RetrogeneDB ID: retro_hsap_3480

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:64190038..64190431(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000225121
• 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_3480
ATGGGTTTCAGAGACCTGAAAAGCCCCACTGGCCTCCAGGTGCACAATGGTTACCTGGCTGACCAGAGCTGCAACAAGGG
GTATGTGCCATCACAAGCAGACGTGGCAGTAATTGAAGCAGTCTCCAGTCCATTGTCCGGTAATTTGTGTCATGCTCTAC
ATTGGTATAATTACATCAAGTCTTACGAAAAGGAAAAAGCCAGCCTAGCAGGAATGAAGAAAGCTTTGGGCAAGTATGGA
CCTGCTAATGTGGAAGATAGTAGAGGAAGTGGAGCTACAGATAGTGAAGATGACAATGACATTTATCTATTTGGATTTGA
TAAGGGGGAGGAAAGCAAAGAATCAAAAAGGCAAAGGGAAGAATACCCTGCATAGTATGAATCAAAGAAAGCC

Alignment

ORF - retro_hsap_3480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.57 %
• Parental protein coverage: 58.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGFGDLKSPAGLQVLNDYLADKSYIEGYVPSQADVAVFEAVSSPPPADLCHALRWYNHIKSYEKEKASLP
          MGF.DLKSP.GLQV.N.YLAD.S...GYVPSQADVAV.EAVSSP....LCHAL.WYN.IKSYEKEKASL.
Retrocopy MGFRDLKSPTGLQVHNGYLADQSCNKGYVPSQADVAVIEAVSSPLSGNLCHALHWYNYIKSYEKEKASLA

Parental  GVKKALGKYGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKRLREERLAQYESKKA
          G.KKALGKYGPA.VED..GSGATDS.DD.DI.LFG.D..EES.E.KR.REE..A.YESKKA
Retrocopy GMKKALGKYGPANVEDSRGSGATDSEDDNDIYLFGFDKGEESKESKRQREEYPA*YESKKA

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	0.00 RPM	187.77 RPM
bodymap2_adrenal	0.00 RPM	282.83 RPM
bodymap2_brain	0.00 RPM	104.64 RPM
bodymap2_breast	0.00 RPM	143.58 RPM
bodymap2_colon	0.00 RPM	319.29 RPM
bodymap2_heart	0.00 RPM	61.66 RPM
bodymap2_kidney	0.00 RPM	112.61 RPM
bodymap2_liver	0.00 RPM	139.20 RPM
bodymap2_lung	0.00 RPM	214.31 RPM
bodymap2_lymph_node	0.00 RPM	291.01 RPM
bodymap2_ovary	0.00 RPM	314.33 RPM
bodymap2_prostate	0.00 RPM	279.88 RPM
bodymap2_skeletal_muscle	0.00 RPM	175.31 RPM
bodymap2_testis	0.00 RPM	184.38 RPM
bodymap2_thyroid	0.00 RPM	160.16 RPM
bodymap2_white_blood_cells	0.00 RPM	343.51 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3480 was not detected

EST

No EST(s) were mapped for retro_hsap_3480 retrocopy.

TSS

No TSS is located nearby retro_hsap_3480 retrocopy 5' end.

Lab

retro_hsap_3480 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3480 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2876
Macaca mulatta	retro_mmul_1767

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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,