RetrogeneDB ID: retro_ocun_576

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:102053964..102054318(-)
• Located in intron of: ENSOCUG00000002744

Retrocopy information

• Ensembl ID: ENSOCUG00000024678
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMED2
• Ensembl ID: ENSOCUG00000003453
• Aliases: None
• Description: transmembrane emp24 domain trafficking protein 2 [Source:HGNC Symbol;Acc:16996]

Sequence

>retro_ocun_576
GTGGAGATCACAGGCCCTGACGATAAAGGGATCTACAGAGGGGGCCGGGAGTCCAGTGGGAAGTACACGTTTGCTGCTCA
CATGGACGGGACGTACAAGTTCTGTTTCAGCAACAGGATGTCCACCATGACCCCAAAGATCGTGATGTTCACCATCGACA
TTGAGGAGGCCCCGAAAGGCCAGGACATGGAAACAGAAGCTCACCAGAACAAGCTAGAAGAAATGATCAGTGAGCTGGCA
GTGGCCATGACAGCCGTAAAGCACGAGCAGGAGTACATGGAGGTGCGAGAGAGGATACACAGAGCCATCAACGACAACAC
CAACAGCAGAGTGGTCCTCTGGTCCTTCTTTGAC

Alignment

ORF - retro_ocun_576 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.22 %
• Parental protein coverage: 82.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQITGPDNKGIYKGDRESSGKYTFAAHMDGTYKFCFSNRMSTMTPKIVMFTIDIGEAPKGQDMETEAHQN
          ..ITGPD.KGIY.G.RESSGKYTFAAHMDGTYKFCFSNRMSTMTPKIVMFTIDI.EAPKGQDMETEAHQN
Retrocopy VEITGPDDKGIYRGGRESSGKYTFAAHMDGTYKFCFSNRMSTMTPKIVMFTIDIEEAPKGQDMETEAHQN

Parental  KLEEMINELAVAMTAVKHEQEYMEVRERIHRAINDNTNSRVVLWSFFE
          KLEEMI.ELAVAMTAVKHEQEYMEVRERIHRAINDNTNSRVVLWSFF.
Retrocopy KLEEMISELAVAMTAVKHEQEYMEVRERIHRAINDNTNSRVVLWSFFD

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	3.37 RPM	38.80 RPM
SRP017611_kidney	9.53 RPM	80.38 RPM
SRP017611_liver	4.93 RPM	47.63 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_576 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_576 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_576 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039630	2 retrocopies	retro_btau_52, retro_btau_819,
Macropus eugenii	ENSMEUG00000006459	2 retrocopies	retro_meug_1478, retro_meug_745,
Oryctolagus cuniculus	ENSOCUG00000003453	1 retrocopy	retro_ocun_576 ,
Oryctolagus cuniculus	ENSOCUG00000012427	1 retrocopy	retro_ocun_566,