RetrogeneDB ID: retro_ocun_308

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:134358474..134358954(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000005657
• Aliases: None
• Description: None

Sequence

>retro_ocun_308
CTGCAGGAAATAAGGGATCACAGCAGATGTAAAAAAAGAAAGTTGGGGAAAGATCAAGATGAGAACACAAAGACTAAAAC
TAGTGTCCTTGGGAAAGAAGTGGATGTGAAAGAGTTTAATCTAGAAAAGGACTGTTTCGAGGTACACTGTGTCTATATCA
CAGGTTATAGAAAAGAAACAGAAAAAGTCCTCTTTTGGGAATGCACCATTTTGCTGGGTGCTAAGCCTTCCAAAAATAGG
TGAATCTCAAAGTTTTGCTGGAGCAAATCAAATAAAAACAGCAGCAAAGGAAAAGAGAAGAAAATGGCGTGGGACACAGA
CATTTTCAAGAAAAAGAAGAGGAAAAGGCAGGAAGAAAGGAAATCCAAAAAGGAAGTGACTCCCAGTATTTTGTCAAGTG
GACAGACTAGTCAGGTTGGAAAAATCAAAAATGGAATATTGATTCTAAGCACAACTGGTATTAGGAAAACAAATTGTTCA

Alignment

ORF - retro_ocun_308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.28 %
• Parental protein coverage: 56.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VEVVEFHSRHKKRKLKQAQDGSTKAKTSVLEKGVDVQEFNLEKARLEVHRFGITGYGKGTERVLEQERAI
          ......HSR.KKRKL...QD..TK.KTSVL.K.VDV.EFNLEK...EVH...ITGY.K.TE.VL..E..I
Retrocopy LQEIRDHSRCKKRKLGKDQDENTKTKTSVLGKEVDVKEFNLEKDCFEVHCVYITGYRKETEKVLFWECTI

Parental  MLGAKPPKNSYVNYKVLQEQIKEKQAAKEKEKKMVQDTDIFKKKKRKGQEERKSKKKKSAPSILSSGRAG
          .LGAKP.KN............K.....K..EKKM..DTDIFKKKKRK.QEERKSKK....PSILSSG...
Retrocopy LLGAKPSKNR*ISKFCWSKSNKNSSKGK--EKKMAWDTDIFKKKKRKRQEERKSKKEVT-PSILSSGQTS

Parental  QVGKFKNGTLILSPSDIKKINSS
          QVGK.KNG.LILS...I.K.N.S
Retrocopy QVGKIKNGILILSTTGIRKTNCS

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	2.48 RPM
SRP017611_kidney	0.00 RPM	2.64 RPM
SRP017611_liver	0.00 RPM	3.85 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_308 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_308 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_308 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000009357	1 retrocopy	retro_mdom_1277,
Oryctolagus cuniculus	ENSOCUG00000005657	1 retrocopy	retro_ocun_308 ,