RetrogeneDB ID: retro_ocun_360

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:48888337..48888879(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MND1
• Ensembl ID: ENSOCUG00000004594
• Aliases: None
• Description: meiotic nuclear divisions 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24839]

Sequence

>retro_ocun_360
GATGTGTTTCAACGAAAAGACATGGAGAAGATTGCTCCCAAAGAAAACAGTGTTACTACCACGTCAGGAAAAGACATCCC
CAGAGTTTAGTTGATGATGGTGTGGTTGACTGTGAGAGGATTGGAACGTCGAGTTACTACTGGGCTTTTCCTAGGAAAGC
TCTTCATGCAAGGAATCGCAAGGTGGAGGTTCTGGAATCCCAGTTGTCTGAAGGAAACCAGAAGTATGCAAACCACAGGA
AAACATGGAGAAAGCTAAAATTGGCCTACACGAGATGGAAGAACGAGCCATGATAGCAAAAGAGCTTTCTTCACTGCCAG
AAGAAAGGGAGCAGCTAAAAGCACAAGTGGAGAAATTATGAGGAATGTGATCCACAAGTTGTGGAAGAAATACGTCAAGC
AAATAAAATAGCCAAAGAAGCTGGTAACAGATAGACTGATAACATAGTTGCAATAAAATCTTGGGCCAAAAGAAAATTTT
GATTGGAAGAAAATAAAATTGATAAAAATTTGGGAATCCCGGAAGACTTTAACAACATAGAC

Alignment

ORF - retro_ocun_360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.07 %
• Parental protein coverage: 88.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DVFQLKDMEKIAPKEKGITAMSVKDVL-QSLVDDGMVDCERIGTSNYYWAFPSKALHVRKRKVEVLESQL
          DVFQ.KDMEKIAPKE...T..S.KD...QSLVDDG.VDCERIGTS.YYWAFP.KALH.R.RKVEVLESQL
Retrocopy DVFQRKDMEKIAPKENSVTTTSGKDIP<QSLVDDGVVDCERIGTSSYYWAFPRKALHARNRKVEVLESQL

Parental  SEGNQKYANLQK-NIEKAKIGRHETEERAMIAKELSSLREERDQLKAEVEK-YKECDPQVVEEIRQANKI
          SEGNQKYAN..K.N.EKAKIG.HE.EERAMIAKELSSL.EER.QLKA.VEK.Y.ECDPQVVEEIRQANKI
Retrocopy SEGNQKYANHRK<NMEKAKIGLHEMEERAMIAKELSSLPEEREQLKAQVEK>YEECDPQVVEEIRQANKI

Parental  AKEAANRWTDNIFAIKSWAKRKFGLEENKIDKNFGIPEDFDYID
          AKEA.NR.TDNI.AIKSWAKRKF.LEENKIDKN.GIPEDF..ID
Retrocopy AKEAGNR*TDNIVAIKSWAKRKF*LEENKIDKNLGIPEDFNNID

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	0.44 RPM
SRP017611_kidney	0.00 RPM	0.10 RPM
SRP017611_liver	0.00 RPM	0.23 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_360 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_360 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_360 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018446	1 retrocopy	retro_amel_1745,
Callithrix jacchus	ENSCJAG00000001993	5 retrocopies	retro_cjac_1495, retro_cjac_1907, retro_cjac_2624, retro_cjac_2946, retro_cjac_3979,
Dipodomys ordii	ENSDORG00000004514	1 retrocopy	retro_dord_99,
Felis catus	ENSFCAG00000022084	1 retrocopy	retro_fcat_1833,
Macaca mulatta	ENSMMUG00000004937	1 retrocopy	retro_mmul_395,
Mus musculus	ENSMUSG00000033752	2 retrocopies	retro_mmus_1172, retro_mmus_3281,
Nomascus leucogenys	ENSNLEG00000005936	1 retrocopy	retro_nleu_998,
Oryctolagus cuniculus	ENSOCUG00000004594	2 retrocopies	retro_ocun_1865, retro_ocun_360 ,
Ochotona princeps	ENSOPRG00000015738	1 retrocopy	retro_opri_1121,
Sorex araneus	ENSSARG00000011001	1 retrocopy	retro_sara_417,
Tupaia belangeri	ENSTBEG00000004475	1 retrocopy	retro_tbel_1734,