RetrogeneDB ID: retro_ocun_1485

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:83369924..83370378(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000003923
• Aliases: None
• Description: None

Sequence

>retro_ocun_1485
ATGGCTGGAAATGCAGAAAAGGCCAAAAGGGCCTTACCAAGGGTTCACCAAGCTCAACAGGAAGAGGGAACGGTGAACAA
ACAGAAGCCCTTCCTTGCTTTGAAATGTACAGAGCTGCCCAAGGCTGAGAAGTGGAGAGACAGATCATTGGAGCGATCAC
TAAAAAAAAAAGTGGCATATATCCAGAATGCTGGGTTAGGTGTATTCTGAATAGGTGAAATTAACAAGCTGCTAAGAGAG
AAAAGACACTGGCAATTTTGAGTAAAAGAGTGGGGTTGTCCTGATTATGGAAAAAATGGCCCTAAAATTTTAGATCATGA
AGGGAAAGAAGTCTCAGGAAACCAAGGATACAAGCATTCTGGAGCAGCAAAAAAATTTGCCTCCTGTCAGAGAGTTTGAA
AAAGAACCTCTTGCCCCTCCCAGGAAGACATATGCTGAGCTCACGAAGGTATTA

Alignment

ORF - retro_ocun_1485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.52 %
• Parental protein coverage: 54.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARNAEKAMTALARFRQAQLEEGKVKERRPFLASECTELPKAEKWR-RQIIGEISKKVAQIQNAGLGEFR
          MA.NAEKA..AL.R..QAQ.EEG.V....PFLA..CTELPKAEKWR.R.......KKVA.IQNAGLG.F.
Retrocopy MAGNAEKAKRALPRVHQAQQEEGTVNKQKPFLALKCTELPKAEKWRDRSLERSLKKKVAYIQNAGLGVF*

Parental  IRDLNDEINKLLREKGHWEVRVKELGGPDYGKVGPKMLDHEGKEVPGNRGYKYFGAA-KDLPGVRELFEK
          I.....EINKLLREK.HW...VKE.G.PDYGK.GPK.LDHEGKEV.GN.GYK..GAA.K.LP.VRE.FEK
Retrocopy I----GEINKLLREKRHWQF*VKEWGCPDYGKNGPKILDHEGKEVSGNQGYKHSGAA>KNLPPVRE-FEK

Parental  EPLPPPRKTRAELMKAI
          EPL.PPRKT.AEL.K..
Retrocopy EPLAPPRKTYAELTKVL

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	35.98 RPM
SRP017611_kidney	0.00 RPM	35.07 RPM
SRP017611_liver	0.00 RPM	17.03 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1485 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1485 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1485 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000006886	1 retrocopy	retro_dord_331,
Ficedula albicollis	ENSFALG00000000023	1 retrocopy	retro_falb_5,
Loxodonta africana	ENSLAFG00000004015	2 retrocopies	retro_lafr_1070, retro_lafr_1170,
Myotis lucifugus	ENSMLUG00000011804	1 retrocopy	retro_mluc_1401,
Oryctolagus cuniculus	ENSOCUG00000003923	1 retrocopy	retro_ocun_1485 ,
Taeniopygia guttata	ENSTGUG00000003998	1 retrocopy	retro_tgut_5,