RetrogeneDB ID: retro_ocun_359

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:47261248..47261482(-)
• Located in intron of: ENSOCUG00000006819

Retrocopy information

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

Parental gene information

• Parental gene symbol: TEX12
• Ensembl ID: ENSOCUG00000002174
• Aliases: None
• Description: testis expressed 12 [Source:HGNC Symbol;Acc:11734]

Sequence

>retro_ocun_359
ATGATGGCCAATCACCTTGTAAAACCTGATATTGGAAATTCAATGAGGCCAGGAGAACTGAAGCATCAAATACCAGATGC
TTCAGAGCTGCCCTCTCTTGGAAATTCAGATTCACATTACTCTGAGAACTCTCAGCGATTTTATAAAGATGAGGCCCTGA
AGAAATACTTGAATGATATAAGCAAGGGAATTACTCTAAAGTTATTTAAATATACAGAGAGTGAGAGAAGCAGT

Alignment

ORF - retro_ocun_359 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55. %
• Parental protein coverage: 65.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMASHLVKPDTRSCKRPRETEPQMPDSPQLSSLGKSDSLCSESSGLFYKDEALEKDLNEMSKEINLMLST
          MMA.HLVKPD.....RP.E...Q.PD...L.SLG.SDS..SE.S..FYKDEAL.K.LN..SK.I.L.L..
Retrocopy MMANHLVKPDIGNSMRPGELKHQIPDASELPSLGNSDSHYSENSQRFYKDEALKKYLNDISKGITLKLFK

Parental  YAKILSERAA
          Y....SER..
Retrocopy YTE--SERSS

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	0.17 RPM
SRP017611_kidney	0.00 RPM	0.10 RPM
SRP017611_liver	0.00 RPM	0.23 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_359 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_359 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_359 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000009900	1 retrocopy	retro_cpor_1327,
Oryctolagus cuniculus	ENSOCUG00000002174	1 retrocopy	retro_ocun_359 ,
Tarsius syrichta	ENSTSYG00000006348	1 retrocopy	retro_tsyr_335,