RetrogeneDB ID: retro_ocun_1679

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018762:472287..472987(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000022261
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LYPLA1
• Ensembl ID: ENSOCUG00000006751
• Aliases: None
• Description: lysophospholipase I (LYPLA1), mRNA [Source:RefSeq mRNA;Acc:NM_001109817]

Sequence

>retro_ocun_1679
TGTTGGCTTAGTCTGTGTATGTGTGGTAATACCATGCCTGCTCCACTGTAAGCCATAGTGCCTTGCACCAGGAAGGATGC
CACTGTGGTAATTTTCCTTCATGATTGGAAGATCCTGGACATGGATGGGCAGAAGCCTTTGCAGGTAGCACAAGTTCACA
TGCCAGATGTATCAGCCTGCATGCACCCATTGTGCCTGTTGCATTAAATATAAACATGGCTATGCCTTTTTGGTTTGATA
ATATTGGACTTTCACCAGACTCACCGGAGGATGAATCTAGAATTAAACAAGCAACAGAAAATGTAAAGGCTTTGATAGAT
CAAGAGGTGACGAGTAGCATTGCTTCTAACAGAATTATTTTGGGAGGATTTCCTCAGGGAGGAGCTTTATATACTGCTCT
TACCACATAGCAGAAACTGGTGGTGTCACTGCACTCAGTTGCTGGCTTCCACTTCGGGCTTCATTTCCACAGGGTCCTAT
CAGTGGTGCTAATAGAGATGTTTCTATTCTCCAGTGCCATGGAGATTGCAACTCTTTAGTTCCACTCATGTTTGGTTCTC
TTACTGTGGAAAAACTAAACACATTGCTAAATCTGGCCAGTGTAACCTTTAAGGCCTATGAAGGCATGAGTCACAGTTCC
TGTCAGCAGGAAATGATGGATGTCAAGCAATTCATTGGTAAAATCCTACCTCCAATTGAT

Alignment

ORF - retro_ocun_1679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.73 %
• Parental protein coverage: 99.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CRPSQCMCGNTMSAPLPAIVPAARKATAAVIFLHG-LGDTGHGWAEAFAGIRSSHIKYICPHAPVMPVTL
          C..S.CMCGNTM.APL.AIVP..RK....VIFLH..L.D.GHGWAEAFAG..SSH...I..HAP..PV.L
Retrocopy CWLSLCMCGNTMPAPL*AIVPCTRKDATVVIFLHD<LEDPGHGWAEAFAGSTSSHARCISLHAPIVPVAL

Parental  NMNMAMPSWFDIIGLSPDSQEDEPGIKQAAENVKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTQ
          N.NMAMP.WFD.IGLSPDS.EDE..IKQA.ENVKALIDQEV...I.SNRIILGGF.QGGAL..YTALTT.
Retrocopy NINMAMPFWFDNIGLSPDSPEDESRIKQATENVKALIDQEVTSSIASNRIILGGFPQGGAL--YTALTT*

Parental  QKLA-GVTALSCWLPLRASFPQGPISGANRDISILQCHGDCDPLVPLMFGSLTVEKLKTLVNPANVTFKT
          QKL..GVTALSCWLPLRASFPQGPISGANRD.SILQCHGDC..LVPLMFGSLTVEKL.TL.N.A.VTFK.
Retrocopy QKLV<GVTALSCWLPLRASFPQGPISGANRDVSILQCHGDCNSLVPLMFGSLTVEKLNTLLNLASVTFKA

Parental  YEGMMHSSCQQEMMDVKQFIDKLLPPID
          YEGM.HSSCQQEMMDVKQFI.K.LPPID
Retrocopy YEGMSHSSCQQEMMDVKQFIGKILPPID

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	11.98 RPM
SRP017611_kidney	0.00 RPM	25.04 RPM
SRP017611_liver	0.00 RPM	6.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1679 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1679 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1679 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006978	1 retrocopy	retro_cfam_523,
Callithrix jacchus	ENSCJAG00000011562	2 retrocopies	retro_cjac_1260, retro_cjac_3100,
Cavia porcellus	ENSCPOG00000022715	3 retrocopies	retro_cpor_142, retro_cpor_549, retro_cpor_782,
Dipodomys ordii	ENSDORG00000001479	1 retrocopy	retro_dord_88,
Equus caballus	ENSECAG00000016530	1 retrocopy	retro_ecab_238,
Echinops telfairi	ENSETEG00000001727	2 retrocopies	retro_etel_612, retro_etel_791,
Homo sapiens	ENSG00000120992	3 retrocopies	retro_hsap_3078, retro_hsap_3485, retro_hsap_3897,
Myotis lucifugus	ENSMLUG00000008208	1 retrocopy	retro_mluc_1683,
Macaca mulatta	ENSMMUG00000013157	3 retrocopies	retro_mmul_1734, retro_mmul_2459, retro_mmul_2474,
Mus musculus	ENSMUSG00000025903	1 retrocopy	retro_mmus_3700,
Nomascus leucogenys	ENSNLEG00000001027	4 retrocopies	retro_nleu_1137, retro_nleu_2015, retro_nleu_2817, retro_nleu_2869,
Oryctolagus cuniculus	ENSOCUG00000006751	3 retrocopies	retro_ocun_1510, retro_ocun_1623, retro_ocun_1679 ,
Otolemur garnettii	ENSOGAG00000003767	3 retrocopies	retro_ogar_1528, retro_ogar_1530, retro_ogar_1532,
Pongo abelii	ENSPPYG00000018590	3 retrocopies	retro_pabe_2550, retro_pabe_3177, retro_pabe_3565,
Pteropus vampyrus	ENSPVAG00000005246	2 retrocopies	retro_pvam_224, retro_pvam_838,
Rattus norvegicus	ENSRNOG00000008320	3 retrocopies	retro_rnor_1747, retro_rnor_2612, retro_rnor_406,
Tupaia belangeri	ENSTBEG00000014207	8 retrocopies	retro_tbel_1839, retro_tbel_2439, retro_tbel_2478, retro_tbel_2907, retro_tbel_3127, retro_tbel_3466, retro_tbel_371, retro_tbel_4145,
Tarsius syrichta	ENSTSYG00000012350	6 retrocopies	retro_tsyr_1287, retro_tsyr_1303, retro_tsyr_1465, retro_tsyr_1901, retro_tsyr_1996, retro_tsyr_2158,
Tursiops truncatus	ENSTTRG00000011836	3 retrocopies	retro_ttru_1643, retro_ttru_169, retro_ttru_291,