RetrogeneDB ID: retro_ocun_1279

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 6:1790401..1791522(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000001209
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PIM2
• Ensembl ID: ENSOCUG00000015757
• Aliases: None
• Description: pim-2 oncogene [Source:HGNC Symbol;Acc:8987]

Sequence

>retro_ocun_1279
GTAGCACTGGGGCTGGCGCGCGCGGCGAATCTTAACGCTGCGCCGTCTGCGGACGCTTCCGGGCCACCGGTTTCCCTGCC
TTCCACCCTGGCGCCCCCAGCCCTGGCTCCCCGGCTGCCCTGCCCCAGGCGTCCACGCCCTGCGGGCTCAGCGGATTCAG
CGGGCTCAATCTGCGCAGCACCTCCTCCATGTTGACCAAGCCTCTGCAGGGGCTCCCCGCGCCCCCGGTGACCCCCACGC
CGCCACCAGGAGGCAAGGATCGGGAAGCGTTCGAGGCCGAGTACCGACTTGGCCCCCTCCTGGGTAAGGGGGGATTTGGC
ACGGTCTTCGCGGGACATCGCGTCACAGATCGACTCCAGGTGGCCATCAAAGTGATCCCTCGGAATCGTGTGTTGGGCTG
GTCCTCCTTGTCCGACTCAGTCTCATGCCCCCTCGAAGTGGCACTGCTCTGGAAGGTGTGTGCAGGTGGTGGGCACCCTG
GTGTCATCCGCCTGCTCGACTGGTTTGAGACACCTGAGGGCTTCATGCTGGTCCTCGAGCGGCCTCTGCCGGCCCAGGAT
CTCTTTGACTACATCACAGAGAAGGGCCCGCTGGGGGAAGGCCGAAGCCGCAGCTTCTTTGGCCAGGTGGTGGCAGCTGT
CCAACACTGCCACGCCCGTGGAGTCGTCCACCGTGACATCAAGGACGAGAACATCCTGATAGACCTACGCCGGGGCTGCG
CCAAGCTCATCGATTTTGGTTCGGGTGCCCTGCTTCATGATGAACCTTACACTGACTTTGATGGGACAAGGGTGTACAGC
CCGCCGGAGTGGATCTCCCGACACCAGTACCACGCGCTCCCGGCCACTGTCTGGTCCCTGGGCATCCTCCTTTATGACAT
GGTGTGTGGGGACATTCCCTTCAAGAGGGACCAGGAGATTTTGGAGGCTGAACTCCATTTCCCGGGTCATGTCTCCCCAG
ACTGCTGTGCCCTGATCCGCCGGTGCCTGGCCCCTAAACCCTCTTCCCGACCGTCACTGGAGGAGATCCTGCTGGACCCC
TGGATGCAAACACCAGCTGAAGATGCACCCCTCAACCCCCCCAAAGGAGGTCCCTCCCCCTTGGCCTGGTCCCTGCTGCC
C

Alignment

ORF - retro_ocun_1279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VALGLARAANLNAAPSADASGPPVSLPSTLAPP-SPGSPAALPRASTPCGLSGFSGLNLRSTSSMLTKPL
          VALGLARAANLNAAPSADASGPPVSLPSTLAPP.SPGSPAALP.ASTPCGLSGFSGLNLRSTSSMLTKPL
Retrocopy VALGLARAANLNAAPSADASGPPVSLPSTLAPP<SPGSPAALPQASTPCGLSGFSGLNLRSTSSMLTKPL

Parental  QGLPAPPVTPTPPPGGKDREAFEAEYRLGPLLGKGGFGTVFAGHRVTDRLQVAIKVIPRNRVLGWSSLLQ
          QGLPAPPVTPTPPPGGKDREAFEAEYRLGPLLGKGGFGTVFAGHRVTDRLQVAIKVIPRNRVLGWSSL..
Retrocopy QGLPAPPVTPTPPPGGKDREAFEAEYRLGPLLGKGGFGTVFAGHRVTDRLQVAIKVIPRNRVLGWSSL--

Parental  SDSVSCPLEVALLWKVCAGGGHPGVIRLLDWFETPEGFMLVLERPLPAQDLFDYITEKGPLGEGRSRSFF
          SDSVSCPLEVALLWKVCAGGGHPGVIRLLDWFETPEGFMLVLERPLPAQDLFDYITEKGPLGEGRSRSFF
Retrocopy SDSVSCPLEVALLWKVCAGGGHPGVIRLLDWFETPEGFMLVLERPLPAQDLFDYITEKGPLGEGRSRSFF

Parental  GQVVAAVQHCHARGVVHRDIKDENILIDLRRGCAKLIDFGSGALLHDEPYTDFDGTRVYSPPEWISRHQY
          GQVVAAVQHCHARGVVHRDIKDENILIDLRRGCAKLIDFGSGALLHDEPYTDFDGTRVYSPPEWISRHQY
Retrocopy GQVVAAVQHCHARGVVHRDIKDENILIDLRRGCAKLIDFGSGALLHDEPYTDFDGTRVYSPPEWISRHQY

Parental  HALPATVWSLGILLYDMVCGDIPFERDQEILEAELHFPGHVSPDCCALIRRCLAPKPSSRPSLEEILLDP
          HALPATVWSLGILLYDMVCGDIPF.RDQEILEAELHFPGHVSPDCCALIRRCLAPKPSSRPSLEEILLDP
Retrocopy HALPATVWSLGILLYDMVCGDIPFKRDQEILEAELHFPGHVSPDCCALIRRCLAPKPSSRPSLEEILLDP

Parental  WMQTPAEDAPLNPPKGGPSPLAWSLLP
          WMQTPAEDAPLNPPKGGPSPLAWSLLP
Retrocopy WMQTPAEDAPLNPPKGGPSPLAWSLLP

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	0.55 RPM	6.02 RPM
SRP017611_kidney	0.41 RPM	3.95 RPM
SRP017611_liver	0.15 RPM	0.31 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1279 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1279 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1279 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007968	1 retrocopy	retro_etel_401,
Mus musculus	ENSMUSG00000031155	2 retrocopies	retro_mmus_2005, retro_mmus_3178,
Oryctolagus cuniculus	ENSOCUG00000015757	1 retrocopy	retro_ocun_1279 ,
Otolemur garnettii	ENSOGAG00000009613	1 retrocopy	retro_ogar_3049,
Sorex araneus	ENSSARG00000008832	3 retrocopies	retro_sara_222, retro_sara_223, retro_sara_395,