RetrogeneDB ID: retro_ocun_554

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:32878304..32878632(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB22A
• Ensembl ID: ENSOCUG00000004414
• Aliases: None
• Description: RAB22A, member RAS oncogene family [Source:HGNC Symbol;Acc:9764]

Sequence

>retro_ocun_554
GACATCACGAATAAGAAACATTTTCTACATGAAAGAACTGGGGAGTAAGAGAGCTTTGACAGCTTGGGCCACCTGCTAGC
CTAATTGTCATTGCAGGAATAAGTGTGATCTTATCAATGTGAGAGAAGCCACGGGGAGAGATGCTAAGGACTATACTGGC
TCCATTCACGCAATTTTTGTAGAGACCAGTGCAGAAAACGCAATAAACATACATGAACTGTTTATAGAAATTAGCGGAAG
ACTTCCTTCCCACGTCGCCAAACTGCCATCTGATGGTGATAGCTTCAGACTCCAAAGGCAGCCTTCAGAGCCGAGACAAA
ACTGCTGC

Alignment

ORF - retro_ocun_554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.96 %
• Parental protein coverage: 58.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DITKE-ETFSTLKNW-VKELRQHGPPNIVVAIAG-NKCDLIDVREVMERDAKDYADSIHAIFVETSAKNA
          DIT...ETFST.KNW.V.EL.Q.GPP.....IAG.NKCDLI.VRE...RDAKDY..SIHAIFVETSA.NA
Retrocopy DITNK<ETFST*KNWGVREL*QLGPPASLIVIAG<NKCDLINVREATGRDAKDYTGSIHAIFVETSAENA

Parental  ININELFIEISRRIPSGDTSQPSGSKGFKLRRQPSEPRRSCC
          INI.ELFIEIS.R.PS.....PS....F.L.RQPSEPR..CC
Retrocopy INIHELFIEISGRLPSHVAKLPSDGDSFRLQRQPSEPRQNCC

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	17.94 RPM
SRP017611_kidney	0.00 RPM	15.81 RPM
SRP017611_liver	0.00 RPM	5.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_554 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_554 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_554 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012646	1 retrocopy	retro_amel_617,
Canis familiaris	ENSCAFG00000012101	1 retrocopy	retro_cfam_501,
Callithrix jacchus	ENSCJAG00000019039	2 retrocopies	retro_cjac_1715, retro_cjac_842,
Microcebus murinus	ENSMICG00000008382	1 retrocopy	retro_mmur_1546,
Oryctolagus cuniculus	ENSOCUG00000004414	1 retrocopy	retro_ocun_554 ,
Oryctolagus cuniculus	ENSOCUG00000012200	1 retrocopy	retro_ocun_1034,
Oryctolagus cuniculus	ENSOCUG00000013895	1 retrocopy	retro_ocun_1193,
Otolemur garnettii	ENSOGAG00000015779	1 retrocopy	retro_ogar_2851,