RetrogeneDB ID: retro_hsap_3799

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:139218986..139219298(+)
• Located in intron of: ENSG00000236279

Retrocopy information

• Ensembl ID: ENSG00000254270
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ERH
• Ensembl ID: ENSG00000100632
• Aliases: None
• Description: enhancer of rudimentary homolog (Drosophila) [Source:HGNC Symbol;Acc:3447]

Sequence

>retro_hsap_3799
ATGTCTCACACCATTTTGCTGATACAGACTACCAAGAGGCCAGAAGGCAGAACTTATGCTGACTACGAATCTGTGAATGA
ATGCATGGAAGGCGTTTGTAAAATGTATGAAGACATGTGAAAAGAATGAATCCCAACAGTCCCTCTATCAAATATGACAT
CAGTCAGTTGTTTGATTTCATCAATGATCTGGCAGACCTCAGCTGCCTGGTTTACCGAGCTGATACCCAGACATACCAGC
CTTATAAAAAAAGACTGGATTAAAGAGAAGATCTACATGCTTCTTCATCGGCAGGCTCAACAGGCTGATAAA

Alignment

ORF - retro_hsap_3799 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSHTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEE-HLKRMNPNSPSITYDISQLFDFIDDLADLSC
          MSHTILL.Q.TKRPEGRTYADYESVNECMEGVCKMYE..H.KRMNPNSPSI.YDISQLFDFI.DLADLSC
Retrocopy MSHTILLIQTTKRPEGRTYADYESVNECMEGVCKMYED<HVKRMNPNSPSIKYDISQLFDFINDLADLSC

Parental  LVYRADTQTYQPY-NKDWIKEKIYVLLRRQAQQAGK
          LVYRADTQTYQPY..KDWIKEKIY.LL.RQAQQA.K
Retrocopy LVYRADTQTYQPY>KKDWIKEKIYMLLHRQAQQADK

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	49.50 RPM
bodymap2_adrenal	0.00 RPM	77.07 RPM
bodymap2_brain	0.21 RPM	62.63 RPM
bodymap2_breast	0.00 RPM	49.22 RPM
bodymap2_colon	0.00 RPM	60.93 RPM
bodymap2_heart	0.00 RPM	31.37 RPM
bodymap2_kidney	0.00 RPM	59.99 RPM
bodymap2_liver	0.00 RPM	50.46 RPM
bodymap2_lung	0.00 RPM	53.69 RPM
bodymap2_lymph_node	0.00 RPM	53.98 RPM
bodymap2_ovary	0.00 RPM	88.60 RPM
bodymap2_prostate	0.00 RPM	69.04 RPM
bodymap2_skeletal_muscle	0.00 RPM	34.52 RPM
bodymap2_testis	0.00 RPM	86.84 RPM
bodymap2_thyroid	0.00 RPM	73.76 RPM
bodymap2_white_blood_cells	0.00 RPM	68.49 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3799 was not detected

EST

No EST(s) were mapped for retro_hsap_3799 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_171608	246 libraries	216 libraries	945 libraries	329 libraries	93 libraries

The graphical summary, for retro_hsap_3799 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_3799 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3799 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017798	4 retrocopies	retro_btau_1260, retro_btau_438, retro_btau_651, retro_btau_795,
Callithrix jacchus	ENSCJAG00000014940	2 retrocopies	retro_cjac_209, retro_cjac_846,
Equus caballus	ENSECAG00000019178	1 retrocopy	retro_ecab_45,
Erinaceus europaeus	ENSEEUG00000007758	6 retrocopies	retro_eeur_105, retro_eeur_108, retro_eeur_115, retro_eeur_116, retro_eeur_185, retro_eeur_546,
Echinops telfairi	ENSETEG00000016172	5 retrocopies	retro_etel_1122, retro_etel_1451, retro_etel_715, retro_etel_716, retro_etel_975,
Homo sapiens	ENSG00000100632	2 retrocopies	retro_hsap_3594, retro_hsap_3799 ,
Myotis lucifugus	ENSMLUG00000011879	1 retrocopy	retro_mluc_142,
Oryctolagus cuniculus	ENSOCUG00000004636	1 retrocopy	retro_ocun_42,
Ochotona princeps	ENSOPRG00000000086	2 retrocopies	retro_opri_1140, retro_opri_519,
Pongo abelii	ENSPPYG00000005939	2 retrocopies	retro_pabe_2954, retro_pabe_3104,
Sus scrofa	ENSSSCG00000002307	1 retrocopy	retro_sscr_748,
Tursiops truncatus	ENSTTRG00000013963	2 retrocopies	retro_ttru_1671, retro_ttru_614,
Vicugna pacos	ENSVPAG00000006444	1 retrocopy	retro_vpac_423,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 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	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 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).