RetrogeneDB ID: retro_hsap_2555

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 22:31298140..31298765(+)
• Located in intron of: ENSG00000184792

Retrocopy information

• Ensembl ID: ENSG00000237977
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF4H
• Ensembl ID: ENSG00000263344
• Aliases: None
• Description: eukaryotic translation initiation factor 4H [Source:HGNC Symbol;Acc:12741]

Sequence

>retro_hsap_2555
AGAGGGTCCCACGGCAGTACTGGTGGCCATGGTTCCCGTAGCCAGAAGGAGTCGCTCACAGAGCCCCACACACAGCATAT
GTAGGGAATCTACCTTTTAATATGGTTCAGGGCGACATAGATGCTATCTTTAAGGATCTCAGCATAAGGAGTGTACGGGT
AGTCAGAGACAAAGACACAGATAAATTTAAAGGATTCTGCTATATAGAATTCGATGAAGTGGATTCCCTTAAGGAAGCTT
GACATACGATGGTGCACTGTTGGGCAATCAGTCACTTCATGTGGACATTGCAGAAGGCAGAAAACAAGATAAAGGTGGCT
TTGGATTCAGAAAAGGTGTACCAGATGACGAAGCTTCAGGGATGACTTCTTAGGAGGCAGGGGAGGTAGTCACCCAGGTG
ACTGGGAAACAGGCCCCCAACTGGGCAGCCACTTCAGAGATGGTCCTCCCTTCCACGATCCAACATGGATTTCAAAGAAC
CGACAGAGGAGGGAAGAGCACAAAGACCACGACTCCAGCTTAAACCTCGAATGTTGTGACGCCCCTCAATGAAGTAGCCG
ATCCCAACTCTGCTATCTTCAGGGGTGCCAGACCCAGAGTGGAATTCGTTCACAAGGAGCAAGAA

Alignment

ORF - retro_hsap_2555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.26 %
• Parental protein coverage: 92.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RGSRGSAGGHGSRSQKELPTEP-PYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYV
          RGS.GS.GGHGSRSQKE..TEP.P.TAYVGNLPFN.VQGDIDAIFKDLSIRSVR.VRDKDTDKFKGFCY.
Retrocopy RGSHGSTGGHGSRSQKESLTEP<PHTAYVGNLPFNMVQGDIDAIFKDLSIRSVRVVRDKDTDKFKGFCYI

Parental  EFDEVDSLKEA-LTYDGALLGDRSLRVDIAEGRKQDKGGFGFRKGGPDD-RGFRDDFLGGRGGSRPGDRR
          EFDEVDSLKEA.LTYDGALLG..SL.VDIAEGRKQDKGGFGFRKG.PDD.R.FRDDFLGGRGGS.PGD..
Retrocopy EFDEVDSLKEA<LTYDGALLGNQSLHVDIAEGRKQDKGGFGFRKGVPDD<RSFRDDFLGGRGGSHPGDWE

Parental  TGPPMGSRFRDGPP-LRGSNMDFREPTEEERAQRPRLQLKPR-TVATPLNQVANPNSAIFGGARPREEVV
          TGP..GS.FRDGPP.L..SNMDF.EPTEE.RAQRPRLQLKPR..V.TPLN.VA.PNSAIF.GARPR.E.V
Retrocopy TGPQLGSHFRDGPP<LPRSNMDFKEPTEEGRAQRPRLQLKPR<NVVTPLNEVADPNSAIFRGARPRVEFV

Parental  QKEQE
          .KEQE
Retrocopy HKEQE

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	0.00 RPM
bodymap2_adrenal	0.76 RPM	0.00 RPM
bodymap2_brain	1.29 RPM	0.00 RPM
bodymap2_breast	0.16 RPM	0.00 RPM
bodymap2_colon	0.52 RPM	0.00 RPM
bodymap2_heart	0.20 RPM	0.00 RPM
bodymap2_kidney	0.31 RPM	0.00 RPM
bodymap2_liver	0.15 RPM	0.00 RPM
bodymap2_lung	0.18 RPM	0.00 RPM
bodymap2_lymph_node	1.15 RPM	0.00 RPM
bodymap2_ovary	0.25 RPM	0.00 RPM
bodymap2_prostate	0.66 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	0.96 RPM	0.00 RPM
bodymap2_thyroid	0.21 RPM	0.00 RPM
bodymap2_white_blood_cells	0.04 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2555 was not detected

EST

No EST(s) were mapped for retro_hsap_2555 retrocopy.

TSS

No TSS is located nearby retro_hsap_2555 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: CCTTAAGGAAGCTTGACATACGA (23 nt long)
• Reverse primer: GGCGTCACAACATTCGAGG (19 nt long)
• Annealing temperature: 60 °C
• (Expected) product size: 317
• Electrophoresis gel image:
• Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2555 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1489
Gorilla gorilla	retro_ggor_1598
Pongo abelii	retro_pabe_1879
Macaca mulatta	retro_mmul_619

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000263344	2 retrocopies	retro_hsap_2555 , retro_hsap_3833,