RetrogeneDB ID: retro_hsap_593

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:74960120..74960983(+)
• Located in intron of: ENSG00000213551

Retrocopy information

• Ensembl ID: ENSG00000227382
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF4A2
• Ensembl ID: ENSG00000156976
• Aliases: EIF4A2, BM-010, DDX2B, EIF4A, EIF4F, eIF-4A-II, eIF4A-II
• Description: eukaryotic translation initiation factor 4A2 [Source:HGNC Symbol;Acc:3284]

Sequence

>retro_hsap_593
CAAAAGGTGATTCTGGCACTTGGAGATTATATGGGAGCAACCTGTCATGCCTGCATTGGTGGAACAAATGTTCAAAATGA
ATGCAAAAACTGCAGGCTGAAGTACCACATATTGTTGGTACACCAGGGAGAATGTGTGATATGTTAAACAGAAGATACCT
TTTTTCCAAAATGGATCAAAATGTTTGTTTTGGATGAAGCAGATGAAATGTTCAGCCAAGGGTTTAAGGATCAAATCTAT
GAGATTTTCCAAAAATTAAATACAAGTATTTAGGTTGTGTTGCTTTCTGCCATGATGCCAACTGATGTGTTGGAAGTGAC
CAAAAAATTCACTAAAGATCCTATTCAAATTCTGGTGAAAAAGGAAGACTTGAACCTTGAAGGAATCGAACAGTTTTATA
TCAGTGTTGAGCAGGAGGAATGGAAGTTGGATATACTTTGTGACTTGTACAAGGCACCATTAAACAGGCTGTTATTTTTC
TCAATACAAGGTGCAAGGTGGACTGGCTGACTGAGAAAATACATGCCAGGGACGTCACAGTTTTTGCTCTGCATGGCGAC
ATGGACCAGAAGGAGAGAGATACTATCATGAGGGAATTCTGATCAGGGTCAAGCCCTGTTCTGATCACTATTTACTTGTT
GGCACGTGGGACTGATGTCCAACAAGTGTCTTCGGTTATAAACTATGATCTACCTAGCAGTCATGAAAACTGTATTCGCA
GAATTGGCAGAGGGGTCAATTTGGTAGAAAAGGTGTGGCTAAAAACTTTGTTACTGAGGAAGGCAAGAGGATTCTTCGTG
ACACTGAGATTTGTATGCAATACTACAGTGAAGGAAATGCCCATAAATGTAGCTGACCGTATT

Alignment

ORF - retro_hsap_593 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.66 %
• Parental protein coverage: 92.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QKVILALGDYMGATCHACIGGTNVRNE-MQKLQAEAPHIVVGTPGRVFDMLNRRYLS-PKWIKMFVLDEA
          QKVILALGDYMGATCHACIGGTNV.NE.MQKLQAE.PHIV.GTPGR..DMLNRRYL..PKWIKMFVLDEA
Retrocopy QKVILALGDYMGATCHACIGGTNVQNE<MQKLQAEVPHIV-GTPGRMCDMLNRRYLF>PKWIKMFVLDEA

Parental  DEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVE
          DEM.S.GFKDQIYEIFQKLNTSI.VVLLSA.MPTDVLEVTKKF..DPI.ILVKKE.L.LEGI.QFYI.VE
Retrocopy DEMFSQGFKDQIYEIFQKLNTSI*VVLLSAMMPTDVLEVTKKFTKDPIQILVKKEDLNLEGIEQFYISVE

Parental  REEWKLDTLCDLYETLTITQAVIF-LNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSGSS
          .EEWKLD.LCDLY..........F.LNTR.KVDWLTEK.HARD.TV.ALHGDMDQKERD.IMREF.SGSS
Retrocopy QEEWKLDILCDLYKA-PLNRLLFF<LNTRCKVDWLTEKIHARDVTVFALHGDMDQKERDTIMREF*SGSS

Parental  RVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRG-GRFGRKGVAINFVTEEDKRILRDIET-FY
          .VLIT..LLARG.DVQQVS.VINYDLP...EN.I.RIGRG.G.FGRKGVA.NFVTEE.KRILRD.E....
Retrocopy PVLITIYLLARGTDVQQVSSVINYDLPSSHENCIRRIGRG<GQFGRKGVAKNFVTEEGKRILRDTEI>VC

Parental  NTTVEEMPMNVADLI
          NTTV.EMP.NVAD.I
Retrocopy NTTVKEMPINVADRI

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	203.43 RPM
bodymap2_adrenal	0.37 RPM	423.29 RPM
bodymap2_brain	0.09 RPM	1018.52 RPM
bodymap2_breast	0.33 RPM	317.26 RPM
bodymap2_colon	0.12 RPM	1022.71 RPM
bodymap2_heart	0.00 RPM	263.13 RPM
bodymap2_kidney	0.08 RPM	383.66 RPM
bodymap2_liver	0.00 RPM	114.05 RPM
bodymap2_lung	0.12 RPM	530.19 RPM
bodymap2_lymph_node	0.00 RPM	664.69 RPM
bodymap2_ovary	0.39 RPM	698.82 RPM
bodymap2_prostate	0.09 RPM	806.01 RPM
bodymap2_skeletal_muscle	0.13 RPM	578.94 RPM
bodymap2_testis	0.02 RPM	536.84 RPM
bodymap2_thyroid	0.08 RPM	856.03 RPM
bodymap2_white_blood_cells	0.24 RPM	366.33 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_593 was not detected

EST

No EST(s) were mapped for retro_hsap_593 retrocopy.

TSS

No TSS is located nearby retro_hsap_593 retrocopy 5' end.

Lab

retro_hsap_593 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_593 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_437
Gorilla gorilla	retro_ggor_525
Pongo abelii	retro_pabe_596
Macaca mulatta	retro_mmul_2450

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014724	2 retrocopies	retro_btau_258, retro_btau_522,
Canis familiaris	ENSCAFG00000013659	1 retrocopy	retro_cfam_378,
Cavia porcellus	ENSCPOG00000011183	1 retrocopy	retro_cpor_639,
Dasypus novemcinctus	ENSDNOG00000011502	5 retrocopies	retro_dnov_1264, retro_dnov_2018, retro_dnov_2066, retro_dnov_648, retro_dnov_869,
Echinops telfairi	ENSETEG00000018565	3 retrocopies	retro_etel_1174, retro_etel_2164, retro_etel_451,
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	ENSGGOG00000005867	2 retrocopies	retro_ggor_525, retro_ggor_712,
Macropus eugenii	ENSMEUG00000011737	1 retrocopy	retro_meug_237,
Microcebus murinus	ENSMICG00000007377	1 retrocopy	retro_mmur_525,
Macaca mulatta	ENSMMUG00000003702	2 retrocopies	retro_mmul_1055, retro_mmul_2450,
Nomascus leucogenys	ENSNLEG00000006633	1 retrocopy	retro_nleu_2589,
Oryctolagus cuniculus	ENSOCUG00000005011	3 retrocopies	retro_ocun_392, retro_ocun_696, retro_ocun_763,
Otolemur garnettii	ENSOGAG00000010729	2 retrocopies	retro_ogar_2830, retro_ogar_943,
Ochotona princeps	ENSOPRG00000004170	1 retrocopy	retro_opri_498,
Pongo abelii	ENSPPYG00000014384	2 retrocopies	retro_pabe_596, retro_pabe_677,
Pan troglodytes	ENSPTRG00000015718	1 retrocopy	retro_ptro_437,
Rattus norvegicus	ENSRNOG00000001815	2 retrocopies	retro_rnor_1163, retro_rnor_2340,
Ictidomys tridecemlineatus	ENSSTOG00000012601	1 retrocopy	retro_itri_858,
Tupaia belangeri	ENSTBEG00000002268	11 retrocopies	retro_tbel_114, retro_tbel_1488, retro_tbel_1500, retro_tbel_2048, retro_tbel_2524, retro_tbel_2729, retro_tbel_2733, retro_tbel_3159, retro_tbel_3793, retro_tbel_4599, retro_tbel_841,
Takifugu rubripes	ENSTRUG00000005660	2 retrocopies	retro_trub_14, retro_trub_6,
Tarsius syrichta	ENSTSYG00000013050	3 retrocopies	retro_tsyr_1905, retro_tsyr_903, retro_tsyr_935,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.11 RPM
CEU_NA11843	0.11 RPM
CEU_NA11930	0.16 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.10 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.24 RPM
CEU_NA12872	0.16 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.08 RPM
FIN_HG00277	0.22 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.09 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.17 RPM
GBR_HG00111	0.11 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	0.07 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.14 RPM
GBR_HG00134	0.11 RPM
GBR_HG00137	0.08 RPM
GBR_HG00142	0.08 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.10 RPM
TSI_NA20518	0.08 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.18 RPM
TSI_NA20756	0.15 RPM
TSI_NA20765	0.15 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.13 RPM
TSI_NA20798	0.16 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.08 RPM
YRI_NA19213	0.07 RPM
YRI_NA19214	0.10 RPM
YRI_NA19223	0.12 RPM

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Indel association:

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