RetrogeneDB ID: retro_ocun_922

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:63803448..63803915(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1B3
• Ensembl ID: ENSOCUG00000009848
• Aliases: EEF1B3, EEF1B, EF1B
• Description: eukaryotic translation elongation factor 1 beta 3 (EEF1B3), mRNA [Source:RefSeq mRNA;Acc:NM_001082399]

Sequence

>retro_ocun_922
ATGGGTTTCAGAGACCTAAAAAGCCTCACCTGCCTCTGGCTCAATGATTACGGGGCAGACAAGAGTTATATCAGAGGGCA
TGTGCCATCACAAGCAGCTTTGGCAGTATTTGAAGCAGTCTCTGGCCACACAACCTACCGACCTGTGATCATACCCTACG
CTGGTATATCACATCAAATCTTATGAGAAGGAGAAGCCCAGCCTGCCAGGAGTTAAAAAAAAGCTCTGGACAAGAATGGC
CCTGCAGATGTGGAAGACACCACAGGAAGTGGAACCACAGATAGTGATAATGACATTGACCTCTTTGGACCAGATAAGAA
GGAGGAACATGAAGATGGAAGGGGCTAAGGGAGGAATAACTTGCACAGTCTGAGTCAAAGTCAAAAGCTACCCTTGTTGC
CAAGACTTCCATCTTTCATGATATAAAATCTTGGGATGACAAAACAAATAGGACAAAATTGGATGAG

Alignment

ORF - retro_ocun_922 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.66 %
• Parental protein coverage: 71.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MGFGDLKSPAGLQVLNDYLADKSYIEGYVPSQADVAVFEAVSG-PPPADL-CHALRWY-NHIKSYEKEKA
          MGF.DLKS...L..LNDY.ADKSYI.G.VPSQA..AVFEAVSG...P.DL..H.LRWY..HIKSYEKEK.
Retrocopy MGFRDLKSLTCLW-LNDYGADKSYIRGHVPSQAALAVFEAVSG>TQPTDL>DHTLRWY<YHIKSYEKEKP

Parental  SLPGIKKAL-GRYGP-ADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEA-KRLREERLAQYESKKAKKP
          SLPG.KK.L.G...P.ADVEDTTGSG.TDS..D.DIDLFG.D..EE.E...K.LREE.LAQ.ESK...K.
Retrocopy SLPGVKKKL>GQEWP>ADVEDTTGSGTTDS--DNDIDLFGPDKKEEHEDG<KGLREE*LAQSESK--SKA

Parental  ALVAKSSILLDVKPWDDETDMVKLEE
          .LVAK.SI..D.K.WDD.T...KL.E
Retrocopy TLVAKTSIFHDIKSWDDKTNRTKLDE

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	124.78 RPM
SRP017611_kidney	0.00 RPM	188.93 RPM
SRP017611_liver	0.00 RPM	93.72 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_922 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_922 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_922 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029635	1 retrocopy	retro_cfam_56,
Callithrix jacchus	ENSCJAG00000005805	2 retrocopies	retro_cjac_176, retro_cjac_341,
Cavia porcellus	ENSCPOG00000014496	4 retrocopies	retro_cpor_1116, retro_cpor_1381, retro_cpor_1407, retro_cpor_296,
Gorilla gorilla	ENSGGOG00000007002	2 retrocopies	retro_ggor_134, retro_ggor_2000,
Macropus eugenii	ENSMEUG00000002654	8 retrocopies	retro_meug_1418, retro_meug_1846, retro_meug_1917, retro_meug_240, retro_meug_241, retro_meug_52, retro_meug_775, retro_meug_949,
Myotis lucifugus	ENSMLUG00000016602	8 retrocopies	retro_mluc_1035, retro_mluc_1068, retro_mluc_1104, retro_mluc_1167, retro_mluc_1542, retro_mluc_1578, retro_mluc_1681, retro_mluc_1857,
Oryctolagus cuniculus	ENSOCUG00000009848	4 retrocopies	retro_ocun_1014, retro_ocun_1240, retro_ocun_544, retro_ocun_922 ,
Oreochromis niloticus	ENSONIG00000017630	1 retrocopy	retro_onil_28,
Ochotona princeps	ENSOPRG00000017163	3 retrocopies	retro_opri_1192, retro_opri_294, retro_opri_748,
Oryzias latipes	ENSORLG00000018533	1 retrocopy	retro_olat_16,
Pongo abelii	ENSPPYG00000013107	7 retrocopies	retro_pabe_1251, retro_pabe_1656, retro_pabe_2163, retro_pabe_2389, retro_pabe_2419, retro_pabe_2746, retro_pabe_2876,
Sarcophilus harrisii	ENSSHAG00000017853	1 retrocopy	retro_shar_208,
Ictidomys tridecemlineatus	ENSSTOG00000005437	3 retrocopies	retro_itri_1263, retro_itri_813, retro_itri_873,
Xiphophorus maculatus	ENSXMAG00000006050	1 retrocopy	retro_xmac_21,