RetrogeneDB ID: retro_ocun_270

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:8841739..8841980(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGST3
• Ensembl ID: ENSOCUG00000010376
• Aliases: None
• Description: microsomal glutathione S-transferase 3 (MGST3), mRNA [Source:RefSeq mRNA;Acc:NM_001082138]

Sequence

>retro_ocun_270
CTGCAATCAGCTCACCAGAACATGTTAGAAGTGTACCTTCCCTTCTTGTTTTTTTTCTGGTTGTTGAAGGTGTTTATCAC
CATGGGTAGTTCTGGCTTCGGCTGGGTCTGGATGGTTCGGTGGGTCCTTTACACTTCATGGCTATTACTTGGGAGATCTC
AGCAAGTGCTATGGAGGAGCCGTGTCCTCACTGGCCCTCGTCCTTTTGATGGGCACCACTGTGTGCTCTGCTTTCCAGCA
T

Alignment

ORF - retro_ocun_270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.41 %
• Parental protein coverage: 52.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IQRAHQNTLEVY-PPFL-FFLAVGGVYH-PRIV-SGLGWVWIVGRVLYA-YGYYTGDPSKRYRGAVSSLA
          .Q.AHQN.LEVY.P..L.FFL.V.GVYH.P..V.SG.GWVW.V..VLY...GYY.GD.SK.Y.GAVSSLA
Retrocopy LQSAHQNMLEVY<PSLLVFFLVVEGVYH<PWVV<SGFGWVWMVRWVLYT>HGYYLGDLSKCYGGAVSSLA

Parental  LFGLMGTTVCSAFQH
          L..LMGTTVCSAFQH
Retrocopy LVLLMGTTVCSAFQH

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	87.69 RPM
SRP017611_kidney	0.00 RPM	154.97 RPM
SRP017611_liver	0.00 RPM	91.10 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_270 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_270 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_270 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006658	1 retrocopy	retro_amel_1210,
Canis familiaris	ENSCAFG00000013353	1 retrocopy	retro_cfam_35,
Choloepus hoffmanni	ENSCHOG00000012723	2 retrocopies	retro_chof_1872, retro_chof_356,
Echinops telfairi	ENSETEG00000003507	3 retrocopies	retro_etel_1328, retro_etel_1527, retro_etel_1544,
Mustela putorius furo	ENSMPUG00000003817	1 retrocopy	retro_mputfur_1251,
Mus musculus	ENSMUSG00000026688	1 retrocopy	retro_mmus_2709,
Oryctolagus cuniculus	ENSOCUG00000010376	1 retrocopy	retro_ocun_270 ,
Procavia capensis	ENSPCAG00000015774	2 retrocopies	retro_pcap_385, retro_pcap_393,
Rattus norvegicus	ENSRNOG00000004245	1 retrocopy	retro_rnor_195,
Tupaia belangeri	ENSTBEG00000005299	2 retrocopies	retro_tbel_2989, retro_tbel_752,