RetrogeneDB ID: retro_rnor_2612

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:20218655..20219135(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lypla1
• Ensembl ID: ENSRNOG00000008320
• Aliases: Lypla1, 25KDL, Pla1a
• Description: Acyl-protein thioesterase 1 [Source:UniProtKB/Swiss-Prot;Acc:P70470]

Sequence

>retro_rnor_2612
TCTTGGTTTGATATTATTGGACTTTCACCAGATTCCCAGGAGGATGAATCTGGAATTAAACAGGTGGCAGAAACTATAAA
AGCCTTGATGGATCAAGAAGTGAAGAATGGCATTCCTTCTAACAGAATTATTTTGGGAGGATTTTCTCAATGAGGAGACT
TCTGTTTATGCATTGCTCTCACAACACAGCAGAAACCAGCTAGTGTCACTGCACTCAGTTGCTGGGTTCCACTTCAGGCT
TCGTTTTCACAGGGGCCTATCAATAGTGCTATTTGAGATATTTCTGTTACCCTGTGTCATTGAGATTGTGACACTTTAGT
TTCCCTAATGTTTGGTTCTCTTACTATTGAAAGACAAAAAGCATTGGTAAATCCAGCCAACGTAACCTTCAAAGTCTATG
AAGGCATGATGCATAGATCATGTCAGCAAGAAATGATGGATGTCAAGTACTTCATTGGTAAGCTCCAACCTCCAATAGAT

Alignment

ORF - retro_rnor_2612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.75 %
• Parental protein coverage: 69.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SWFDIIGLSPDSQEDESGIKQAAETVKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTQQKLAGVT
          SWFDIIGLSPDSQEDESGIKQ.AET.KAL.DQEVKNGIPSNRIILGGFSQ.G...L..ALTTQQK.A.VT
Retrocopy SWFDIIGLSPDSQEDESGIKQVAETIKALMDQEVKNGIPSNRIILGGFSQ*GDFCLCIALTTQQKPASVT

Parental  ALSCWLPLRASFSQGPINSANRDISVLQCHGDCDPLVPLMFGSLTVERLKGLVNPANVTFKVYEGMMHSS
          ALSCW.PL.ASFSQGPINSA..DISV..CH.DCD.LV.LMFGSLT.ER.K.LVNPANVTFKVYEGMMH.S
Retrocopy ALSCWVPLQASFSQGPINSAI*DISVTLCH*DCDTLVSLMFGSLTIERQKALVNPANVTFKVYEGMMHRS

Parental  CQQEMMDVKYFIDKLLPPID
          CQQEMMDVKYFI.KL.PPID
Retrocopy CQQEMMDVKYFIGKLQPPID

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	16.82 RPM
SRP017611_kidney	0.00 RPM	179.13 RPM
SRP017611_liver	0.00 RPM	96.42 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2612 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2612 has 0 orthologous retrocopies within eutheria group .

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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,