RetrogeneDB ID: retro_ocun_1184

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:19170979..19171635(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021117
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000013434
• Aliases: None
• Description: None

Sequence

>retro_ocun_1184
ATGGCTGAATAATTAGCTTCGATATTCGGGACTGAGAGGACAAGGTTAACCGTTCTTTTTACTTTAATATCGGGGCCTGC
CGGCACGGAGACCAGTGCTCTCGGCTTCACAACAAACCGACTTTCAGCCAGACCATAGTGCTGCTCAACCTGTACCGGAA
TCCACAGAACACGGCCCAAACAGCAGACGGCTCGCATTGTCACGTGAGCGACGTGGAGGTGCAGGAACACTACGATAACT
TCTTCGAGGAGGTGTTCACAGAGCTGCAGGAGAAGTACGGGGAGATCGAGGAGATGAATGTCTGCGACAACCTGGGCGAC
CACCTCGTGGGCAACGTCTACGTCAAGTTCCGGCGGGAGGAGGATGCGGAGCGGGCAGTGGCTGAACTCCATAACCGCTG
GTTCAATGGGCAAGCCGTGCACGCAGAGCTGTCTCCTGTCACCGACTTCCGGGAGTCGTGCTGTCGGCAGTACGAGATGG
GGGAATGCACCCGAGGCGGCTTCTGCAACTTCAGGCACCTGCGGCCCATTTCCCGGAACCTGCGGCGGCAGCTCTACGGG
CGGGGACCCAGGCGCAGGTCACCCCCAAGGTCCCACGCTGGCCATCGTCCCCGAGAGAGGAACAGACGGCATTCTCCGGA
CCACCGGCACGGCCGC

Alignment

ORF - retro_ocun_1184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.91 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEYLASIFGTEK-DKVNCSFYFKIGACRHGDRCSRLHNKPTFSQTIVLLNLYRNPQNTAQTADGSHCHV
          MAE.LASIFGTE..DKVN.SFYF.IGACRHGD.CSRLHNKPTFSQTIVLLNLYRNPQNTAQTADGSHCHV
Retrocopy MAE*LASIFGTER<DKVNRSFYFNIGACRHGDQCSRLHNKPTFSQTIVLLNLYRNPQNTAQTADGSHCHV

Parental  SDVEVQEHYDNFFEEVFTELQEKYGEIEEMNVCDNLGDHLVGNVYVKFRREEDAERAVAELNNRWFNGQA
          SDVEVQEHYDNFFEEVFTELQEKYGEIEEMNVCDNLGDHLVGNVYVKFRREEDAERAVAEL.NRWFNGQA
Retrocopy SDVEVQEHYDNFFEEVFTELQEKYGEIEEMNVCDNLGDHLVGNVYVKFRREEDAERAVAELHNRWFNGQA

Parental  VHAELSPVTDFRESCCRQYEMGECTRGGFCNFMHLRPISRNL-RQLYGRGPRRRSPPRSHAGHRPRERNR
          VHAELSPVTDFRESCCRQYEMGECTRGGFCNF.HLRPISRNL.RQLYGRGPRRRSPPRSHAGHRPRERNR
Retrocopy VHAELSPVTDFRESCCRQYEMGECTRGGFCNFRHLRPISRNLRRQLYGRGPRRRSPPRSHAGHRPRERNR

Parental  RHSPDHRHGR
          RHSPDHRHGR
Retrocopy RHSPDHRHGR

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	2.15 RPM	38.47 RPM
SRP017611_kidney	2.23 RPM	21.39 RPM
SRP017611_liver	0.46 RPM	6.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1184 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1184 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000006383	1 retrocopy	retro_fcat_1650,
Gorilla gorilla	ENSGGOG00000016828	1 retrocopy	retro_ggor_150,
Loxodonta africana	ENSLAFG00000012923	1 retrocopy	retro_lafr_1090,
Mus musculus	ENSMUSG00000078765	1 retrocopy	retro_mmus_540,
Oryctolagus cuniculus	ENSOCUG00000013434	1 retrocopy	retro_ocun_1184 ,
Sus scrofa	ENSSSCG00000002896	1 retrocopy	retro_sscr_543,