RetrogeneDB ID: retro_ocun_320

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:163370885..163371702(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTR3C
• Ensembl ID: ENSOCUG00000000459
• Aliases: None
• Description: ARP3 actin-related protein 3 homolog C (yeast) [Source:HGNC Symbol;Acc:37282]

Sequence

>retro_ocun_320
TGTGTGGTAGACTGTGGCATGGGGTGTATAAAACTAGGAAATGCTGGAAATACAGAACCACAGTTTATCATCTCTTCCTG
TAATGCTGTTAAGGAGTCAGAAAAGTGAGTGATCAGGCTCAATGGAGGGTGATGAAAAGTGTTGATGACCTAGACTTTTT
CATTGGTGATAAAGCAATAGAAAAACCTATATATGCAACAAAGTAGCCAATTCACCACGGTATAGTTGAAGGTTGGAATT
TGATGGAAAGGTTTATGGAACAAGTGATCTTTAAATGTTTAAGGGCAGAACCTGAAGATCATTATTTTCTTTTGACTGAA
CCTCAACTGAATACTCCAGAAAACAAGGGATATACTGCTGAAATAATGTTTTAGTCTTTCAGTGTTTCAGGCATGTACAT
TACTGTGCAGACTGTTCTTGACTTAGCGCATCCTGGACCTCAGTACAAGTAGAACAGACATTGACTGGTATGGTAATAAG
ACAGTGGAGATGGTGTCACTAATGTCATTCCTGTGGCTGAAGGGTATGTGATTGGCAGCTGTATTAAACACATTGAATTG
CACGATGGGATATAACATAGTAGATTCAGCAACTGCTGAGAGACTAAGAAGTAGGAATCCTTTCAGAACAATCCCTTGAA
ACTGCTAAGGTAGAATGAGTGCTATAGATATTCCCAGATTTAATAAAGGAACTTAACAATTATGACACAGATGCATCAAA
GTGGGTTAAGCAATATATTGGAATCAATACTATCGCTAAGAAAGAATTTTCCATTGATGTTGGTTATGAGAGATTCCTGG
GACCTGAAGTTTTTTTT

Alignment

ORF - retro_ocun_320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.14 %
• Parental protein coverage: 66.03 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CVVDCGTGYTKLGYAGNTEPQFIIPSCIAIRESAK-VVDQAQRRVLRGVDDLDFFIGDEAIDKPTYATKW
          CVVDCG.G..KLG.AGNTEPQFII.SC.A..ES.K.V.DQAQ.RV...VDDLDFFIGD.AI.KP.YATK.
Retrocopy CVVDCGMGCIKLGNAGNTEPQFIISSCNAVKESEK<VSDQAQWRVMKSVDDLDFFIGDKAIEKPIYATK*

Parental  PIRHGIIEDWDLMERFMEQVVFKYLRAEPEDHYFLMTEPPLNTPENREYLAEIMFESFNVPGLYIAVQAV
          PI.HGI.E.W.LMERFMEQV.FK.LRAEPEDHYFL.TEP.LNTPEN..Y.AEIMF.SF.V.G.YI.VQ.V
Retrocopy PIHHGIVEGWNLMERFMEQVIFKCLRAEPEDHYFLLTEPQLNTPENKGYTAEIMF*SFSVSGMYITVQTV

Parental  LALA-ASWTSRQVGERTLTGIVI-DSGDGVTHVIPVAEGYVIGSCIKHIP-IAGRDITYFIQQLLREREV
          L.LA.ASWTS.QV.E.TLTG.VI.DSGDGVT.VIPVAEGYVIGSCIKHI..IA..DIT..IQQLLR..EV
Retrocopy LDLA<ASWTSVQV-EQTLTGMVI>DSGDGVTNVIPVAEGYVIGSCIKHIE<IARWDIT**IQQLLRD*EV

Parental  GIPPEQSLETAKAIKEKYCYICPDIVKEFAKYDMDPRKWIKQYTGINAINQKKFIIDVGYERFLGPEIFF
          GI..EQSLETAK...E....I.PD..KE...YD.D..KW.KQY.GIN.I..K.F.IDVGYERFLGPE.FF
Retrocopy GILSEQSLETAKV--E*VL*IFPDLIKELNNYDTDASKWVKQYIGINTIAKKEFSIDVGYERFLGPEVFF

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	85.98 RPM
SRP017611_kidney	0.00 RPM	16.22 RPM
SRP017611_liver	0.00 RPM	8.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_320 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_320 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_320 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007730	5 retrocopies	retro_chof_1134, retro_chof_1204, retro_chof_1899, retro_chof_208, retro_chof_2171,
Dasypus novemcinctus	ENSDNOG00000019288	2 retrocopies	retro_dnov_1143, retro_dnov_2539,
Homo sapiens	ENSG00000133627	7 retrocopies	retro_hsap_1676, retro_hsap_2126, retro_hsap_2540, retro_hsap_2966, retro_hsap_4334, retro_hsap_4921, retro_hsap_561,
Macropus eugenii	ENSMEUG00000004885	5 retrocopies	retro_meug_1340, retro_meug_1477, retro_meug_2105, retro_meug_330, retro_meug_899,
Oryctolagus cuniculus	ENSOCUG00000000459	1 retrocopy	retro_ocun_320 ,
Otolemur garnettii	ENSOGAG00000003249	2 retrocopies	retro_ogar_1307, retro_ogar_3388,