RetrogeneDB ID: retro_ocun_613

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:61416403..61416766(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GMNN
• Ensembl ID: ENSOCUG00000000728
• Aliases: None
• Description: geminin, DNA replication inhibitor [Source:HGNC Symbol;Acc:17493]

Sequence

>retro_ocun_613
ACACATGAGTCTTCCAGCTCTGGAGTTTTTATTGTCCCAGAACACAGTGAAAATAAAAATCTTGAAGGAGTCACTGAGAA
CCATTTGATTTTTTGATTAAAGAAAATCCATTTCCTTAGTCTTGAAAAGAAGTGGCAAAAAAATGGAGGAAGTCTCTCTG
CAAAGCACTAAGTTAATCAAGTAACTTTGTAAAGAAATCAAATGAAAGGACAATGCAATTTGTCACCTGAAAAAGGAGAA
TACAGAATTGGAGGAAGTAGCAGAACATGTTCAGTTGTGGCAAAGGTAATAGGGAGAGTGAACGATGGACTGCTGGCTGA
CTTTGAATCACTGGATAGTCAGGAATTTGATTATAAAGAAGAA

Alignment

ORF - retro_ocun_613 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.8 %
• Parental protein coverage: 58.65 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TAKTSSPGVVTVSEHSENKNLEGVTQ-EAFDLMVKENASSQYWKEVAENRRKALYETLKENEK-LHKEIE
          T...SS.GV..V.EHSENKNLEGVT..E.FD...KEN......KEVA...RK.L...L......L.KEI.
Retrocopy THESSSSGVFIVPEHSENKNLEGVTE<EPFDFLIKENPFP*S*KEVAKKWRKSLCKALS*SSN<LCKEIK

Parental  QKDNEIARLKKENKELAEVAEHVQ-YMAQVIETLSDRTLHDFESPDSQEFDSEEE
          .KDN.I..LKKEN.EL.EVAEHVQ...A.VI....D..L.DFES.DSQEFD..EE
Retrocopy *KDNAICHLKKENTELEEVAEHVQ<VVAKVIGRVNDGLLADFESLDSQEFDYKEE

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	6.84 RPM
SRP017611_kidney	0.00 RPM	6.39 RPM
SRP017611_liver	0.00 RPM	8.17 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_613 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_613 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_613 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006161	1 retrocopy	retro_cjac_1012,
Microcebus murinus	ENSMICG00000014010	1 retrocopy	retro_mmur_594,
Myotis lucifugus	ENSMLUG00000014849	2 retrocopies	retro_mluc_1589, retro_mluc_743,
Monodelphis domestica	ENSMODG00000011682	1 retrocopy	retro_mdom_1800,
Mus musculus	ENSMUSG00000006715	2 retrocopies	retro_mmus_1525, retro_mmus_2213,
Oryctolagus cuniculus	ENSOCUG00000000728	1 retrocopy	retro_ocun_613 ,
Otolemur garnettii	ENSOGAG00000004982	1 retrocopy	retro_ogar_1726,
Ochotona princeps	ENSOPRG00000007969	1 retrocopy	retro_opri_439,
Rattus norvegicus	ENSRNOG00000018782	1 retrocopy	retro_rnor_820,
Sarcophilus harrisii	ENSSHAG00000004058	2 retrocopies	retro_shar_581, retro_shar_769,
Tupaia belangeri	ENSTBEG00000010502	2 retrocopies	retro_tbel_1028, retro_tbel_353,