RetrogeneDB ID: retro_ocun_742

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:20542079..20542588(-)
• Located in intron of: ENSOCUG00000000996

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000013664
• Aliases: None
• Description: None

Sequence

>retro_ocun_742
GTAAAGGTTACTATATGAAAAATAAAGATACCAGGAAGAGTAAAGAGGTTGCATTTATTTTGTTTTTGGATAAAGACTGC
ACAAAACTGCACCAGGGTGATAAACAACAAACAGTATTTGTAGAGTGAAAAAGCAAGCATTGCTGTCTACAGTGGAAGAG
TGGCTGAATTCATCCGAAGACGAAACTACTTTCAGAAATCCAAGTGCTGTGAACGTGGGGAACGTGGACACTTAAGTTAT
GCCTGACCTAAAAATATGCTTGGAGCACATGAACCTCCAAAGAAGAAAGAGAAAAAAGTTCCTGAACCAGAGGAAGCAGA
AGAAAGTGAAGACGAAGGGGAGGACCCTGCTCGGGACAGCCTCACCAGGCCATAGCCTTCCCGCAAGCCCAGCTGAAGAC
GAACAAGGACATGGAGACCCAGTCCAGGGGTCCCTCCACATCCGATGACTCGAGACGGCCGAGGATGAAGAAAAGCACAT
GCTTCAGTGATGAGGAGGAGCTCGGTGAC

Alignment

ORF - retro_ocun_742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LRVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAIDNGRAAEFIRRRNYFDKSK
          ..VTI.K.K.....K......F..K..AQNCTR.I.N........KASIA...GR.AEFIRRRNYF.KSK
Retrocopy VKVTI*KIKIPGRVKRLHLFCFWIK-TAQNCTRVI-NNKQYL*SEKASIAVYSGRVAEFIRRRNYFQKSK

Parental  CYECGESGHLSYACPKNMLGEREPPVPEPEE--EIEEVEESEDEGEDPALDSLS-QAIAFQQAKI-EEEQ
          C.E.GE.GHLSYA.PKNMLG..EPP........E.EE.EESEDEGEDPA.DSL..QAIAF.QA...E.EQ
Retrocopy CCERGERGHLSYA*PKNMLGAHEPPKKKEKKVPEPEEAEESEDEGEDPARDSLT<QAIAFPQAQL<EDEQ

Parental  -RKWRPGPG-GPSTSDDSRRPRIKKSTYFSDEEELSD
          .R.WRP.PG.GPSTSDDSRRPR.KKST.FSDEEEL.D
Retrocopy <RTWRPSPG<GPSTSDDSRRPRMKKSTCFSDEEELGD

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	0.06 RPM	9.27 RPM
SRP017611_kidney	0.20 RPM	11.66 RPM
SRP017611_liver	0.15 RPM	5.78 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_742 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_742 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_742 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019119	2 retrocopies	retro_btau_1637, retro_btau_830,
Choloepus hoffmanni	ENSCHOG00000004490	1 retrocopy	retro_chof_1549,
Callithrix jacchus	ENSCJAG00000017749	3 retrocopies	retro_cjac_2009, retro_cjac_2662, retro_cjac_4174,
Cavia porcellus	ENSCPOG00000014554	1 retrocopy	retro_cpor_757,
Dasypus novemcinctus	ENSDNOG00000010107	11 retrocopies	retro_dnov_1075, retro_dnov_1120, retro_dnov_1127, retro_dnov_1357, retro_dnov_1599, retro_dnov_1673, retro_dnov_1846, retro_dnov_2146, retro_dnov_2432, retro_dnov_2466, retro_dnov_888,
Equus caballus	ENSECAG00000012174	1 retrocopy	retro_ecab_184,
Erinaceus europaeus	ENSEEUG00000000397	1 retrocopy	retro_eeur_298,
Echinops telfairi	ENSETEG00000019302	1 retrocopy	retro_etel_2080,
Gorilla gorilla	ENSGGOG00000015647	1 retrocopy	retro_ggor_3029,
Loxodonta africana	ENSLAFG00000008847	2 retrocopies	retro_lafr_1183, retro_lafr_783,
Microcebus murinus	ENSMICG00000017422	3 retrocopies	retro_mmur_1236, retro_mmur_236, retro_mmur_466,
Myotis lucifugus	ENSMLUG00000001332	3 retrocopies	retro_mluc_2290, retro_mluc_319, retro_mluc_364,
Monodelphis domestica	ENSMODG00000008893	1 retrocopy	retro_mdom_114,
Mus musculus	ENSMUSG00000022635	1 retrocopy	retro_mmus_847,
Oryctolagus cuniculus	ENSOCUG00000013664	2 retrocopies	retro_ocun_742 , retro_ocun_896,
Otolemur garnettii	ENSOGAG00000013178	2 retrocopies	retro_ogar_43, retro_ogar_812,
Ochotona princeps	ENSOPRG00000011095	2 retrocopies	retro_opri_729, retro_opri_927,
Procavia capensis	ENSPCAG00000011749	2 retrocopies	retro_pcap_458, retro_pcap_64,
Pan troglodytes	ENSPTRG00000004838	1 retrocopy	retro_ptro_3231,
Pteropus vampyrus	ENSPVAG00000006651	2 retrocopies	retro_pvam_1343, retro_pvam_697,