCTATAAGAGATATTGATCAACTTGGTATCCAGATTGTCATGGAATAGACATTTGATCCCCTGACTGGCAAAAG
ACAAAGGGTAATCCATCTGAGATTTGATATTGAAGCATTTGATCCTACACTGCCTCAAACCAAGGGAACCCATGTTTCCA
GGGAACTAACCTATCAAGAAATCATGCACATTATTTAGGATGTACATAAATAAGGGCTTCTGTCATCACTGGACCTTTTT
GAAGTCAATCTTTGCTTAGCTGCTTGAGAGGAAGAGGTGAAGGCTACAGCTAGCCTGGCA

Alignment

ORF - retro_ocun_277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.56 %
• Parental protein coverage: 50.85 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLCVVWVDAHADINTPLTTSSGNLHGQPVSFLLRELQDKVPQLPGFSWIKPCISSPSIVYIGLRDVDPPE
          DL.VVWVDAH.DINT.LTTS...L.GQPVSFLLR.L.DK.PQ...FS.IK.CISS..IVYIGLRD..PPE
Retrocopy DLFVVWVDAHGDINTSLTTSPRILCGQPVSFLLRQLLDKLPQISRFS*IKLCISSSGIVYIGLRDMVPPE

Parental  HFILKKYDIQYFSMRDIDRLGIQKVMEQTFDLLIGKRQRPIHLSFDIDAFDPTLAPATGTPVVGGLTYRE
          HFILK.YDIQYFS.RDID.LGIQ.VME.TFD.L.GKRQR.IHL.FDI.AFDPTL....GT.V...LTY.E
Retrocopy HFILKNYDIQYFSIRDIDQLGIQIVME*TFDPLTGKRQRVIHLRFDIEAFDPTLPQTKGTHVSRELTYQE

Parental  GMYISEEIHNTGLLSALDLVEVNPRLAASDEEAKATASLA
          .M.I....H..GLLS.LDL.EVN..LAA..EE.KATASLA
Retrocopy IMHII*DVHK*GLLSSLDLFEVNLCLAA*EEEVKATASLA

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	28.04 RPM
SRP017611_kidney	0.00 RPM	86.76 RPM
SRP017611_liver	0.00 RPM	6.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_277 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_277 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_277 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005722	1 retrocopy	retro_acar_91,
Choloepus hoffmanni	ENSCHOG00000007159	1 retrocopy	retro_chof_1179,
Callithrix jacchus	ENSCJAG00000015277	4 retrocopies	retro_cjac_1933, retro_cjac_2357, retro_cjac_2561, retro_cjac_902,
Dasypus novemcinctus	ENSDNOG00000004808	1 retrocopy	retro_dnov_251,
Homo sapiens	ENSG00000081181	1 retrocopy	retro_hsap_3501,
Gorilla gorilla	ENSGGOG00000005615	1 retrocopy	retro_ggor_2367,
Microcebus murinus	ENSMICG00000010837	1 retrocopy	retro_mmur_874,
Monodelphis domestica	ENSMODG00000009978	1 retrocopy	retro_mdom_257,
Nomascus leucogenys	ENSNLEG00000000741	2 retrocopies	retro_nleu_2875, retro_nleu_792,
Oryctolagus cuniculus	ENSOCUG00000000584	1 retrocopy	retro_ocun_277 ,
Pongo abelii	ENSPPYG00000005926	1 retrocopy	retro_pabe_2893,
Pan troglodytes	ENSPTRG00000006467	1 retrocopy	retro_ptro_2373,