RetrogeneDB ID: retro_ocun_199

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018751:1341725..1342373(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000012617
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000003942
• Aliases: None
• Description: None

Sequence

>retro_ocun_199
ACAATTGGTGACATGAGTGACACAGAAGATGACGATACTCCTCAGCTTTCTTCCCACGCCTTAGCAGCTCTCCAGGAATT
TTATGCTGAGCAGAAGCAACAAGCTGACCCAGGTGCACATGATAAATATAACATTGGAATAATAGAAGAGAACTGGCAAC
TGAGCCAGTTTTGGTATAGTCCGGAAACTGCCCTACGACTCGCACAGGAAGTGATTACAGCTGCTGGAGAAGGTGGCAGA
ATCGCCTGTGTGAGCGCCCCCAGTGTTTACCAGAAGCTCCGAGAGCTGCACAGAGAAGACTTTTCCATTTGCATCTTTGA
ATATGACAAAAGGTTTGCCATGTATGGAGAGGACTTTATCTTCTATGATTACAATAATCCACTGGATCTACCTGAACACA
TCCCTACACATAGCTTTGACGTCGTGGTGGCGGATCCTCCATATCTTTCTGAGGAGTGTCTCAGGAAGACATCAGAAACC
ATCAAGTACTTGACCAAGGCCAAGATTTTGCTGTGCACAGGGGCCGTCATGGAAGAACAGGCCGCACAGCTCCTGGGGGT
GAAGATGTGCAAGTTCATTCCACGGCACACCCGAAACCTGGCAAATGAGTTCCGCTGTTACATGAATTTCGATTCTGGGC
TGGACTGC

Alignment

ORF - retro_ocun_199 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.64 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDTEDDDTPQLSSHALAALQEFYAEQKQQADPGAHDKYNIGIIEENWQLSQFWYSPETALRLAQEVITA
          MSDTEDDDTPQLSSHALAALQEFYAEQKQQADPGAHDKYNIGIIEENWQLSQFWYSPETALRLAQEVITA
Retrocopy MSDTEDDDTPQLSSHALAALQEFYAEQKQQADPGAHDKYNIGIIEENWQLSQFWYSPETALRLAQEVITA

Parental  AGEGGRIACVSAPSVYQKLRELHREDFSVCIFEYDKRFAIYGEDFIFYDYNNPLDLPEHIPAHSFDVVVA
          AGEGGRIACVSAPSVYQKLRELHREDFS.CIFEYDKRFA.YGEDFIFYDYNNPLDLPEHIP.HSFDVVVA
Retrocopy AGEGGRIACVSAPSVYQKLRELHREDFSICIFEYDKRFAMYGEDFIFYDYNNPLDLPEHIPTHSFDVVVA

Parental  DPPYLSEECLRKTSETIKYLTKAKILLCTGAVMEEQAAQLLGVKMCKFIPRHTRNLANEFRCYVNFNSGL
          DPPYLSEECLRKTSETIKYLTKAKILLCTGAVMEEQAAQLLGVKMCKFIPRHTRNLANEFRCY.NF.SGL
Retrocopy DPPYLSEECLRKTSETIKYLTKAKILLCTGAVMEEQAAQLLGVKMCKFIPRHTRNLANEFRCYMNFDSGL

Parental  DC
          DC
Retrocopy DC

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	0.50 RPM	4.91 RPM
SRP017611_kidney	0.41 RPM	4.97 RPM
SRP017611_liver	0.31 RPM	2.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_199 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_199 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_199 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008296	1 retrocopy	retro_btau_746,
Oryctolagus cuniculus	ENSOCUG00000003942	1 retrocopy	retro_ocun_199 ,