RetrogeneDB ID: retro_ocun_391

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:138471074..138471659(-)
• Located in intron of: ENSOCUG00000017463

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTP1
• Ensembl ID: ENSOCUG00000002230
• Aliases: None
• Description: glutathione S-transferase pi 1 [Source:HGNC Symbol;Acc:4638]

Sequence

>retro_ocun_391
GGGCACTGTGAAGCTGTGTACACGCTGCCGGCTGGCCAGAGCCAGAGTCAGAGCCTGAAGGAGGAGGTGGTGGGCCTGCA
GACCTGGCCACAGAGCTCAGTCAAGGCCTCCTGTCTGTACAGGCAGTTCCCCAAGTTCCCAGACAGAGACATCACTGGTG
CCAGTCCAGTGCCAATCTGTGATATTTGGGCCACACTCTGTGTTCTATGGGAAGGTGGTCCTGCTGGACATTTTGAATGA
TGGTGTGGAGGACCTGCAGGACAAATACGTCACCCTCATCTACACCAGCTACAATGCAGGCCAGGCCATCTAATGTGAAG
GCTCTGCCTGGGTACCTGAAACCTTTTGAGAATCTTCTGCCTTAGAACCAGGAAGCCAGCCCTTCATCATGGGCAACGAG
ATCTCCTAGACTTACTACACCTCCTGGACTTGCTGCTAACCCACCAGATCATGGCCTCTGGCTGCCTAGATGCCTTTCCC
ATGCTCTCGACCTACATGGCACACCCCAGTGCCTGGACCAAGCTCAAAGCTTTACTGACCTCCTCTGCCCATGTGAACTG
CCCCATCAATGGTGATGGGAAAAGG

Alignment

ORF - retro_ocun_391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.54 %
• Parental protein coverage: 94.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GRCEAMRMLLT--DQGQSWKEEVVNLETWSQGSLKASCLYGQLPKLQDGDLT-LYQSNAILRHLGRTLG-
          G.CEA...L.....Q.QS.KEEVV.L.TW.Q.S.KASCLY.Q.PK..D.D.T...QS.A.L..LG.TL..
Retrocopy GHCEAVYTLPAGQSQSQSLKEEVVGLQTWPQSSVKASCLYRQFPKFPDRDIT<WCQSSANL*YLGHTLC<

Parental  IYGKDQREAALLDMVNDGVEDLRIKYITLIYTNYDAG-KDSYVKALPGHLKPFETLLSQNKDG-KSFIVG
          .YGK......LLD..NDGVEDL..KY.TLIYT.Y.AG...S.VKALPG.LKPFE.LL..N......FI.G
Retrocopy FYGK----VVLLDILNDGVEDLQDKYVTLIYTSYNAG>RPSNVKALPGYLKPFENLLP*NQEA<QPFIMG

Parental  DQISFADY-NLLDLLLTHQILAPGCLDAFPLLSAYVARLSARPKLKAFLASPEHVNRPINANGKK
          ..IS...Y..LLDLLLTHQI.A.GCLDAFP.LS.Y.A..SA..KLKA.L.S..HVN.PIN..GK.
Retrocopy NEIS*TYY<HLLDLLLTHQIMASGCLDAFPMLSTYMAHPSAWTKLKALLTSSAHVNCPINGDGKR

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	130.02 RPM
SRP017611_kidney	0.00 RPM	230.59 RPM
SRP017611_liver	0.00 RPM	8.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_391 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_391 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_391 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001020	3 retrocopies	retro_amel_1921, retro_amel_249, retro_amel_778,
Canis familiaris	ENSCAFG00000011349	4 retrocopies	retro_cfam_143, retro_cfam_2043, retro_cfam_46, retro_cfam_617,
Callithrix jacchus	ENSCJAG00000000879	1 retrocopy	retro_cjac_3321,
Macropus eugenii	ENSMEUG00000001519	2 retrocopies	retro_meug_1519, retro_meug_1762,
Mustela putorius furo	ENSMPUG00000004029	2 retrocopies	retro_mputfur_1215, retro_mputfur_1463,
Mus musculus	ENSMUSG00000038155	1 retrocopy	retro_mmus_521,
Oryctolagus cuniculus	ENSOCUG00000002230	1 retrocopy	retro_ocun_391 ,
Rattus norvegicus	ENSRNOG00000018237	4 retrocopies	retro_rnor_2140, retro_rnor_2567, retro_rnor_2842, retro_rnor_769,
Tursiops truncatus	ENSTTRG00000003746	1 retrocopy	retro_ttru_1416,
Vicugna pacos	ENSVPAG00000008003	1 retrocopy	retro_vpac_73,