RetrogeneDB ID: retro_hsap_4836

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:52862115..52862937(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000224781
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSG00000161960
• Aliases: EIF4A1, DDX2A, EIF-4A, EIF4A, eIF-4A-I, eIF4A-I
• Description: eukaryotic translation initiation factor 4A1 [Source:HGNC Symbol;Acc:3282]

Sequence

>retro_hsap_4836
TCCATGGATTATAACAGAGAACGTGGCAGCCCAGAGGGAATGGACCCTGATGGTGCCATTGAGAGCAACTGTAATGAGAT
CGTTGATAACTTTGATGATATGAATTTAAAGGAGTCTCTTCTTTGGGGCATCTATGCTTACGATTTTGAGAAGTCTTCTG
CTATTCAGCAGAGAGCTATTATTACCTGTATGAAAGGGTATGATGTGATTGCTCAAGCTCAGTCAGGTACTGGCAAGACA
GCCACATTTGCTATTTCCATCCTGCAACAGTTGGAGACCCAAGCACTAATGCTGGCCCCCACCAGAGAACTGGCTCCACA
GATCCAAAAGGTAATTCTGGCACTTGGAGACTATATGGGAGCAACTTGTCATGCCTGCATTGGTGGAACAAATGTTCAAA
CTGAAATGCAAAAACTGCAGGCTGAAGCACCACATATTGTTGTTGGTACACTTGGGAGAGTGTTTGATATGTTAAACAGA
AGATATCTTTTTCCAAAATGGATCAAAATGCTTGTTTTGGATGAAGCAGATGAAATGTTGAGCCATGGGTTTAAGGATGA
AATCTATGAGATTTTCCAAAAACTAAATACAAGTATTCAGGTTGTGTTGCTTTCTGCCACAATGCCAACTGATGTGTTGG
AAGTGACCAAAAAATTCATGAGAGATCCAATTTGAATTCTGGTGAAAAAGGAATAATTGACCCTTGAAGGAATCAAACAG
TTTTATATTAATGTTGAGAGAGAAGAATGGAAGTTGGATACACTTTGTGACTTGTATGAGACACCGACCATTACGCAGGC
TGTTATTTTTCTCAAGGCCCAA

Alignment

ORF - retro_hsap_4836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.55 %
• Parental protein coverage: 68.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVI
          S.D.......P.GM.P.G.IESN.NEIVD.FDDMNL.ESLL.GIYAY.FEK.SAIQQRAI..C.KGYDVI
Retrocopy SMDYNRERGSPEGMDPDGAIESNCNEIVDNFDDMNLKESLLWGIYAYDFEKSSAIQQRAIITCMKGYDVI

Parental  AQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAE
          A..Q...G...T....I.....L....TQAL.LAPTRELA.QIQKV..ALGDYMGA.CHACIGGTNV..E
Retrocopy A--QAQSGTGKTATFAISILQQLE---TQALMLAPTRELAPQIQKVILALGDYMGATCHACIGGTNVQTE

Parental  VQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLS
          .QKLQ.EAPHI.VGT.GRVFDMLNRRYL.PK.IKM.VLDEADEMLS.GFKD.IY.IFQKLN...QVVLLS
Retrocopy MQKLQAEAPHIVVGTLGRVFDMLNRRYLFPKWIKMLVLDEADEMLSHGFKDEIYEIFQKLNTSIQVVLLS

Parental  ATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTR
          ATMP.DVLEVTKKFMRDPI.ILVKKE.LTLEGI.QFYINVEREEWKLDTLCDLYET.TITQAVIF....
Retrocopy ATMPTDVLEVTKKFMRDPI*ILVKKE*LTLEGIKQFYINVEREEWKLDTLCDLYETPTITQAVIFLKAQ

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	4.06 RPM
bodymap2_adrenal	0.00 RPM	24.05 RPM
bodymap2_brain	0.05 RPM	3.59 RPM
bodymap2_breast	0.00 RPM	7.61 RPM
bodymap2_colon	0.00 RPM	3.27 RPM
bodymap2_heart	0.04 RPM	1.90 RPM
bodymap2_kidney	0.00 RPM	4.74 RPM
bodymap2_liver	0.00 RPM	1.94 RPM
bodymap2_lung	0.02 RPM	11.81 RPM
bodymap2_lymph_node	0.04 RPM	10.49 RPM
bodymap2_ovary	0.00 RPM	12.09 RPM
bodymap2_prostate	0.05 RPM	5.92 RPM
bodymap2_skeletal_muscle	0.07 RPM	1.07 RPM
bodymap2_testis	0.00 RPM	1.85 RPM
bodymap2_thyroid	0.06 RPM	6.67 RPM
bodymap2_white_blood_cells	0.00 RPM	3.11 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4836 was not detected

EST

No EST(s) were mapped for retro_hsap_4836 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_200342	209 libraries	367 libraries	1112 libraries	105 libraries	36 libraries

The graphical summary, for retro_hsap_4836 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_4836 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4836 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004900	1 retrocopy	retro_cpor_1088,
Erinaceus europaeus	ENSEEUG00000003581	1 retrocopy	retro_eeur_610,
Felis catus	ENSFCAG00000024897	1 retrocopy	retro_fcat_370,
Homo sapiens	ENSG00000156976	2 retrocopies	retro_hsap_593, retro_hsap_878,
Homo sapiens	ENSG00000161960	10 retrocopies	retro_hsap_1004, retro_hsap_1182, retro_hsap_1252, retro_hsap_1270, retro_hsap_1796, retro_hsap_2520, retro_hsap_4836 , retro_hsap_4873, retro_hsap_4931, retro_hsap_610,
Gorilla gorilla	ENSGGOG00000024702	8 retrocopies	retro_ggor_1321, retro_ggor_1572, retro_ggor_3015, retro_ggor_537, retro_ggor_798, retro_ggor_920, retro_ggor_983, retro_ggor_998,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Myotis lucifugus	ENSMLUG00000003415	3 retrocopies	retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta	ENSMMUG00000013499	1 retrocopy	retro_mmul_1280,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Mus musculus	ENSMUSG00000059796	7 retrocopies	retro_mmus_1810, retro_mmus_1853, retro_mmus_2320, retro_mmus_2473, retro_mmus_3122, retro_mmus_325, retro_mmus_527,
Nomascus leucogenys	ENSNLEG00000009547	7 retrocopies	retro_nleu_2109, retro_nleu_2117, retro_nleu_230, retro_nleu_2470, retro_nleu_2769, retro_nleu_440, retro_nleu_701,
Pan troglodytes	ENSPTRG00000008694	10 retrocopies	retro_ptro_1201, retro_ptro_1465, retro_ptro_2954, retro_ptro_3112, retro_ptro_3247, retro_ptro_450, retro_ptro_750, retro_ptro_810, retro_ptro_862, retro_ptro_870,
Rattus norvegicus	ENSRNOG00000030628	3 retrocopies	retro_rnor_1059, retro_rnor_2213, retro_rnor_2306,
Sorex araneus	ENSSARG00000006017	7 retrocopies	retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605, retro_sara_89,
Ictidomys tridecemlineatus	ENSSTOG00000024814	1 retrocopy	retro_itri_610,