RetrogeneDB ID: retro_ocun_1014

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 19:10040242..10040918(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000028136
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1014
ATGGGTTTCGGAGACCTGAAAAGCCCCGCCGGCCTACAGGTGTTCAACGATTACCTGGCAGACAAGAGCTACATCGAGGG
GTATGTGCCGTCCCAGGCAGATGTGGCAGGATTCGAAGCCGTCTCCGGCCCGCCGCCTGCCGACTTGTGTCATGCCCTAC
GCTGGTATAATCACATCAAGTCCTACGAGAAGGAGAAGGTCAGCTTGCCAGGAATAAAAAAAGCTTTGGGCAAGTATGGC
CCTGCGGATGTGGAAGACACCACAGGAAGCGGAGCCACAGTTAGTAAAGATGACGATGACATTGACCTCTTTCGATCCGA
TGAGGAGGAGGAAAGTGAAGAGGCAAAGAGGTTAAGGGAAGAACGACTTGCACAGTATGAGTCAAAGAAAGCCAAAAAAC
CTGCACTTGTTGCCAAGTCTTCCATCTTACTAGATGTGAAACCCTGGGATGACGAAACAGATATGGTAAAATTGGAGGAG
TGTGTCAGAAGCATTCAAGCAGATGGCTTGGTCTGGGGCTCCTCTAAACTAAGTTCCAGTGGGGTATGGAATTAAGAAGC
TTCAAATACAGTGTGTAGTTGAAGATGACAAAGCTGGAACAGATATGCTGGAGGAGCAGATCACGGCTTTTGAGGACTAT
GTGCAATCCATGGATGTGGCTGCTTTCAACAAGATC

Alignment

ORF - retro_ocun_1014 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.02 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGFGDLKSPAGLQVLNDYLADKSYIEGYVPSQADVAVFEAVSGPPPADLCHALRWYNHIKSYEKEKASLP
          MGFGDLKSPAGLQV.NDYLADKSYIEGYVPSQADVA.FEAVSGPPPADLCHALRWYNHIKSYEKEK.SLP
Retrocopy MGFGDLKSPAGLQVFNDYLADKSYIEGYVPSQADVAGFEAVSGPPPADLCHALRWYNHIKSYEKEKVSLP

Parental  GIKKALGRYGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKRLREERLAQYESKKAKKPALVAKS
          GIKKALG.YGPADVEDTTGSGAT.SKDDDDIDLF.SD.EEESEEAKRLREERLAQYESKKAKKPALVAKS
Retrocopy GIKKALGKYGPADVEDTTGSGATVSKDDDDIDLFRSDEEEESEEAKRLREERLAQYESKKAKKPALVAKS

Parental  SILLDVKPWDDETDMVKLEECVRSIQADGLVWGSSKL-VPVGYGIKKLQIQCVVEDDKVGTDMLEEQITA
          SILLDVKPWDDETDMVKLEECVRSIQADGLVWGSSKL.VPVGYGIKKLQIQCVVEDDK.GTDMLEEQITA
Retrocopy SILLDVKPWDDETDMVKLEECVRSIQADGLVWGSSKL>VPVGYGIKKLQIQCVVEDDKAGTDMLEEQITA

Parental  FEDYVQSMDVAAFNKI
          FEDYVQSMDVAAFNKI
Retrocopy FEDYVQSMDVAAFNKI

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	0.33 RPM	124.78 RPM
SRP017611_kidney	1.22 RPM	188.93 RPM
SRP017611_liver	0.08 RPM	93.72 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1014 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1014 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1014 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,