RetrogeneDB ID: retro_ocun_1243

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:75633377..75633809(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000023212
• Aliases: None
• Description: None

Sequence

>retro_ocun_1243
CTGGCCGGGGTCTCCATGAGTGAGACAGGAAAATATAAAATTGTCAGAGTAGATGATGCAAATAAGAAGGGGCTCATCCC
TGCCCACCTCCGCGTTGCCATGGCAGAGCCGGCCACTAAGCATTCAGAATAGGTGGGAGTCATACCTGGAAAAGCCCTCA
GAAAGAGCGAGTGGAGACCGTGGAGGTGCTAAGACACCATCAAGGGAAGCCAGCGGTGGCCGCTGTGATCAGCAGCAGAG
CTCTCTGGTGCTGGCGAGGTCTGGGCGGAGAGCAAGTGGGCGCCACGAAGACCAAGTTCCATTCAGAAAATAACCCCTGA
AGCCACAAGCAAAAGGTGTGCCAAAGGTGAAGCTGCTGTGTGGGGCAGATTTACTGGAGCCCTTTTGCGTTCCCAAATGT
GGAAGAGTGAGGATAACGCCCACACTGTGGCT

Alignment

ORF - retro_ocun_1243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.93 %
• Parental protein coverage: 50.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LSGTGKYNVVKGIISPVGDAYKKKGLIPAHHRVVMAELATKHSEWVEV-DTWESLQKEWVETVKVLRHHR
          L.G.......K..I..V.DA..KKGLIPAH.RV.MAE.ATKHSE.V.V..TW.S.QKE.VETV.VLRHH.
Retrocopy LAGVSMSETGKYKIVRVDDA-NKKGLIPAHLRVAMAEPATKHSE*VGV<HTWKSPQKERVETVEVLRHHQ

Parental  EKLAAS-HCGQQQSSPVPERPARKR-KWADQRPDSRQKK-PLEPKTEGVPKVKLLCGADLLESFGVP-NL
          .K.A....C.QQQSS.V..R..R...KWA..RP.S.QK..PL.P...GVPKVKLLCGADLLE.F.VP...
Retrocopy GKPAVA<RCDQQQSSLVLARSGRRA<KWAPRRPSSIQKI>PLKPQAKGVPKVKLLCGADLLEPFCVP<QM

Parental  WKSEDIAHIVA
          WKSED.AH.VA
Retrocopy WKSEDNAHTVA

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	1.10 RPM
SRP017611_kidney	0.00 RPM	5.78 RPM
SRP017611_liver	0.00 RPM	6.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1243 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1243 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1243 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001361	2 retrocopies	retro_btau_1153, retro_btau_1654,
Callithrix jacchus	ENSCJAG00000005483	1 retrocopy	retro_cjac_1690,
Homo sapiens	ENSG00000173614	3 retrocopies	retro_hsap_247, retro_hsap_2740, retro_hsap_2989,
Macaca mulatta	ENSMMUG00000005863	2 retrocopies	retro_mmul_1488, retro_mmul_446,
Nomascus leucogenys	ENSNLEG00000009375	2 retrocopies	retro_nleu_1072, retro_nleu_741,
Oryctolagus cuniculus	ENSOCUG00000023212	1 retrocopy	retro_ocun_1243 ,
Otolemur garnettii	ENSOGAG00000033037	2 retrocopies	retro_ogar_1088, retro_ogar_637,