RetrogeneDB ID: retro_ocun_1709

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018799:124065..124341(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000006840
• Aliases: None
• Description: None

Sequence

>retro_ocun_1709
CCTCAAAAATTTATAAATGTGAGCCTAGCAGTGACCTGGAAGTTTGGAGGAAGTTCAACTTTGAATGGCTGTCCATAGGC
AGGTCCTATGTTGACAGATAATGGGAATTTTATCCTGGACTGGAAGTTTGATTGTGTACACAAATGTAGTCAAGTGAACA
TGGCTATCAAAATGATCCCAGGCATGGTGGACACAGGGCTGTTCATCAACATGGCTGAGACAGTCTTCTTTGGGATGCAG
AAAGGTTAAGTGAACGTGTGAGAGAAACCCTTCTGT

Alignment

ORF - retro_ocun_1709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 68.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PMAYVPVSRAVTWKFGGEVQLQMAVHKAGPVVTDNGNFILDWKFDCAHKWSEVNIAIKMILSVVDTGLFI
          P.....VS.AVTWKFGG...L......AGP..TDNGNFILDWKFDC.HK.S.VN.AIKMI...VDTGLFI
Retrocopy PQKFINVSLAVTWKFGGSSTLN-GCP*AGPMLTDNGNFILDWKFDCVHKCSQVNMAIKMIPGMVDTGLFI

Parental  NMVERVYFGMQDGSVTVREKPFC
          NM.E.V.FGMQ.G.V.V.EKPFC
Retrocopy NMAETVFFGMQKG*VNV*EKPFC

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.15 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1709 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1709 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002866	1 retrocopy	retro_btau_1373,
Equus caballus	ENSECAG00000011754	1 retrocopy	retro_ecab_645,
Macropus eugenii	ENSMEUG00000008256	1 retrocopy	retro_meug_1506,
Microcebus murinus	ENSMICG00000006462	1 retrocopy	retro_mmur_722,
Myotis lucifugus	ENSMLUG00000005384	1 retrocopy	retro_mluc_1129,
Monodelphis domestica	ENSMODG00000009649	1 retrocopy	retro_mdom_320,
Oryctolagus cuniculus	ENSOCUG00000006840	3 retrocopies	retro_ocun_1541, retro_ocun_1708, retro_ocun_1709 ,
Otolemur garnettii	ENSOGAG00000034178	2 retrocopies	retro_ogar_1218, retro_ogar_518,
Tarsius syrichta	ENSTSYG00000006406	8 retrocopies	retro_tsyr_1081, retro_tsyr_1088, retro_tsyr_1902, retro_tsyr_2028, retro_tsyr_393, retro_tsyr_709, retro_tsyr_725, retro_tsyr_994,
Tursiops truncatus	ENSTTRG00000000876	2 retrocopies	retro_ttru_1175, retro_ttru_799,