RetrogeneDB ID: retro_hsap_3906

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:132719369..132720680(-)
• Located in intron of: ENSG00000106554

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1G
• Ensembl ID: ENSG00000254772
• Aliases: EEF1G, EF1G, GIG35
• Description: eukaryotic translation elongation factor 1 gamma [Source:HGNC Symbol;Acc:3213]

Sequence

>retro_hsap_3906
ATGGCGGCTGGGACCCTGTACACGTATCCTGAAAACTGGAGGGCCTTCAAGGCTCTCATCGCTGCTCAGTACAGCGGGGC
TCAGATCCGCGTGCTCTCCGCACCACCCCACTTCCATTTTGGCCAAACCAACCGCACCTCTGAATTTCTTCGCAAATTTC
CTGCCGGCAAGGTCCCAGCATTTGAGGGTGATGATGGATTCTGTGTGTTTGAGAGCAACGCCATTGCCTACTATGTGAGC
AATGAGGAGCTGCGGGGAAGTACTCCAGAGGCAGCAGCCCAGGTGGTGCAGTGGGTGAGCTTTGCTGATTCCGATATAGT
GCCCCCAGCCAGTACCTGGGTGTTCCCCACCTTGGGCATCATGCACCACAACAAACAGGCCACTGAGAATGCAAAGGAGG
AAGTGAGGCGAATTCTGGGGCTGCTGGATGCTTACTTGAAGACGAGGACTTTTCTGGTGGGCGAACGAGTGACATTGGCT
GACATCACAGTTGTCTGCACCCTGTTGTGGCTCTATAAGCAGGTTCTAGAGCCTTCTTTCCGCCGGGCCTTTCGCAATAC
CAACCGCTGGTTCCTCACCTGCATTAACCAGCCCCAGTTCCGGGCTGTCTTGGGGGAACTGAAACTGTGTGAGAAGATGG
CCCAGTTTGATGCTAAAAAGTTTGCAGAGACCCAGCCTAAAAAGGACACACCACGGAAAGAGAAGGGTTCACGGGAAGAG
AAGCAGAAGCCCCAGGCTGAGCGGAAGGAGGAGAAAAAGGCGGCTGCCCCTGCTCCTGAGGAGGAGATGGATGAATGTGA
GCAGGCGCTGGCTGCTGAGCCCAAGGCCAAGGACCCCTTCGCTCACCTGCCCAAGAGTACCTTTGTGTTGGATGAATTTA
AGCGCAAGTACTCCAATGAGGACACACTCTCTGTGGCACTGCCATATTTCTGGGAGCACTTTGATAAGGACGGCTGGTCC
CTGTGGTACTCAGAGTATCGCTTCCCTGAAGAACTCACTCAGACCTTCATGAGCTGCAATCTCATCACTGGAATGTTCCA
GCGACTGGACAAGCTGAGGAAGAATGCCTTCGCCAGTGTCATCCTTTTTGGAACCAACAATAGCAGCTCCATTTCTGGAG
TCTGGGTCTTCCGAGGCCAGGAGCTTGCCTTTCCGCTGAGTCCAGATTGGCAGGTGGACTACGAGTCATACACATGGCGG
AAACTGGATCCTGGCAGAGAGGAGACCCAGACGCTGGTTCGAGAGTACTTTTCCTGGGAGGGGGCCTTCCAGCATGTGGG
CAAAGCCTTCAATCACGGCAAGATCTTCAAG

Alignment

ORF - retro_hsap_3906 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.4 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF
          MAAGTLYTYPENWRAFKALIAAQYSGAQ.RVLSAPPHFHFGQTNRT.EFLRKFPAGKVPAFEGDDGFCVF
Retrocopy MAAGTLYTYPENWRAFKALIAAQYSGAQIRVLSAPPHFHFGQTNRTSEFLRKFPAGKVPAFEGDDGFCVF

Parental  ESNAIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILG
          ESNAIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILG
Retrocopy ESNAIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILG

Parental  LLDAYLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAVLGEVKLC
          LLDAYLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFR.AF.NTNRWFLTCINQPQFRAVLGE.KLC
Retrocopy LLDAYLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRRAFRNTNRWFLTCINQPQFRAVLGELKLC

Parental  EKMAQFDAKKFAETQPKKDTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPF
          EKMAQFDAKKFAETQPKKDTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPF
Retrocopy EKMAQFDAKKFAETQPKKDTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPF

Parental  AHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYSEYRFPEELTQTFMSCNLITGMFQRLD
          AHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYSEYRFPEELTQTFMSCNLITGMFQRLD
Retrocopy AHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYSEYRFPEELTQTFMSCNLITGMFQRLD

Parental  KLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEETQTLVREYFSWE
          KLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPG.EETQTLVREYFSWE
Retrocopy KLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGREETQTLVREYFSWE

Parental  GAFQHVGKAFNQGKIFK
          GAFQHVGKAFN.GKIFK
Retrocopy GAFQHVGKAFNHGKIFK

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	5.01 RPM	0.14 RPM
bodymap2_adrenal	8.78 RPM	0.16 RPM
bodymap2_brain	1.03 RPM	0.02 RPM
bodymap2_breast	5.16 RPM	0.04 RPM
bodymap2_colon	6.67 RPM	0.04 RPM
bodymap2_heart	2.07 RPM	0.00 RPM
bodymap2_kidney	4.61 RPM	0.04 RPM
bodymap2_liver	2.15 RPM	0.06 RPM
bodymap2_lung	1.55 RPM	0.16 RPM
bodymap2_lymph_node	8.75 RPM	0.00 RPM
bodymap2_ovary	9.62 RPM	0.06 RPM
bodymap2_prostate	13.70 RPM	0.09 RPM
bodymap2_skeletal_muscle	6.66 RPM	0.00 RPM
bodymap2_testis	3.22 RPM	0.02 RPM
bodymap2_thyroid	5.67 RPM	0.62 RPM
bodymap2_white_blood_cells	11.91 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3906 was not detected

EST

No EST(s) were mapped for retro_hsap_3906 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_171152	387 libraries	701 libraries	698 libraries	37 libraries	6 libraries
TSS #2	TSS_171153	96 libraries	29 libraries	391 libraries	569 libraries	744 libraries

The graphical summary, for retro_hsap_3906 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_3906 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3906 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2633

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Erinaceus europaeus	ENSEEUG00000001231	1 retrocopy	retro_eeur_575,
Homo sapiens	ENSG00000254772	4 retrocopies	retro_hsap_2778, retro_hsap_2982, retro_hsap_3906 , retro_hsap_4744,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Loxodonta africana	ENSLAFG00000003339	1 retrocopy	retro_lafr_381,
Macaca mulatta	ENSMMUG00000006598	5 retrocopies	retro_mmul_1447, retro_mmul_1905, retro_mmul_2528, retro_mmul_736, retro_mmul_802,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Mus musculus	ENSMUSG00000071644	7 retrocopies	retro_mmus_1447, retro_mmus_1839, retro_mmus_2350, retro_mmus_2765, retro_mmus_3080, retro_mmus_425, retro_mmus_989,
Nomascus leucogenys	ENSNLEG00000003528	2 retrocopies	retro_nleu_1510, retro_nleu_681,
Pan troglodytes	ENSPTRG00000003768	3 retrocopies	retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Rattus norvegicus	ENSRNOG00000020075	8 retrocopies	retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,
Ictidomys tridecemlineatus	ENSSTOG00000002851	2 retrocopies	retro_itri_852, retro_itri_886,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	13.35 RPM
CEU_NA11843	16.75 RPM
CEU_NA11930	22.00 RPM
CEU_NA12004	8.24 RPM
CEU_NA12400	15.05 RPM
CEU_NA12751	12.31 RPM
CEU_NA12760	26.95 RPM
CEU_NA12827	16.56 RPM
CEU_NA12872	11.76 RPM
CEU_NA12873	14.93 RPM
FIN_HG00183	16.20 RPM
FIN_HG00277	18.93 RPM
FIN_HG00315	11.65 RPM
FIN_HG00321	11.12 RPM
FIN_HG00328	9.94 RPM
FIN_HG00338	13.86 RPM
FIN_HG00349	18.55 RPM
FIN_HG00375	13.82 RPM
FIN_HG00377	11.30 RPM
FIN_HG00378	11.47 RPM
GBR_HG00099	12.64 RPM
GBR_HG00111	12.81 RPM
GBR_HG00114	11.39 RPM
GBR_HG00119	11.04 RPM
GBR_HG00131	10.38 RPM
GBR_HG00133	11.05 RPM
GBR_HG00134	10.46 RPM
GBR_HG00137	14.79 RPM
GBR_HG00142	14.39 RPM
GBR_HG00143	11.07 RPM
TSI_NA20512	13.59 RPM
TSI_NA20513	8.32 RPM
TSI_NA20518	21.59 RPM
TSI_NA20532	15.27 RPM
TSI_NA20538	15.62 RPM
TSI_NA20756	18.22 RPM
TSI_NA20765	7.96 RPM
TSI_NA20771	18.50 RPM
TSI_NA20786	10.62 RPM
TSI_NA20798	11.26 RPM
YRI_NA18870	17.50 RPM
YRI_NA18907	9.67 RPM
YRI_NA18916	9.30 RPM
YRI_NA19093	9.34 RPM
YRI_NA19099	11.72 RPM
YRI_NA19114	13.47 RPM
YRI_NA19118	13.07 RPM
YRI_NA19213	7.89 RPM
YRI_NA19214	7.50 RPM
YRI_NA19223	8.40 RPM

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Indel association:

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