RetrogeneDB ID: retro_ocun_1130

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 20:5396953..5397800(+)
• Located in intron of: ENSOCUG00000000898

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC1A
• Ensembl ID: ENSOCUG00000003944
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 1A, 41kDa [Source:HGNC Symbol;Acc:703]

Sequence

>retro_ocun_1130
GCCTATGTGTGGAGTCAGAAAGTTGGAATCTGAAAGCCAACCCTAGTGATCCTGAGGATTAACTGTGTGTTAACTTTTGT
GATGCAGTCCTCCCTGGAGAACAAATTTGCTGTGGGAAGTGGAGCACAATTCATTTCTGTTTGTTACTTGAGTCTGAAAA
TGAATGGTATGTAAGCAAACACATCAAAAAGCCAAAACACTCCACAGTCCTCAGCTTGGACCGGCATCTAAACAGTGTTT
TGCTGGCAGCAAGAACCTGTAACTTCAAATGCTGAGTGTTTTCTGCCTACATTAAAGAAATGGATGAAAAGCCAGCCAGT
ATTCCCTGGAGCAGCAAGATGCCTTTTGGTCAGCTGCTGTCATAGTCTGGTGACAGTGCTATTGGTGGCTAGGTCCACAG
GGTCAGTTTCTCTGCCAGTGGAAATCTCCTGGCTTGGGCCAGTCATAGCACTGTATCCATTGTGGATGCATCAAAAAGCG
TGCAGGTCTCCACTCTGAAAACCAAGTTCCTGCCACTCCTCAGTGTGAACTTTGTCTCAGATAATAGCACTGTAGCTGCT
GGCCATGACTGCTGCCCAGTGTTCTTTAACTATGATGACCGCAGCTGCCTGACCTTTATCTCCAAGCTGGACATTCCAAA
ACAGAGCACCCAGTGCAATATGTCTGCCATGGAACGCTTTTGCAACACAGACAAGAAAGCCATGACCAAAGACTGCAACA
GGGCCCTGGAGGCGCTGTACCAGAACAGCATCACTCAAATGTCTATGAAGTGGATAAGCAAGATTGTTGCAAATTTTGCA
CAACTGGCATCCACGGAGCCATGACAATTTGAGATTTTAAGACCTTA

Alignment

ORF - retro_ocun_1130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.56 %
• Parental protein coverage: 77.03 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AYVWSQKDGVWKPTLVILRINRAATFVKWSPLENKFAVGSGARLISVCYF-ESENDWWVSKHIKKPIRST
          AYVWSQK.G..KPTLVILRIN...TFV..S.LENKFAVGSGA..ISVCY..ESEN.W.VSKHIKKP..ST
Retrocopy AYVWSQKVGI*KPTLVILRINCVLTFVMQSSLENKFAVGSGAQFISVCYL<ESENEWYVSKHIKKPKHST

Parental  VLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKPASTPWGSKMPFGQLMSEFGGSGTGGWVHGVSFSA
          VLSLD.H.N.VLLAA..C.FKC.VFSAYIKE.DEKPAS.PW.SKMPFGQL.S..G.S..GG.VH.VSFSA
Retrocopy VLSLDRHLNSVLLAARTCNFKC*VFSAYIKEMDEKPASIPWSSKMPFGQLLS*SGDSAIGG*VHRVSFSA

Parental  SGSRLAWVSHDSTVSVADASKSVQVSTLKTEFLPLLSVSFVSENSVVAAGHDCCPMLFNYDDRGCLTFVS
          SG..LAW.SH.STVS..DASKSVQVSTLKT.FLPLLSV.FVS.NS.VAAGHDCCP..FNYDDR.CLTF.S
Retrocopy SGNLLAWASH-STVSIVDASKSVQVSTLKTKFLPLLSVNFVSDNSTVAAGHDCCPVFFNYDDRSCLTFIS

Parental  KLDIPKQSIQRNMSAMERFRNMDKRATTEDRNTALETLHQNSITQVSIYEVDK-QDCRKFCTTGIDGAMT
          KLDIPKQS.Q.NMSAMERF.N.DK.A.T.D.N.ALE.L.QNSITQ.S.....K...C..FCTTGI.GAMT
Retrocopy KLDIPKQSTQCNMSAMERFCNTDKKAMTKDCNRALEALYQNSITQMSMKWISK<DCCK-FCTTGIHGAMT

Parental  IWDFKTL
          I.DFKTL
Retrocopy I*DFKTL

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	115.07 RPM
SRP017611_kidney	0.00 RPM	73.48 RPM
SRP017611_liver	0.08 RPM	36.15 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1130 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1130 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1130 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006322	1 retrocopy	retro_amel_1431,
Bos taurus	ENSBTAG00000004242	1 retrocopy	retro_btau_1486,
Callithrix jacchus	ENSCJAG00000015859	3 retrocopies	retro_cjac_2141, retro_cjac_2165, retro_cjac_2263,
Cavia porcellus	ENSCPOG00000001777	2 retrocopies	retro_cpor_452, retro_cpor_981,
Dasypus novemcinctus	ENSDNOG00000005984	5 retrocopies	retro_dnov_1615, retro_dnov_1839, retro_dnov_1966, retro_dnov_2257, retro_dnov_941,
Dipodomys ordii	ENSDORG00000016059	1 retrocopy	retro_dord_593,
Equus caballus	ENSECAG00000016467	1 retrocopy	retro_ecab_185,
Homo sapiens	ENSG00000241685	2 retrocopies	retro_hsap_2010, retro_hsap_3191,
Loxodonta africana	ENSLAFG00000014024	1 retrocopy	retro_lafr_1006,
Macropus eugenii	ENSMEUG00000005609	8 retrocopies	retro_meug_1033, retro_meug_1081, retro_meug_1495, retro_meug_1668, retro_meug_1755, retro_meug_1912, retro_meug_2179, retro_meug_492,
Myotis lucifugus	ENSMLUG00000010912	1 retrocopy	retro_mluc_1432,
Macaca mulatta	ENSMMUG00000019342	2 retrocopies	retro_mmul_1383, retro_mmul_2012,
Monodelphis domestica	ENSMODG00000001303	9 retrocopies	retro_mdom_1360, retro_mdom_1380, retro_mdom_1438, retro_mdom_1551, retro_mdom_1796, retro_mdom_1917, retro_mdom_686, retro_mdom_699, retro_mdom_808,
Mus musculus	ENSMUSG00000029621	1 retrocopy	retro_mmus_1373,
Nomascus leucogenys	ENSNLEG00000010852	2 retrocopies	retro_nleu_1663, retro_nleu_2069,
Oryctolagus cuniculus	ENSOCUG00000003944	1 retrocopy	retro_ocun_1130 ,
Otolemur garnettii	ENSOGAG00000010870	6 retrocopies	retro_ogar_1547, retro_ogar_2690, retro_ogar_2697, retro_ogar_381, retro_ogar_610, retro_ogar_656,
Pongo abelii	ENSPPYG00000025816	4 retrocopies	retro_pabe_1647, retro_pabe_1648, retro_pabe_2537, retro_pabe_2647,
Pan troglodytes	ENSPTRG00000033819	2 retrocopies	retro_ptro_1340, retro_ptro_2253,
Sarcophilus harrisii	ENSSHAG00000010673	2 retrocopies	retro_shar_180, retro_shar_727,
Sus scrofa	ENSSSCG00000007609	1 retrocopy	retro_sscr_387,
Ictidomys tridecemlineatus	ENSSTOG00000001660	1 retrocopy	retro_itri_1834,
Tupaia belangeri	ENSTBEG00000011381	3 retrocopies	retro_tbel_1237, retro_tbel_1241, retro_tbel_82,
Tursiops truncatus	ENSTTRG00000003002	4 retrocopies	retro_ttru_1621, retro_ttru_1838, retro_ttru_575, retro_ttru_853,