RetrogeneDB ID: retro_ocun_1706

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018790:924505..924912(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOLT1B
• Ensembl ID: ENSOCUG00000008797
• Aliases: None
• Description: golgi transport 1B [Source:HGNC Symbol;Acc:20175]

Sequence

>retro_ocun_1706
ATGATCTCCTTAACAGACACCCAGAAAATTGGAATGGGATTGCAGGATTTGGAGTGTTTTTCCTGTTCTTTGGAATGGTT
CTCTTTTTTGACAAAGTGTTACTTCCTATTGAAATGTTTTGTTTGTGGCTGGCTTGGCTTTTGTAATTGGTTTAGAAAGA
ACATTCAGATTCTTTCAAACACATAAAATGAAAGCCACTGGATTTTTCCTGGGTGGTGTATTTGTAGTCCTCATCGGTTG
GCCTTTGGTAGGTGTGTTTTTCAAAGCTTATGGATTCTTTCTCTTGTTCGGGGGCTTTTCCTGTGGTGGTTGGCTTTATT
AGAAGAGTGTCAGTGCTTGGATACCTCTGAAATTTACCTGGAAATAGATCATTTGTGAATAAAGTTGGAGAAAGCAACAA
TATGATA

Alignment

ORF - retro_ocun_1706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MISLTDTQKIGMGL-TGFGVFFLFFGMILFFDKALLAIG-NVLFVAGLAFVIGLERTFRFFFQKHKMKAT
          MISLTDTQKIGMGL..GFGVFFLFFGM.LFFDK.LL.I..NVLFVAGLAFVIGLERTFRFF.Q.HKMKAT
Retrocopy MISLTDTQKIGMGL<AGFGVFFLFFGMVLFFDKVLLPIE<NVLFVAGLAFVIGLERTFRFF-QTHKMKAT

Parental  GFFLGGVFVVLIGWPLIGMIFEIYGFFL-LFRGF-FPVVVGFIRRVPVLGSLLNLPGIRSFVDKVGESNN
          GFFLGGVFVVLIGWPL.G..F..YGFFL.L.RG..FPVVVGFIRRV.VLG.L.NLPG.RSFV.KVGESNN
Retrocopy GFFLGGVFVVLIGWPLVGVFFKAYGFFL<LVRGL<FPVVVGFIRRVSVLGYL*NLPGNRSFVNKVGESNN

Parental  MV
          M.
Retrocopy MI

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	29.91 RPM
SRP017611_kidney	0.00 RPM	19.56 RPM
SRP017611_liver	0.00 RPM	4.78 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1706 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1706 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1706 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016231	1 retrocopy	retro_amel_604,
Canis familiaris	ENSCAFG00000012256	1 retrocopy	retro_cfam_1835,
Dasypus novemcinctus	ENSDNOG00000013576	2 retrocopies	retro_dnov_158, retro_dnov_1730,
Felis catus	ENSFCAG00000028655	1 retrocopy	retro_fcat_1782,
Oryctolagus cuniculus	ENSOCUG00000008797	1 retrocopy	retro_ocun_1706 ,
Otolemur garnettii	ENSOGAG00000004756	1 retrocopy	retro_ogar_3234,
Ictidomys tridecemlineatus	ENSSTOG00000006352	1 retrocopy	retro_itri_1786,