RetrogeneDB ID: retro_hsap_4795

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:24806511..24807186(-)
• Located in intron of: ENSG00000101868

Retrocopy information

• Ensembl ID: ENSG00000232472
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EEF1B2
• Ensembl ID: ENSG00000114942
• Aliases: EEF1B2, EEF1B, EEF1B1, EF1B
• Description: eukaryotic translation elongation factor 1 beta 2 [Source:HGNC Symbol;Acc:3208]

Sequence

>retro_hsap_4795
ATGGGTTTCAGAGACCTGAAAAGCCCCGCCGGCCTCCAGGTGCTCAACGATTACCTGGCGGACAAGAGCTACATCGAGGG
GTATGTGCCATCACAAGCAGATGTGGCAGTATTTGAAGCCGTGTCCAGCCCACTGCCTGCCGACTTGTGTCATGCCCTAC
GTTGGTATAATCACATCAAGTCTTACGAAAAGGAAAAGGCCAGCCTGCCAGGAGTGAAGAAAGCTTTGGGCAAGTATGGT
CCTGCCGATGTGGAAGACACTACAGGAAGTGGAGCTACAGATAGTAAAGATGATGATGACATTGACCTCTTTGGATCTGA
TGATGAGGAGGAAAGTGAAGAAGCAAAGAGGCTAAGGGAAGAACGTCTTGCACAATATGAATCAAAGAAAGCCAAAAAAC
CTGCACTTGTTGCCAAGTCTTCCATCTTACTAGATGTGAAACCTTGGGATGATGAGACAGATATGGCGAAATTAGAGGAG
CGCGTCAGAAGCATTCAAGCAGACGGCTTAGTCTGGGGCTCATCTAAACTAGTTCCAGTGGGATACGGAATTAAGAAACT
TCAAATACAGTGTGTAGTTGAAGATGATAAAGTCGGAACAGATATGCTGGAGGAGCAGATCACTGCTTTTGAGGACTACG
TGCAGTCCATGGATGTGGCTGCTTTCAACAAGATC

Alignment

ORF - retro_hsap_4795 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.67 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGFGDLKSPAGLQVLNDYLADKSYIEGYVPSQADVAVFEAVSSPPPADLCHALRWYNHIKSYEKEKASLP
          MGF.DLKSPAGLQVLNDYLADKSYIEGYVPSQADVAVFEAVSSP.PADLCHALRWYNHIKSYEKEKASLP
Retrocopy MGFRDLKSPAGLQVLNDYLADKSYIEGYVPSQADVAVFEAVSSPLPADLCHALRWYNHIKSYEKEKASLP

Parental  GVKKALGKYGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKRLREERLAQYESKKAKKPALVAKS
          GVKKALGKYGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKRLREERLAQYESKKAKKPALVAKS
Retrocopy GVKKALGKYGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKRLREERLAQYESKKAKKPALVAKS

Parental  SILLDVKPWDDETDMAKLEECVRSIQADGLVWGSSKLVPVGYGIKKLQIQCVVEDDKVGTDMLEEQITAF
          SILLDVKPWDDETDMAKLEE.VRSIQADGLVWGSSKLVPVGYGIKKLQIQCVVEDDKVGTDMLEEQITAF
Retrocopy SILLDVKPWDDETDMAKLEERVRSIQADGLVWGSSKLVPVGYGIKKLQIQCVVEDDKVGTDMLEEQITAF

Parental  EDYVQSMDVAAFNKI
          EDYVQSMDVAAFNKI
Retrocopy EDYVQSMDVAAFNKI

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
bodymap2_adipose	0.76 RPM	187.77 RPM
bodymap2_adrenal	1.13 RPM	282.83 RPM
bodymap2_brain	0.30 RPM	104.64 RPM
bodymap2_breast	0.33 RPM	143.58 RPM
bodymap2_colon	1.60 RPM	319.29 RPM
bodymap2_heart	0.09 RPM	61.66 RPM
bodymap2_kidney	0.60 RPM	112.61 RPM
bodymap2_liver	0.34 RPM	139.20 RPM
bodymap2_lung	0.44 RPM	214.31 RPM
bodymap2_lymph_node	0.57 RPM	291.01 RPM
bodymap2_ovary	1.02 RPM	314.33 RPM
bodymap2_prostate	0.92 RPM	279.88 RPM
bodymap2_skeletal_muscle	0.84 RPM	175.31 RPM
bodymap2_testis	0.30 RPM	184.38 RPM
bodymap2_thyroid	0.79 RPM	160.16 RPM
bodymap2_white_blood_cells	0.69 RPM	343.51 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4795 was not detected

EST

No EST(s) were mapped for retro_hsap_4795 retrocopy.

TSS

No TSS is located nearby retro_hsap_4795 retrocopy 5' end.

Lab

retro_hsap_4795 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4795 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_134

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 95 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003015	1 retrocopy	retro_amel_427,
Bos taurus	ENSBTAG00000021979	8 retrocopies	retro_btau_1127, retro_btau_1309, retro_btau_1786, retro_btau_366, retro_btau_367, retro_btau_450, retro_btau_512, retro_btau_792,
Canis familiaris	ENSCAFG00000029635	1 retrocopy	retro_cfam_56,
Choloepus hoffmanni	ENSCHOG00000013835	1 retrocopy	retro_chof_725,
Callithrix jacchus	ENSCJAG00000005805	2 retrocopies	retro_cjac_176, retro_cjac_341,
Dipodomys ordii	ENSDORG00000003669	2 retrocopies	retro_dord_510, retro_dord_592,
Felis catus	ENSFCAG00000010239	1 retrocopy	retro_fcat_1735,
Homo sapiens	ENSG00000114942	9 retrocopies	retro_hsap_1154, retro_hsap_1500, retro_hsap_2397, retro_hsap_2883, retro_hsap_3332, retro_hsap_3480, retro_hsap_3657, retro_hsap_3903, retro_hsap_4795 ,
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,
Microcebus murinus	ENSMICG00000010607	3 retrocopies	retro_mmur_1067, retro_mmur_615, retro_mmur_78,
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,
Macaca mulatta	ENSMMUG00000001054	6 retrocopies	retro_mmul_1456, retro_mmul_1767, retro_mmul_1881, retro_mmul_2140, retro_mmul_894, retro_mmul_969,
Nomascus leucogenys	ENSNLEG00000007098	8 retrocopies	retro_nleu_1220, retro_nleu_1676, retro_nleu_2078, retro_nleu_2107, retro_nleu_2521, retro_nleu_2630, retro_nleu_624, retro_nleu_834,
Otolemur garnettii	ENSOGAG00000011229	3 retrocopies	retro_ogar_2628, retro_ogar_616, retro_ogar_862,
Oreochromis niloticus	ENSONIG00000017630	1 retrocopy	retro_onil_28,
Oryzias latipes	ENSORLG00000018533	1 retrocopy	retro_olat_16,
Procavia capensis	ENSPCAG00000013348	1 retrocopy	retro_pcap_154,
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,
Pteropus vampyrus	ENSPVAG00000017334	2 retrocopies	retro_pvam_1055, retro_pvam_56,
Sorex araneus	ENSSARG00000001524	1 retrocopy	retro_sara_463,
Sarcophilus harrisii	ENSSHAG00000017853	1 retrocopy	retro_shar_208,
Sus scrofa	ENSSSCG00000016128	1 retrocopy	retro_sscr_766,
Ictidomys tridecemlineatus	ENSSTOG00000005437	3 retrocopies	retro_itri_1263, retro_itri_813, retro_itri_873,
Tupaia belangeri	ENSTBEG00000005657	13 retrocopies	retro_tbel_161, retro_tbel_2046, retro_tbel_2094, retro_tbel_2298, retro_tbel_2700, retro_tbel_2776, retro_tbel_3143, retro_tbel_3541, retro_tbel_3542, retro_tbel_4050, retro_tbel_4073, retro_tbel_4205, retro_tbel_611,
Xiphophorus maculatus	ENSXMAG00000006050	1 retrocopy	retro_xmac_21,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	3.34 RPM
CEU_NA11843	4.72 RPM
CEU_NA11930	5.35 RPM
CEU_NA12004	1.94 RPM
CEU_NA12400	2.98 RPM
CEU_NA12751	2.21 RPM
CEU_NA12760	4.67 RPM
CEU_NA12827	3.87 RPM
CEU_NA12872	2.72 RPM
CEU_NA12873	4.05 RPM
FIN_HG00183	3.82 RPM
FIN_HG00277	3.77 RPM
FIN_HG00315	2.32 RPM
FIN_HG00321	2.48 RPM
FIN_HG00328	1.89 RPM
FIN_HG00338	2.51 RPM
FIN_HG00349	4.75 RPM
FIN_HG00375	3.77 RPM
FIN_HG00377	2.70 RPM
FIN_HG00378	2.80 RPM
GBR_HG00099	3.23 RPM
GBR_HG00111	2.34 RPM
GBR_HG00114	2.87 RPM
GBR_HG00119	2.04 RPM
GBR_HG00131	2.21 RPM
GBR_HG00133	2.75 RPM
GBR_HG00134	2.75 RPM
GBR_HG00137	3.22 RPM
GBR_HG00142	2.92 RPM
GBR_HG00143	2.81 RPM
TSI_NA20512	2.60 RPM
TSI_NA20513	2.10 RPM
TSI_NA20518	7.58 RPM
TSI_NA20532	3.57 RPM
TSI_NA20538	3.69 RPM
TSI_NA20756	2.97 RPM
TSI_NA20765	1.47 RPM
TSI_NA20771	3.15 RPM
TSI_NA20786	2.04 RPM
TSI_NA20798	2.40 RPM
YRI_NA18870	4.57 RPM
YRI_NA18907	2.01 RPM
YRI_NA18916	1.85 RPM
YRI_NA19093	2.34 RPM
YRI_NA19099	2.77 RPM
YRI_NA19114	2.80 RPM
YRI_NA19118	3.56 RPM
YRI_NA19213	1.55 RPM
YRI_NA19214	1.89 RPM
YRI_NA19223	2.51 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).