RetrogeneDB ID: retro_hsap_3833

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:27497784..27498468(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000233830
• 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_3833
ATGGCGGACTTCGACACCTACGACGATCAGGCCTACAGCAGCTTCGGCAGCGGCAGAGGGTCCCGCGGCAGTGCTGGTGG
CCATGGTTCCCGTAGCCAGAAGGAGTTGCCCACAGAGCCCCCCTACACAGCATACGTAGGAAATCTACCTTTCAATACGG
TTCGGGGCGACATAGATGCTATCTTTAAGGATCTCAGCATAAGGAGTGTACGGCTAGTCAGAGACAAAGACACAGATAAA
TTTAAAGGATTCTGCTATGTAGAATTCGATGAAGTGGATTCCCTTAAGGAAGCCTTGACATACGATGGTGCACTGTTGGG
CGATCGGTCACTTCGTGTGGACATTGCAGAAGGCAGAAAACAAGATAAAGGTGGCTTTGGATTCAGAAAAGGTGGACCAG
ATGACAGAGGCTTCAGGGATGACTTCTTAGGGGGCAGGGGAGGTAGTCGCCCAGGCGACCGGCGAACAGGCCCCCCCATG
GGCAGCCGCTTCGGAGATGGCCCTCCCCTCGGTGGATCCAACATGGATTTCAGAGAACCCACAGAAGAGGAAAGCGCACA
GAGACCACGACTCCAGCTTAAACCTCGAACAGTCGCGACGCCCCTCAATCAAGTAGCCAATCCCAACTCTGCTATCTTCG
GGGGTGCCAGGCCTAGAGAGGAAGTTGTTCAAAAGGAGCAAAAA

Alignment

ORF - retro_hsap_3833 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.93 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADFDTYDDRAYSSFGGGRGSRGSAGGHGSRSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSV
          MADFDTYDD.AYSSFG.GRGSRGSAGGHGSRSQKELPTEPPYTAYVGNLPFNTV.GDIDAIFKDLSIRSV
Retrocopy MADFDTYDDQAYSSFGSGRGSRGSAGGHGSRSQKELPTEPPYTAYVGNLPFNTVRGDIDAIFKDLSIRSV

Parental  RLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKGGFGFRKGGPDDRGFRD
          RLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKGGFGFRKGGPDDRGFRD
Retrocopy RLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKGGFGFRKGGPDDRGFRD

Parental  DFLGGRGGSRPGDRRTGPPMGSRFRDGPPLRGSNMDFREPTEEERAQRPRLQLKPRTVATPLNQVANPNS
          DFLGGRGGSRPGDRRTGPPMGSRF.DGPPL.GSNMDFREPTEEE.AQRPRLQLKPRTVATPLNQVANPNS
Retrocopy DFLGGRGGSRPGDRRTGPPMGSRFGDGPPLGGSNMDFREPTEEESAQRPRLQLKPRTVATPLNQVANPNS

Parental  AIFGGARPREEVVQKEQE
          AIFGGARPREEVVQKEQ.
Retrocopy AIFGGARPREEVVQKEQK

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	0.26 RPM	0.00 RPM
bodymap2_adrenal	0.31 RPM	0.00 RPM
bodymap2_brain	0.16 RPM	0.00 RPM
bodymap2_breast	0.23 RPM	0.00 RPM
bodymap2_colon	0.17 RPM	0.00 RPM
bodymap2_heart	0.11 RPM	0.00 RPM
bodymap2_kidney	0.31 RPM	0.00 RPM
bodymap2_liver	0.06 RPM	0.00 RPM
bodymap2_lung	0.02 RPM	0.00 RPM
bodymap2_lymph_node	0.11 RPM	0.00 RPM
bodymap2_ovary	0.08 RPM	0.00 RPM
bodymap2_prostate	0.17 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.47 RPM	0.00 RPM
bodymap2_testis	0.19 RPM	0.00 RPM
bodymap2_thyroid	0.34 RPM	0.00 RPM
bodymap2_white_blood_cells	0.08 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3833 was not detected

EST

No EST(s) were mapped for retro_hsap_3833 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_174477	452 libraries	911 libraries	458 libraries	8 libraries	0 libraries

The graphical summary, for retro_hsap_3833 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_3833 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3833 has 0 orthologous retrocopies within eutheria group .

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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 ,