RetrogeneDB ID: retro_ocun_290

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:70956119..70956447(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM18
• Ensembl ID: ENSOCUG00000008527
• Aliases: None
• Description: RNA binding motif protein 18 [Source:HGNC Symbol;Acc:28413]

Sequence

>retro_ocun_290
CTGGAGAATGCATCCGTGCTCCCAGCAGGCTCTCTGCAGGAAGGCAGATTATGGGTTGGCAACCTGGACCCCAGAACCAC
AGAATACCATCTTCTCATGCTGCTCCAGAAGTTTGGCAAGGTGAAGCAGTTTGACTTCGTCTTCCACAAGTCGAGTGCTT
TGAGGGACAGCCTCAGGGTACTGCTTTGTTAACTTTGAAACCAAGCAGAAGGCAGAACAAGCCAACCAGTGTCTCAGTGG
CAAGCCGGCTCTGTCTAAGAAGCTGGTGGCGCAATGGGCACATGCATAAGTAAAGAGATATGATCATGACAAGAATGATA
AGGTCCTT

Alignment

ORF - retro_ocun_290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.65 %
• Parental protein coverage: 58.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LENASILSEGSLQEGHRLWIGNLDPKITEYHLLKLLQRFGKVKQFDFLFHKSGAL-EGQPR-GYCFVNFE
          LENAS.L..GSLQEG.RLW.GNLDP..TEYHLL.LLQ.FGKVKQFDF.FHKS.AL.EGQP..GYCFVNFE
Retrocopy LENASVLPAGSLQEG-RLWVGNLDPRTTEYHLLMLLQKFGKVKQFDFVFHKSSAL<EGQPQ<GYCFVNFE

Parental  TKQEAEQAIQCLNGKLALSKKLVVRWAHAQVKRYDHNKNDKIL
          TKQ.AEQA.QCL.GK.ALSKKLV..WAHA.VKRYDH.KNDK.L
Retrocopy TKQKAEQANQCLSGKPALSKKLVAQWAHA*VKRYDHDKNDKVL

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	19.76 RPM
SRP017611_kidney	0.00 RPM	14.90 RPM
SRP017611_liver	0.00 RPM	5.93 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_290 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_290 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013811	1 retrocopy	retro_cpor_237,
Myotis lucifugus	ENSMLUG00000004794	1 retrocopy	retro_mluc_298,
Monodelphis domestica	ENSMODG00000019688	1 retrocopy	retro_mdom_1462,
Oryctolagus cuniculus	ENSOCUG00000008527	1 retrocopy	retro_ocun_290 ,
Otolemur garnettii	ENSOGAG00000015104	1 retrocopy	retro_ogar_846,
Ochotona princeps	ENSOPRG00000010381	2 retrocopies	retro_opri_1123, retro_opri_360,
Ictidomys tridecemlineatus	ENSSTOG00000022388	1 retrocopy	retro_itri_1882,
Tupaia belangeri	ENSTBEG00000016520	1 retrocopy	retro_tbel_2898,