RetrogeneDB ID: retro_ocun_29

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:48624340..48625207(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000007184
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: OTUD6B
• Ensembl ID: ENSOCUG00000000218
• Aliases: None
• Description: OTU domain containing 6B [Source:HGNC Symbol;Acc:24281]

Sequence

>retro_ocun_29
TTACCGTTAAACATCATGGAGCGCGACAAGCAGCAGATCCTTCAGCGCCAGCGCCGCGAGGAGAGAGAGCTCCAGGCCCG
CATCCAGGCCATGAAGCACACAGTCCCAAAGAACGATAAGAAGAGAAGAAAGCAGCTTCTCCAAGAAATGGCCCACCTCG
AGGCCAAGATGGAGGAGAAGCACCAGCAGGAGCTGGAGCTGTACTTCGAGAGGCGCTCCCGCAGCACCAACGTCGATTCT
GTCACTGATGAGCTGGCCAGGATGGCTCTCGAGAACCAGTCACTGTACCTCTCGAGAGCACAGCGAAGGCACGAAAGAAA
GGCAGCCCACCAGCAGGAGCATCAGGAGAGGATCGAGGTGCTGGAGATGGAGGATCTGGCCAGCTACCGCCGGGAGGAGG
AGGAGAAGCTGGCCGCCATCCTGCGCGCCAAGAATCTGGAGATGAAGAATATCCCGGCCGACGGCCACTGCATGTACCGC
GCCATCCAAGACCAGCTGATGTCCTTTGTGACTGTGGATAGCCTTCGTCACTGCACCTCCGAGTACATGCAGAAGCACGT
CGACGACTTCCTGCCATTCTTCAGCAACCCCAACATCTGCGACGGCTGCGCACGCGCCGACTTCCTGAAATACTGCCAGG
ACATCGTGAGACGTGCCTCGTGGGGAACCCAGCTCGAGCTGAGAGCCCTGTCGCACATCCTGCAGACCCGCATCGAGGTG
ATCCGGGCCGATTCGCCAGCCCTCATTATCGGGGAGGAATACAACACGAAGCCGCTCACCCTCGTCTACCTGCGCCACGC
CTGCGTCACCGGCGAGCACTACAATTCCGTGAAGCTGGTCAAGGCCACGGGCGCCGAAGCTGCGGGC

Alignment

ORF - retro_ocun_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.09 %
• Parental protein coverage: 88.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEQLVRRHRKEKKELQAKIQGMKNAVPKNDKKRRKQLTEDVAKLEKELEQKHKEELEQL--KLTSKNKI
          ...Q...R.R.E..ELQA.IQ.MK..VPKNDKKRRKQL....A.LE...E.KH..ELE............
Retrocopy DKQQILQRQRREERELQARIQAMKHTVPKNDKKRRKQLLQEMAHLEAKMEEKHQQELELYFERRSRSTNV

Parental  DSVAVNISNLVLENQPPRISKAQKRRDKKAALEKEREERIAEAEIENLSGARHIESEKLAQILAARQLEI
          DSV........LENQ....S.AQ.R...KAA...E..ERI...E.E.L...R..E.EKLA.IL.A..LE.
Retrocopy DSVTDELARMALENQSLYLSRAQRRHERKAAHQQEHQERIEVLEMEDLASYRREEEEKLAAILRAKNLEM

Parental  KQIPSDGHCMYRAIEDQLKEQDSAVTVAALRSQTAEYMQSHVEDFLPFLTNPNTGNMYTSEEFGKYCDDI
          K.IP.DGHCMYRAI.DQL....S.VTV..LR..T.EYMQ.HV.DFLPF..NPN.........F.KYC.DI
Retrocopy KNIPADGHCMYRAIQDQLM---SFVTVDSLRHCTSEYMQKHVDDFLPFFSNPNICDGCARADFLKYCQDI

Parental  VNTAAWGGQLELRALSHILQTPIEIIQADSLPIVVGEEYKKKPLILVYMRHAYGLGEHYNSVTQLVNTAT
          V..A.WG.QLELRALSHILQT.IE.I.ADS.....GEEY..KPL.LVY.RHA...GEHYNSV.....T..
Retrocopy VRRASWGTQLELRALSHILQTRIEVIRADSPALIIGEEYNTKPLTLVYLRHACVTGEHYNSVKLVKATGA

Parental  E
          E
Retrocopy E

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	13.36 RPM
SRP017611_kidney	0.00 RPM	8.21 RPM
SRP017611_liver	0.15 RPM	6.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_29 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_29 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_29 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_350
Sus scrofa	retro_sscr_52

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006971	1 retrocopy	retro_amel_74,
Bos taurus	ENSBTAG00000003481	2 retrocopies	retro_btau_236, retro_btau_969,
Choloepus hoffmanni	ENSCHOG00000004266	2 retrocopies	retro_chof_1969, retro_chof_2069,
Cavia porcellus	ENSCPOG00000013595	1 retrocopy	retro_cpor_103,
Equus caballus	ENSECAG00000018205	1 retrocopy	retro_ecab_44,
Felis catus	ENSFCAG00000029900	1 retrocopy	retro_fcat_124,
Loxodonta africana	ENSLAFG00000011002	1 retrocopy	retro_lafr_16,
Microcebus murinus	ENSMICG00000012278	1 retrocopy	retro_mmur_1222,
Myotis lucifugus	ENSMLUG00000016954	1 retrocopy	retro_mluc_1226,
Macaca mulatta	ENSMMUG00000013396	1 retrocopy	retro_mmul_350,
Monodelphis domestica	ENSMODG00000007551	2 retrocopies	retro_mdom_119, retro_mdom_1326,
Mustela putorius furo	ENSMPUG00000009194	1 retrocopy	retro_mputfur_51,
Mus musculus	ENSMUSG00000040550	1 retrocopy	retro_mmus_2456,
Nomascus leucogenys	ENSNLEG00000002420	1 retrocopy	retro_nleu_2365,
Oryctolagus cuniculus	ENSOCUG00000000218	1 retrocopy	retro_ocun_29 ,
Otolemur garnettii	ENSOGAG00000011298	1 retrocopy	retro_ogar_228,
Ochotona princeps	ENSOPRG00000007655	1 retrocopy	retro_opri_413,
Pan troglodytes	ENSPTRG00000020413	1 retrocopy	retro_ptro_3120,
Sus scrofa	ENSSSCG00000006120	1 retrocopy	retro_sscr_52,
Ictidomys tridecemlineatus	ENSSTOG00000002954	1 retrocopy	retro_itri_9,
Tupaia belangeri	ENSTBEG00000017070	1 retrocopy	retro_tbel_304,
Tursiops truncatus	ENSTTRG00000004345	1 retrocopy	retro_ttru_1207,