RetrogeneDB ID: retro_ocun_1035

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:36620431..36621075(+)
• 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_1035
CGAGTGGAGGGCATCCTGCCCTCAAAGGGGAGTCTGAAAGAGTTGGGAAAGGAGGCGGCGGAGAGGAGGAACAAGTGCTC
CAGCAGTCAGTGGTCAGACATATGAAGATACGCCACTGGAAGAACTGGACGGCAATGAAGATGAATTTAATGAAGTGGAA
GAATGTGCTATTGAAACGTACAGGCAGCAAAGACTGGCTGAGTGGAGAGCAACTCAAGAAAAGAATAAATTTGAAGAAGT
TTTAGAGATTTCAGGAAAAGATTACATCTGAGAAGTTACCAAAGCTGGTGAGGACTTCTGGGTAATCTTGCACCTTTACC
AACAAAGGATTCCCCCTGTGCCCTGATAAATCAACACTCTGGTGGACTTGCCAGGAAGTTTCCTGATACGAAGTTTATCA
AAACCATCTCAGCACAATTTAAACCCAATTATCCTGATAGGAATCTGCCCACAGTATTCATTTACCTTGAAGGTGAGATC
AAGGCTCAGCTTATTGGTCCCCTAGTGTTGGGTGGCATGAACTTGACTCAGATAAGTTGGAGTGGAAACTGGCCGAGTCA
GGGGCGATCAAGACGGACCTGCAGGAGAATCCCACGAAGCCAATCAGAGACATGTTGCTGTCCTCAGTGCGGTGTCTATC
CCCA

Alignment

ORF - retro_ocun_1035 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.82 %
• Parental protein coverage: 90.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RKKGILPSKESLKELEKQAEE-EEERALQQSVVK-TYEDMTLEELEDNEDEFNEEDERAIEMYRQQRLAE
          R..GILPSK.SLKEL.K.A.E.EEE..LQQSVV..TYED..LEEL..NEDEFNE..E.AIE.YRQQRLAE
Retrocopy RVEGILPSKGSLKELGKEAAE<EEEQVLQQSVVR<TYEDTPLEELDGNEDEFNEVEECAIETYRQQRLAE

Parental  WRATQEKNKFGEVLEISGKDYVQEVTKAGEGLWVILHLYKQGIP-LCALINQHFSALARKFPDVKFIKAI
          WRATQEKNKF.EVLEISGKDY..EVTKAGE..WVILHLY.Q.IP..CALINQH...LARKFPD.KFIK.I
Retrocopy WRATQEKNKFEEVLEISGKDYI*EVTKAGEDFWVILHLYQQRIP<PCALINQHSGGLARKFPDTKFIKTI

Parental  STTCIPNYPDRNLPTVFVYLEGEIKAQFVGPLVFGGMNLTR-DELEWKLAKSGAIKTDLEENPRKPIEDV
          S....PNYPDRNLPTVF.YLEGEIKAQ..GPLV.GGMNLT..D.LEWKLA.SGAIKTDL.ENP.KPI.D.
Retrocopy SAQFKPNYPDRNLPTVFIYLEGEIKAQLIGPLVLGGMNLTQ<DKLEWKLAESGAIKTDLQENPTKPIRDM

Parental  LLSSVRCSVP
          LLSSVRC..P
Retrocopy LLSSVRCLSP

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_1035 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1035 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1035 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,