RetrogeneDB ID: retro_ocun_1116

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:118053477..118053810(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BET1
• Ensembl ID: ENSOCUG00000017029
• Aliases: None
• Description: Bet1 golgi vesicular membrane trafficking protein [Source:HGNC Symbol;Acc:14562]

Sequence

>retro_ocun_1116
GCAGGCCTGGGGAAAGCAGTACCTCCTGGCCACTCCGGGAACTACGGCGATGCTAGTAGTGCCTGTGAAGAAGAAAACCA
GGGACTCGTTGAAACTGGGAAGCAAAGTAACAGCTACAAAATCTCTGTCCTTTGAAACAGGCTGTGAAATTAAAAATCAA
AATAAATTATTAGCTGAAATGGATTCACAGTTTGACTTTACAATGGGATTTCTAGACAGGACTATGGAAAAACAGAAGGT
TTTTATCCAGAGGAAGCCAAATCCAACTATTGTGCTATATGATGTTGTTTTCACTGTCTGTCTTTTTTTGTCATTTATTT
GATTATTAAACTG

Alignment

ORF - retro_ocun_1116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.38 %
• Parental protein coverage: 96.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AGLGEGVPPGNYGSYGYANSGYSACEEENE-RLTESLRSKVTAIKSLSIEIGHEVKNQNKLLAEMDSQFD
          AGLG..VPPG..G.YG.A....SAC.EE...R....L.SKVTA.KSLS.E.G.E.KNQNKLLAEMDSQFD
Retrocopy AGLGKAVPPGHSGNYGDAS---SAC-EEEN>RDSLKLGSKVTATKSLSFETGCEIKNQNKLLAEMDSQFD

Parental  STTGFLGKTMGKLKI-LSRGSQTKLLCYMMLFSLFV-FFVIYWIIKL
          .T.GFL..TM.K.K..LSRGSQ..LLCYMMLFSL.V.FFVIY.IIKL
Retrocopy FTMGFLDRTMEKQKV>LSRGSQIQLLCYMMLFSLSV>FFVIYLIIKL

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	0.11 RPM	17.99 RPM
SRP017611_kidney	0.00 RPM	20.78 RPM
SRP017611_liver	0.00 RPM	3.78 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1116 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1116 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1116 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003424	1 retrocopy	retro_btau_1054,
Choloepus hoffmanni	ENSCHOG00000001276	1 retrocopy	retro_chof_2211,
Callithrix jacchus	ENSCJAG00000013720	3 retrocopies	retro_cjac_1411, retro_cjac_2019, retro_cjac_3155,
Dasypus novemcinctus	ENSDNOG00000001012	3 retrocopies	retro_dnov_1683, retro_dnov_393, retro_dnov_60,
Homo sapiens	ENSG00000105829	1 retrocopy	retro_hsap_3809,
Gorilla gorilla	ENSGGOG00000002176	1 retrocopy	retro_ggor_2560,
Loxodonta africana	ENSLAFG00000000587	1 retrocopy	retro_lafr_1023,
Macaca mulatta	ENSMMUG00000000007	1 retrocopy	retro_mmul_1656,
Nomascus leucogenys	ENSNLEG00000015441	1 retrocopy	retro_nleu_2151,
Oryctolagus cuniculus	ENSOCUG00000017029	2 retrocopies	retro_ocun_1116 , retro_ocun_355,
Ochotona princeps	ENSOPRG00000004536	4 retrocopies	retro_opri_201, retro_opri_249, retro_opri_388, retro_opri_880,
Pan troglodytes	ENSPTRG00000019408	1 retrocopy	retro_ptro_2584,
Rattus norvegicus	ENSRNOG00000011008	2 retrocopies	retro_rnor_2195, retro_rnor_2196,
Sus scrofa	ENSSSCG00000015325	2 retrocopies	retro_sscr_455, retro_sscr_516,
Tupaia belangeri	ENSTBEG00000000765	2 retrocopies	retro_tbel_3115, retro_tbel_4272,
Tarsius syrichta	ENSTSYG00000009729	2 retrocopies	retro_tsyr_136, retro_tsyr_1843,