RetrogeneDB ID: retro_ocun_34

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:181040692..181041079(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027982
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000026497
• Aliases: None
• Description: None

Sequence

>retro_ocun_34
ACGGCGGTGGCCGTGGTGGGCTGCGTGCTGCGGCGGTTCCAGCAGATGGTTCCTTTATCAGCTTCAGGGCAAATTCGAGG
TTACTACCTAGACTGGAAAACGTCGCGTGATTTGAAGAGAGGAAAACTGGCCTATGAGTATGCAGATGAGAGGCTACGGA
TCAATTCGCTGAGGAAGAATACCATTTTACCAAAAGATCTTCAGGAAGTGGCTGATGAAGAAATTGCTGCCCTTCCCTGG
GATAGCTGTCCTGTTAGAATCAGAAACCGGTGTGCTATGACGTCCCGGCCACGTGGTGTGAAGCGGCGCTGCAGGCTTAG
TCATATCGTCTTCTGTCACTTAGCTGACCACGGGCAGCTTTCTGGGGTGCAGCGAGCAATGTGGTAA

Alignment

ORF - retro_ocun_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.76 %
• Parental protein coverage: 99.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAVVGCVLRRFRQMVPLSASGQIRGYYVDWKMLRDVKRRKLAYEYADERLRINSLRKNTILPKDLQAVA
          A.AVVGCVLRRF.QMVPLSASGQIRGYY.DWK..RD.KR.KLAYEYADERLRINSLRKNTILPKDLQ.VA
Retrocopy AVAVVGCVLRRFQQMVPLSASGQIRGYYLDWKTSRDLKRGKLAYEYADERLRINSLRKNTILPKDLQEVA

Parental  DEEIAALPRDSCPVRIRNRCVMTSRPRGVKRRWRLSRIVFRHLADHGQLSGVQRAMW
          DEEIAALP.DSCPVRIRNRC.MTSRPRGVKRR.RLS.IVF.HLADHGQLSGVQRAMW
Retrocopy DEEIAALPWDSCPVRIRNRCAMTSRPRGVKRRCRLSHIVFCHLADHGQLSGVQRAMW

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	17.27 RPM
SRP017611_kidney	0.00 RPM	20.88 RPM
SRP017611_liver	0.00 RPM	6.40 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_34 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_34 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_34 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001109	1 retrocopy	retro_btau_149,
Callithrix jacchus	ENSCJAG00000008986	1 retrocopy	retro_cjac_136,
Mus musculus	ENSMUSG00000058267	1 retrocopy	retro_mmus_463,
Oryctolagus cuniculus	ENSOCUG00000026497	1 retrocopy	retro_ocun_34 ,
Tupaia belangeri	ENSTBEG00000003335	1 retrocopy	retro_tbel_1199,