RetrogeneDB ID: retro_hsap_3224

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:102368079..102368732(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000175749
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF3K
• Ensembl ID: ENSG00000178982
• Aliases: EIF3K, EIF3-p28, EIF3S12, HSPC029, M9, MSTP001, PLAC-24, PLAC24, PRO1474, PTD001
• Description: eukaryotic translation initiation factor 3, subunit K [Source:HGNC Symbol;Acc:24656]

Sequence

>retro_hsap_3224
ATGGTGATATTTGAGCAGATGAGAGCCAATGTGGGCATGTTGCTCCAGGGTATCAACAGGAACAATCCTGAGAAGCTGGC
CACCCTGGAGTGCTACGTGGAGATGCAGGCCAAGGACACTGCCTATGATCTGGAAGCCAACCCAGTTGTCCTGAAGCTGT
ACCAGTCCAACCCAGTGTTTTTTCAGACCACGGACACTGCCCAGATCCAGCTGAAGGCCCTCACCAACCTGCCACATACC
AACTTCACCCCGTGTAAGTGCATGATTGGCCAGGCACATCAAGAAGAGTGGCCATCTGACAGATTTTGTATCTCAAGGAC
CTGCTGGAGACCAGCCTCTTTCAGGCCTTCTGGGAAGCCCTGGATGAAAACGTGGACCTCTTGGAAGGTATAACTGGCTT
TGAAGACTCTGTCCGAATGTGTATCTGCCCTGTCGTGGGTATCACTTACCAGCACATCGACCACTGGCTGCTGGCCGAGA
TGCCTGGGTATCTGTCGGACAGCCAGCTGAAGGTGTGGATGAGAAAATACACCTGGAGGGCTGATGAGTCCCAGCAGATC
TTCATCTGTAGCCAGGAAGAGAACATTAAGCCCAAGAACCCTGTGGAGAAGATAGACTTTGACAGTGTGTCCAGCATCAT
GGCCTTCTTCCAG

Alignment

ORF - retro_hsap_3224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMFEQMRANVGKLLKGIDRYNPENLATLERYVETQAKENAYDLEANLAVLKLYQFNPAFFQTTVTAQIL
          M..FEQMRANVG.LL.GI.R.NPE.LATLE.YVE.QAK..AYDLEAN..VLKLYQ.NP.FFQTT.TAQI.
Retrocopy MVIFEQMRANVGMLLQGINRNNPEKLATLECYVEMQAKDTAYDLEANPVVLKLYQSNPVFFQTTDTAQIQ

Parental  LKALTNLPHTDFTLCKCMIDQAHQEERP-IRQILYLGDLLETCHFQAFWQALDENMDLLEGITGFEDSVR
          LKALTNLPHT.FT.CKCMI.QAHQEE.P.I.QILYL.DLLET..FQAFW.ALDEN.DLLEGITGFEDSVR
Retrocopy LKALTNLPHTNFTPCKCMIGQAHQEEWP<I*QILYLKDLLETSLFQAFWEALDENVDLLEGITGFEDSVR

Parental  KFICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWMSKYGWSADESGQIFICSQEESIKPKNIVEKIDFDS
          ..IC.VVGITYQHID.WLLAEM.G.LSDSQLKVWM.KY.W.ADES.QIFICSQEE.IKPKN.VEKIDFDS
Retrocopy MCICPVVGITYQHIDHWLLAEMPGYLSDSQLKVWMRKYTWRADESQQIFICSQEENIKPKNPVEKIDFDS

Parental  VSSIMASSQ
          VSSIMA..Q
Retrocopy VSSIMAFFQ

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	0.06 RPM	83.71 RPM
bodymap2_adrenal	0.41 RPM	105.01 RPM
bodymap2_brain	0.02 RPM	48.61 RPM
bodymap2_breast	0.06 RPM	98.35 RPM
bodymap2_colon	0.00 RPM	100.64 RPM
bodymap2_heart	0.09 RPM	122.05 RPM
bodymap2_kidney	0.00 RPM	110.97 RPM
bodymap2_liver	0.00 RPM	59.42 RPM
bodymap2_lung	0.00 RPM	96.92 RPM
bodymap2_lymph_node	0.00 RPM	101.75 RPM
bodymap2_ovary	0.15 RPM	77.22 RPM
bodymap2_prostate	0.00 RPM	154.32 RPM
bodymap2_skeletal_muscle	0.00 RPM	119.53 RPM
bodymap2_testis	0.06 RPM	50.81 RPM
bodymap2_thyroid	0.02 RPM	69.17 RPM
bodymap2_white_blood_cells	0.00 RPM	148.49 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3224 was not detected

EST

No EST(s) were mapped for retro_hsap_3224 retrocopy.

TSS

No TSS is located nearby retro_hsap_3224 retrocopy 5' end.

Lab

retro_hsap_3224 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3224 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2176
Gorilla gorilla	retro_ggor_2192
Pongo abelii	retro_pabe_2673
Macaca mulatta	retro_mmul_2029
Macaca mulatta	retro_mmul_2098

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007594	3 retrocopies	retro_etel_1653, retro_etel_1868, retro_etel_5,
Homo sapiens	ENSG00000178982	2 retrocopies	retro_hsap_2616, retro_hsap_3224 ,
Gorilla gorilla	ENSGGOG00000016808	1 retrocopy	retro_ggor_2192,
Myotis lucifugus	ENSMLUG00000010217	1 retrocopy	retro_mluc_645,
Macaca mulatta	ENSMMUG00000028767	2 retrocopies	retro_mmul_1478, retro_mmul_2029,
Monodelphis domestica	ENSMODG00000013314	3 retrocopies	retro_mdom_1235, retro_mdom_1929, retro_mdom_781,
Otolemur garnettii	ENSOGAG00000026260	1 retrocopy	retro_ogar_413,
Pongo abelii	ENSPPYG00000025857	4 retrocopies	retro_pabe_2342, retro_pabe_2555, retro_pabe_2610, retro_pabe_2673,
Pan troglodytes	ENSPTRG00000010934	2 retrocopies	retro_ptro_1763, retro_ptro_2176,
Sarcophilus harrisii	ENSSHAG00000005313	1 retrocopy	retro_shar_689,
Tarsius syrichta	ENSTSYG00000007001	1 retrocopy	retro_tsyr_1964,

Population studies

Expression level across human populations :

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

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Indel association:

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