RetrogeneDB ID: retro_ocun_1034

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:35990257..35990719(+)
• Located in intron of: ENSOCUG00000027343

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5A
• Ensembl ID: ENSOCUG00000012200
• Aliases: None
• Description: RAB5A, member RAS oncogene family [Source:HGNC Symbol;Acc:9783]

Sequence

>retro_ocun_1034
CTGTGTCTTGATGACACAACAGTAAAATTTGAAATATGAGGGTCAGCTGGTCAAGAACTATACCATAGCCTAGCACTGAT
GTACTACAGAGGGGCACAAGCAGCCTTCACTATTTATGGTATCCCAAACGAGGAGTCCTTTGCAAAAGCAAAAAACTAGG
TTAAAGAGCTTTAGAGGCAAGCACGTCCGAACTTTGTAATAGCTGTATCAGGATACAAGACTGACCTAGCAAATCGAAGA
TCTGTAGGTTTCCATGAAGCACAGGCCTATGCAGGTGACGTTAGTTTATTATTCATGGAGACATCAGCTAAAACATTGAT
GAATGTAAATGAAACATTCATGAAAATAGCTAAAAAGTTGCTAAAGAATGAGCCACAGAATCCAGGAGCAAACTCTGCTA
GAGTCAGAGGGGTAGACCTTACTGAACCTACACAACCAACCAGGAGTTAGGGTTGTAGTAAC

Alignment

ORF - retro_ocun_1034 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.92 %
• Parental protein coverage: 71.63 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALS
          .CLDDTTVKFEI...AGQE.YHSLA.MYYRGAQAA...Y.I.NEESFA.AKN.VKEL.RQA.PN.VIA.S
Retrocopy LCLDDTTVKFEI*GSAGQELYHSLALMYYRGAQAAFTIYGIPNEESFAKAKN*VKEL*RQARPNFVIAVS

Parental  GNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKNEPQNPGGNSARGRGVDL
          G.K.DLAN.R.V.F.EAQ.YA.D.SLLFMETSAKT.MNVNE.FM.IAKKL.KNEPQNPG.NSAR.RGVDL
Retrocopy GYKTDLANRRSVGFHEAQAYAGDVSLLFMETSAKTLMNVNETFMKIAKKLLKNEPQNPGANSARVRGVDL

Parental  TEPTQPTRSQCCSN
          TEPTQPTRS..CSN
Retrocopy TEPTQPTRS*GCSN

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	106.07 RPM
SRP017611_kidney	0.00 RPM	45.51 RPM
SRP017611_liver	0.00 RPM	20.58 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1034 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1034 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1034 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000954	1 retrocopy	retro_amel_958,
Bos taurus	ENSBTAG00000046385	1 retrocopy	retro_btau_300,
Callithrix jacchus	ENSCJAG00000003731	1 retrocopy	retro_cjac_3268,
Cavia porcellus	ENSCPOG00000005322	2 retrocopies	retro_cpor_1213, retro_cpor_219,
Dipodomys ordii	ENSDORG00000012429	1 retrocopy	retro_dord_288,
Felis catus	ENSFCAG00000004455	2 retrocopies	retro_fcat_1349, retro_fcat_984,
Homo sapiens	ENSG00000144566	1 retrocopy	retro_hsap_1074,
Gorilla gorilla	ENSGGOG00000015981	1 retrocopy	retro_ggor_848,
Loxodonta africana	ENSLAFG00000008321	1 retrocopy	retro_lafr_267,
Macaca mulatta	ENSMMUG00000006992	2 retrocopies	retro_mmul_227, retro_mmul_839,
Monodelphis domestica	ENSMODG00000014793	2 retrocopies	retro_mdom_1219, retro_mdom_1993,
Mus musculus	ENSMUSG00000017831	1 retrocopy	retro_mmus_1645,
Nomascus leucogenys	ENSNLEG00000003434	1 retrocopy	retro_nleu_2466,
Oryctolagus cuniculus	ENSOCUG00000004414	1 retrocopy	retro_ocun_554,
Oryctolagus cuniculus	ENSOCUG00000012200	1 retrocopy	retro_ocun_1034 ,
Oryctolagus cuniculus	ENSOCUG00000013895	1 retrocopy	retro_ocun_1193,
Pongo abelii	ENSPPYG00000014074	2 retrocopies	retro_pabe_3094, retro_pabe_894,
Pan troglodytes	ENSPTRG00000014682	1 retrocopy	retro_ptro_731,
Ictidomys tridecemlineatus	ENSSTOG00000026229	1 retrocopy	retro_itri_398,
Tarsius syrichta	ENSTSYG00000007642	3 retrocopies	retro_tsyr_1544, retro_tsyr_315, retro_tsyr_946,
Tursiops truncatus	ENSTTRG00000001374	1 retrocopy	retro_ttru_949,