RetrogeneDB ID: retro_hsap_2438

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 20:61477015..61477261(+)
• Located in intron of: ENSG00000101190

Retrocopy information

• Ensembl ID: ENSG00000233838
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DPH3
• Ensembl ID: ENSG00000154813
• Aliases: None
• Description: diphthamide biosynthesis 3 [Source:HGNC Symbol;Acc:27717]

Sequence

>retro_hsap_2438
ATGGCAGTATTTCATGACGAGGTGGAAATCGAGGACTTCCAATATGACGAGGACTCGGAGACATATTTCTGTCCCTGCCC
ATGCGGAGATAACTTCTCCATCACCAAGGAAGAGCTGGAGAATGGGGAAGGTGTGGCAATGTGTCCAGGCTGCTCTCTCA
TTATAAAAGTGATTTATGACAAAGATCAGTTTGCGTGTGGAGAAACAGTGCCAGTGCCTTCAGTCAACAAAGAATGAGTT
AAATGC

Alignment

ORF - retro_hsap_2438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVFHDEVEIEDFQYDEDSETYFYPCPCGDNFSITKEDLENGEDVATCPSCSLIIKVIYDKDQFVCGETV
          MAVFHDEVEIEDFQYDEDSETYF.PCPCGDNFSITKE.LENGE.VA.CP.CSLIIKVIYDKDQF.CGETV
Retrocopy MAVFHDEVEIEDFQYDEDSETYFCPCPCGDNFSITKEELENGEGVAMCPGCSLIIKVIYDKDQFACGETV

Parental  PAPSANKELVKC
          P.PS.NKE.VKC
Retrocopy PVPSVNKE*VKC

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	0.95 RPM	27.27 RPM
bodymap2_adrenal	0.18 RPM	23.38 RPM
bodymap2_brain	0.89 RPM	25.46 RPM
bodymap2_breast	0.27 RPM	37.20 RPM
bodymap2_colon	0.56 RPM	39.33 RPM
bodymap2_heart	0.28 RPM	34.91 RPM
bodymap2_kidney	0.33 RPM	49.72 RPM
bodymap2_liver	0.04 RPM	25.16 RPM
bodymap2_lung	0.19 RPM	32.98 RPM
bodymap2_lymph_node	0.66 RPM	38.48 RPM
bodymap2_ovary	0.71 RPM	51.57 RPM
bodymap2_prostate	0.47 RPM	36.86 RPM
bodymap2_skeletal_muscle	0.16 RPM	45.83 RPM
bodymap2_testis	0.85 RPM	41.29 RPM
bodymap2_thyroid	0.38 RPM	40.54 RPM
bodymap2_white_blood_cells	0.75 RPM	45.83 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2438 was not detected

EST

No EST(s) were mapped for retro_hsap_2438 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_103296	1318 libraries	398 libraries	110 libraries	3 libraries	0 libraries

The graphical summary, for retro_hsap_2438 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_2438 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2438 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1409
Gorilla gorilla	retro_ggor_174
Pongo abelii	retro_pabe_1795

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012030	1 retrocopy	retro_dnov_39,
Dipodomys ordii	ENSDORG00000011642	1 retrocopy	retro_dord_167,
Erinaceus europaeus	ENSEEUG00000009790	1 retrocopy	retro_eeur_502,
Echinops telfairi	ENSETEG00000016272	1 retrocopy	retro_etel_1879,
Homo sapiens	ENSG00000154813	1 retrocopy	retro_hsap_2438 ,
Gorilla gorilla	ENSGGOG00000022108	1 retrocopy	retro_ggor_174,
Loxodonta africana	ENSLAFG00000025650	3 retrocopies	retro_lafr_31, retro_lafr_545, retro_lafr_87,
Macaca mulatta	ENSMMUG00000022692	2 retrocopies	retro_mmul_2085, retro_mmul_497,
Monodelphis domestica	ENSMODG00000025472	3 retrocopies	retro_mdom_131, retro_mdom_1434, retro_mdom_609,
Mus musculus	ENSMUSG00000021905	1 retrocopy	retro_mmus_196,
Nomascus leucogenys	ENSNLEG00000001096	2 retrocopies	retro_nleu_2876, retro_nleu_2913,
Pongo abelii	ENSPPYG00000014083	1 retrocopy	retro_pabe_1795,
Pan troglodytes	ENSPTRG00000014671	1 retrocopy	retro_ptro_1409,
Tupaia belangeri	ENSTBEG00000011675	1 retrocopy	retro_tbel_58,
Tursiops truncatus	ENSTTRG00000007739	3 retrocopies	retro_ttru_1474, retro_ttru_31, retro_ttru_907,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.21 RPM
CEU_NA11843	0.34 RPM
CEU_NA11930	0.91 RPM
CEU_NA12004	0.15 RPM
CEU_NA12400	0.49 RPM
CEU_NA12751	0.90 RPM
CEU_NA12760	1.08 RPM
CEU_NA12827	0.57 RPM
CEU_NA12872	0.22 RPM
CEU_NA12873	0.51 RPM
FIN_HG00183	0.22 RPM
FIN_HG00277	0.48 RPM
FIN_HG00315	0.86 RPM
FIN_HG00321	0.70 RPM
FIN_HG00328	0.19 RPM
FIN_HG00338	0.32 RPM
FIN_HG00349	0.26 RPM
FIN_HG00375	0.42 RPM
FIN_HG00377	0.45 RPM
FIN_HG00378	0.32 RPM
GBR_HG00099	0.58 RPM
GBR_HG00111	0.41 RPM
GBR_HG00114	0.29 RPM
GBR_HG00119	1.25 RPM
GBR_HG00131	1.78 RPM
GBR_HG00133	0.72 RPM
GBR_HG00134	0.61 RPM
GBR_HG00137	0.63 RPM
GBR_HG00142	0.83 RPM
GBR_HG00143	0.45 RPM
TSI_NA20512	0.23 RPM
TSI_NA20513	1.35 RPM
TSI_NA20518	0.80 RPM
TSI_NA20532	0.58 RPM
TSI_NA20538	0.51 RPM
TSI_NA20756	0.61 RPM
TSI_NA20765	0.37 RPM
TSI_NA20771	0.94 RPM
TSI_NA20786	1.07 RPM
TSI_NA20798	0.25 RPM
YRI_NA18870	0.58 RPM
YRI_NA18907	0.73 RPM
YRI_NA18916	0.57 RPM
YRI_NA19093	0.44 RPM
YRI_NA19099	0.48 RPM
YRI_NA19114	1.15 RPM
YRI_NA19118	0.56 RPM
YRI_NA19213	0.38 RPM
YRI_NA19214	0.84 RPM
YRI_NA19223	0.54 RPM

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Indel association:

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