RetrogeneDB ID: retro_ocun_920

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:62294385..62294949(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCL3
• Ensembl ID: ENSOCUG00000001469
• Aliases: None
• Description: phosducin-like 3 [Source:HGNC Symbol;Acc:28860]

Sequence

>retro_ocun_920
AAGGAGGTGGAAGAGGAGGCGGAGCAGGTGCTCCATCAGTCAGTAGTGAAATGTACGAACATGTGACTTGGAGAGAAGTG
AAACTAATGAACTTAAATTTAAGGAAGAGGATGAACTTGATATCAAAATGCTCAGGCAGCAAAGACTAGCTGAATGGAGA
GCAAATCAACCAAAGAGCAAATTTGGAGAAATTTTGAAGATTTTAGGAAAGGAATTTGTCCAAGATACTATCTAAATTCA
TAAGGACTTGTGGGTAGTCTGTCACCTATGCAAAGAAAGGATTTCCCCCTCTGTGCTCTGATAAAGCACACTTCTGTGGA
CCTGCCAGGAAGATTCCTGATATGAAATATATCAAAGCCATTTTAACAACCTGTGTACCCAGTTATCCTGATAGGAATCC
ACCTACAATATTCATTTACCCTGCAGGGGACACACAAAGTTGAGTTTACCGGTCCTCTGCTGTTTGGGGGCACAGACTTA
AGGAGAGATGAGCTGGAGTGGGAAGTGGCTGAGTCTGGGGGAATGAAGAAAGACCTGGAGGAAAACCCCAAGAAGCCAAC
TGAA

Alignment

ORF - retro_ocun_920 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.79 %
• Parental protein coverage: 78.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KQAEEEEERALQQSVVKT-YEDMT-LEELEDNEDEFNEEDERAIEMYRQQRLAEWRATQEKNKFGEVLEI
          K..EEE.E..L.QSVVK..YE..T.LE..E.NE..F.EEDE..I.M.RQQRLAEWRA.Q.K.KFGE.L.I
Retrocopy KEVEEEAEQVLHQSVVKC<YEHVT<LERSETNELKFKEEDELDIKMLRQQRLAEWRANQPKSKFGEILKI

Parental  SGKDYVQEVTKAGEGLWVILHLYKQ-GIP-LCALINQ-HFSALARKFPDVKFIKAISTTCIPNYPDRNLP
          .GK..VQ........LWV..HL.K..G.P.LCALI...HF...ARK.PD.K.IKAI.TTC.P.YPDRN.P
Retrocopy LGKEFVQDTI*IHKDLWVVCHLCKE>GFP>LCALIKH<HFCGPARKIPDMKYIKAILTTCVPSYPDRNPP

Parental  TVFVY-LEGEIKAQFVGPLVFGGMNLTRDELEWKLAKSGAIKTDLEENPRKPIE
          T.F.Y.L.G..K..F.GPL.FGG..L.RDELEW..A.SG..K.DLEENP.KP.E
Retrocopy TIFIY>LQGTHKVEFTGPLLFGGTDLRRDELEWEVAESGGMKKDLEENPKKPTE

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	20.20 RPM
SRP017611_kidney	0.00 RPM	21.79 RPM
SRP017611_liver	0.00 RPM	7.55 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_920 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_920 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_920 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002226	1 retrocopy	retro_cfam_1740,
Callithrix jacchus	ENSCJAG00000010160	3 retrocopies	retro_cjac_1486, retro_cjac_1599, retro_cjac_2055,
Dipodomys ordii	ENSDORG00000012397	1 retrocopy	retro_dord_702,
Erinaceus europaeus	ENSEEUG00000000224	1 retrocopy	retro_eeur_506,
Homo sapiens	ENSG00000115539	7 retrocopies	retro_hsap_1132, retro_hsap_151, retro_hsap_2684, retro_hsap_2757, retro_hsap_3535, retro_hsap_3961, retro_hsap_4102,
Myotis lucifugus	ENSMLUG00000016446	1 retrocopy	retro_mluc_1443,
Monodelphis domestica	ENSMODG00000001489	1 retrocopy	retro_mdom_734,
Mus musculus	ENSMUSG00000026078	1 retrocopy	retro_mmus_2284,
Nomascus leucogenys	ENSNLEG00000014393	8 retrocopies	retro_nleu_1499, retro_nleu_1575, retro_nleu_2741, retro_nleu_2891, retro_nleu_538, retro_nleu_571, retro_nleu_778, retro_nleu_926,
Oryctolagus cuniculus	ENSOCUG00000001469	2 retrocopies	retro_ocun_1035, retro_ocun_920 ,
Otolemur garnettii	ENSOGAG00000015138	2 retrocopies	retro_ogar_1147, retro_ogar_2959,
Ochotona princeps	ENSOPRG00000011600	2 retrocopies	retro_opri_1070, retro_opri_289,
Tursiops truncatus	ENSTTRG00000006242	1 retrocopy	retro_ttru_1184,