RetrogeneDB ID: retro_ocun_1802

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018922:12494..12849(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHEBL1
• Ensembl ID: ENSOCUG00000016881
• Aliases: None
• Description: Ras homolog enriched in brain like 1 [Source:HGNC Symbol;Acc:21166]

Sequence

>retro_ocun_1802
GAGTACAGCATTCTGCCCTATTCATTCATCATTGGCGTCCATGGTTATGTGCTCGTCTATTCTATCACCTCCCTGCAGAG
CTTCCAAGTCCTTGGAAGTCTCTACCAAAAGCTACATGAAGGCCATGGGAAAACCCGGTTGCCCGTGGTACTAGTGGGGA
ACAAGGCGGATCTCTCTCCAGACAAGAGAGGTGCGGGCAGTCGAAGGGAAGAGGCTGGCAGAGTCCTGGGCTGCGACATT
TATGGAGTCATCTGCTAGAGAGAATCAGCTGGCTGAATGCGTCTTCACCAGAATCATGCAGGAGATCGCCCGGGTGGAGA
ATTCCTACGGGCCGGAGCGGCGCTGCCTCCCCATG

Alignment

ORF - retro_ocun_1802 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.76 %
• Parental protein coverage: 64.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EYSILPYSFIIGVHGYVLVYSITSLHSFQVVESLYQKLHEGHGKTRLPVVLVGNKADLSPD-REVQAVEG
          EYSILPYSFIIGVHGYVLVYSITSL.SFQV..SLYQKLHEGHGKTRLPVVLVGNKADLSPD.REV.AVEG
Retrocopy EYSILPYSFIIGVHGYVLVYSITSLQSFQVLGSLYQKLHEGHGKTRLPVVLVGNKADLSPD>REVRAVEG

Parental  KRLAESWGATFMESSARENQLAQSIFTRIIQEIARVENSYGPERRCLLM
          KRLAESW.ATFMESSARENQLA...FTRI.QEIARVENSYGPERRCL.M
Retrocopy KRLAESWAATFMESSARENQLAECVFTRIMQEIARVENSYGPERRCLPM

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	1.32 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1802 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1802 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1802 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002998	1 retrocopy	retro_cpor_1328,
Erinaceus europaeus	ENSEEUG00000008514	2 retrocopies	retro_eeur_338, retro_eeur_528,
Oryctolagus cuniculus	ENSOCUG00000013173	1 retrocopy	retro_ocun_1309,
Oryctolagus cuniculus	ENSOCUG00000016881	1 retrocopy	retro_ocun_1802 ,
Otolemur garnettii	ENSOGAG00000013477	1 retrocopy	retro_ogar_2338,
Pan troglodytes	ENSPTRG00000004897	1 retrocopy	retro_ptro_115,
Rattus norvegicus	ENSRNOG00000021571	1 retrocopy	retro_rnor_2059,