RetrogeneDB ID: retro_ocun_849

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:92161666..92161972(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC11A
• Ensembl ID: ENSOCUG00000008205
• Aliases: None
• Description: SEC11 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:17718]

Sequence

>retro_ocun_849
CTATGTCTAGACTTCCTGGACAAAGTCCAGAGACCGGACAAGAGCTCTATTTTGGAAGGATTGTCTTCATTTTGGAAGGA
TTGTCTCCTCAGCTCTAGCGGTCTGGAAGGGATTGGTCGGTGTCACCGGAAGCAAAATCCAGTGGTAGTGCTGGCCAGTG
GCAGCATGGAACCTGCATTTCAGAAAGATCTTCTCTTTCAAATAAGTGAGGTTGAAGATCCCATAAGAGTGGGAGAAACT
GGTTTTACGGTAGAGGGAAGACAGAGTCCCTTGGCTGACCAAGTCTCGCAGATTCAAGAAAAGCAA

Alignment

ORF - retro_ocun_849 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.66 %
• Parental protein coverage: 58.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSLDFLDDVRRMNKRQL-YYQVLNFGMIVSSALMIWKGLMVITGS-ESPIVVVLSGSMEPAFHRGDLLFL
          L.LDFLD.V.R..K........L.FG.IVSSAL..WKGL...TGS...P.VV..SGSMEPAF...DLLF.
Retrocopy LCLDFLDKVQRPDKSSI>WKDCLHFGRIVSSALAVWKGLVGVTGS<QNPVVVLASGSMEPAFQK-DLLFQ

Parental  TNRVEDPIRVGEIVVFRIEGREIPIVHRVLKIHEKQ
          ...VEDPIRVGE...F..EGR..P....V..I.EKQ
Retrocopy ISEVEDPIRVGE-TGFTVEGRQSPLADQVSQIQEKQ

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	14.68 RPM
SRP017611_kidney	0.00 RPM	62.54 RPM
SRP017611_liver	0.00 RPM	23.28 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_849 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_849 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_849 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000015328	2 retrocopies	retro_eeur_314, retro_eeur_412,
Macaca mulatta	ENSMMUG00000011486	1 retrocopy	retro_mmul_2343,
Monodelphis domestica	ENSMODG00000019364	1 retrocopy	retro_mdom_726,
Oryctolagus cuniculus	ENSOCUG00000008205	1 retrocopy	retro_ocun_849 ,
Oryctolagus cuniculus	ENSOCUG00000009204	2 retrocopies	retro_ocun_738, retro_ocun_895,
Otolemur garnettii	ENSOGAG00000007281	1 retrocopy	retro_ogar_3315,
Ictidomys tridecemlineatus	ENSSTOG00000019948	1 retrocopy	retro_itri_206,
Tupaia belangeri	ENSTBEG00000012320	3 retrocopies	retro_tbel_1139, retro_tbel_2280, retro_tbel_745,