RetrogeneDB ID: retro_hsap_4873

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:91368243..91369460(-)
• Located in intron of: ENSG00000102290

Retrocopy information

• Ensembl ID: ENSG00000229132
• 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_4873
ATGTCTGTAAGCCAGGATTCCTGATCCAGAGACAATGGCCCCGATGGGATGGAGCCCGAAGGCGTCATCGAGAGTAACTG
GAATGAGATTGTTGACAGCTTTGATGACATGAACCTCTCGGAGTCCCTTCTCCGTGACATCTATGCCTATGGTTTTGAGA
AGCCCTCTGCCATCCAGCAGCAAGCCATTCTACCTTGTATCAGGGGTTATAATGTAATCGCTCAAGCCTGATCTGGGACT
GGGAAAATGGCCACATTTGCCATATCGATTCTGCAGCAGATTGCATTAGATCTAAAAGCCACCCAGGCCTTGGTCCTAGC
ACCCACTCGAGAATTGGCTCAGCAGATACAGAAGGTGGTCATGGCACTAGTAGACTACATGGGTGCCTCCTGTCATGCCT
GTATCAGGGGCACCAATGTGCGTGCTGAGGTGCAGAAACTGCAGATGGAAGCTCCCCACATCATCGTGGGTACCCCTAGC
TGTGTGTTTGATATGCTTAACCGGAGATACCTATCTCCCAAATACATCAAGATGTTTGTACTGGATGAAGCTGACGAAAT
GTTAAGCCGTGGATTCAAGGACCAGATCTATGACATATTCCAAAAGCTCAACAGCAACACCCAGGTAGTTTTGCTGTCAG
CTACAATGCCTTCTGATGTGCTTGAGGTGATCAAGAAGTTCATGAGGGACCCCATTCGGATTCTTGTCAAGAAGGAAGAG
TTGACCCTGGAGGGTATCCGCCAATTCTACATCAACGTGGAACGAGAGGAGTGGAAGCTGGACACACTATGTGACTTGTA
TGAAACCCTGACCATCACCCAGGCAGTCATCTTCATCAATACCCGGAGGAAGGTGGACTGGCTCACCGAGAAGATGCATG
CTCGAGATTTCACTGTCTCCGCCATGCATGGAGATATGGACCAAAAGGAGCGAGACGTGATCACGAGGGAGTTTCGTTCT
GGCTCTAGCAGAGTTTTGATTACCACTGACCTGCTGGCCAGAGGCATTGATGTGCAGCAGGTTTCTTTAGTCATCAACTA
TGACCTTCCCACCAACAGGGAAAACTATATCCACAGAATCAGTCGAGGTGGACAGTTTGGCCGTAAAGATGTGGCTATTA
ACATGGTGACAGAAGAAGACAAGAGGACTCTTCGAGACATTGAGACCTTCTACAACACCTCCATTGAGGAAATGCCCCCA
ATGTTGCTGACCTCATC

Alignment

ORF - retro_hsap_4873 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGY
          MS.SQDS.SRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLR.IYAYGFEKPSAIQQ.AILPCI.GY
Retrocopy MSVSQDS*SRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRDIYAYGFEKPSAIQQQAILPCIRGY

Parental  DVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNV
          .VIAQA.SGTGK.ATFAISILQQI.LDLKATQALVLAPTRELAQQIQKVVMAL.DYMGASCHACI.GTNV
Retrocopy NVIAQA*SGTGKMATFAISILQQIALDLKATQALVLAPTRELAQQIQKVVMALVDYMGASCHACIRGTNV

Parental  RAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV
          RAEVQKLQMEAPHIIVGTP..VFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV
Retrocopy RAEVQKLQMEAPHIIVGTPSCVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV

Parental  LLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFIN
          LLSATMPSDVLEV.KKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFIN
Retrocopy LLSATMPSDVLEVIKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFIN

Parental  TRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP
          TRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVI.REFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP
Retrocopy TRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVITREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP

Parental  TNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMP-LNVADLI
          TNRENYIHRI.RGG.FGRK.VAINMVTEEDKRTLRDIETFYNTSIEEMP..NVADLI
Retrocopy TNRENYIHRISRGGQFGRKDVAINMVTEEDKRTLRDIETFYNTSIEEMP<PNVADLI

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	0.34 RPM	4.06 RPM
bodymap2_adrenal	0.27 RPM	24.05 RPM
bodymap2_brain	0.28 RPM	3.59 RPM
bodymap2_breast	0.14 RPM	7.61 RPM
bodymap2_colon	0.31 RPM	3.27 RPM
bodymap2_heart	0.00 RPM	1.90 RPM
bodymap2_kidney	0.37 RPM	4.74 RPM
bodymap2_liver	0.11 RPM	1.94 RPM
bodymap2_lung	0.12 RPM	11.81 RPM
bodymap2_lymph_node	0.05 RPM	10.49 RPM
bodymap2_ovary	0.21 RPM	12.09 RPM
bodymap2_prostate	0.10 RPM	5.92 RPM
bodymap2_skeletal_muscle	0.07 RPM	1.07 RPM
bodymap2_testis	0.13 RPM	1.85 RPM
bodymap2_thyroid	0.08 RPM	6.67 RPM
bodymap2_white_blood_cells	0.14 RPM	3.11 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4873 was not detected

EST

No EST(s) were mapped for retro_hsap_4873 retrocopy.

TSS

No TSS is located nearby retro_hsap_4873 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: CAAGGAAACCACAGGTATGT (20 nt long)
• Reverse primer: TAGGTATCTCCGGTTAAGCA (20 nt long)
• Anneling temperature: 60 °C
• (Expected) product size: 778
• Electrophoresis gel image:
• Additional comment: Black arrows indicate PCR products of retrogenes undergoing deletions in various human populations (A-J). Lane 1 –GeneRuler Low Range DNA Ladder (Thermo Scientific); 2 –Heart; 3 –Brain; 4 –Placenta; 5 –Lung; 6 –Liver; 7 –Skeletal Muscle; 8 –Kidney; 9 –Pancreas; 10 –Spleen; 11 –Thymus; 12 –Prostate; 13 –Testis; 14 –Ovary, 15 –Small intestine 16 –Colon; 17 –Leukocyte; NTC—No template control (water instead of cDNA).

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4873 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4931
Pan troglodytes	retro_ptro_3247
Pongo abelii	retro_pabe_3792

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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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.39 RPM
CEU_NA11843	0.74 RPM
CEU_NA11930	1.43 RPM
CEU_NA12004	0.34 RPM
CEU_NA12400	0.53 RPM
CEU_NA12751	0.36 RPM
CEU_NA12760	0.94 RPM
CEU_NA12827	0.99 RPM
CEU_NA12872	0.54 RPM
CEU_NA12873	0.41 RPM
FIN_HG00183	0.93 RPM
FIN_HG00277	0.85 RPM
FIN_HG00315	0.63 RPM
FIN_HG00321	0.66 RPM
FIN_HG00328	0.62 RPM
FIN_HG00338	0.53 RPM
FIN_HG00349	1.37 RPM
FIN_HG00375	0.56 RPM
FIN_HG00377	0.73 RPM
FIN_HG00378	0.53 RPM
GBR_HG00099	0.67 RPM
GBR_HG00111	0.56 RPM
GBR_HG00114	0.34 RPM
GBR_HG00119	0.62 RPM
GBR_HG00131	0.55 RPM
GBR_HG00133	0.58 RPM
GBR_HG00134	0.46 RPM
GBR_HG00137	0.52 RPM
GBR_HG00142	0.33 RPM
GBR_HG00143	0.45 RPM
TSI_NA20512	0.48 RPM
TSI_NA20513	0.65 RPM
TSI_NA20518	1.39 RPM
TSI_NA20532	0.65 RPM
TSI_NA20538	0.41 RPM
TSI_NA20756	1.05 RPM
TSI_NA20765	0.62 RPM
TSI_NA20771	0.62 RPM
TSI_NA20786	0.42 RPM
TSI_NA20798	0.44 RPM
YRI_NA18870	1.08 RPM
YRI_NA18907	0.31 RPM
YRI_NA18916	0.38 RPM
YRI_NA19093	0.21 RPM
YRI_NA19099	0.67 RPM
YRI_NA19114	0.39 RPM
YRI_NA19118	0.54 RPM
YRI_NA19213	0.43 RPM
YRI_NA19214	0.27 RPM
YRI_NA19223	0.44 RPM

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Indel association:

The presence of retro_hsap_4873 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_4873 presence in various populations. Based on Kabza et al. 2015 (PubMed).

#	Indel coordinates	AFR, African			AMR, Ad Mixed American			EUR, European					EAS, East Asian
		ASW	YRI	LWK	MXL	PUR	CLM	CEU	IBS	GBR	FIN	TSI	JPT	CHB	CHS
1.	X:91367534..91368800	84.69	88.72	84.93	99.01	98.78	100	100	100	100	100	100	100	100	100

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Indel #1, located at the genomic coordinates X:91367534..91368800.