RetrogeneDB ID: retro_hsap_2370

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:203066105..203066609(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000223825
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DAZAP2
• Ensembl ID: ENSG00000183283
• Aliases: DAZAP2, PRTB
• Description: DAZ associated protein 2 [Source:HGNC Symbol;Acc:2684]

Sequence

>retro_hsap_2370
ATGAACAGCAAAGGTCAATATCCAACACAGCCAACCTAGCCTGTGCAGCCTCCTGGGAATCCAGTCTACCCTCAGACCTT
GCATCTTTCTCAGGCTCTACCCTATACTGATGCTCCGACTGCCTACTCAGAGCTCTATCATCCAAGCTTTGTGCACCCCA
GGGGCTGCCACAGTCCCCACCATGTCGGCCGCTTTCCTGGAGCCTCTCTGTATCTTCCCATGGCCCAGTCTGTGGCTGTT
GGGTCTTTAGGTTCCACAATCCCCATGGCTTATTATCCAGTTGGTCCCATCTATCCACCTGGCTCCACAGTGCTGGTGGA
AGGCGGGTATGATGCAGGTGCCAGATTTGGAGCTGGGGCTACTGCTGGCAACATTCTTCCTCCACCTCCTGGATGCCCTC
CCAGTGCTGCTCAGCTTGCAGTCATGCAGGCAGCCAATGTCCTCGTAACTCAGTGGAAGGGGAACTTCTTCATGGGTGAA
TCAGATGGTGGCTACACCATCTGG

Alignment

ORF - retro_hsap_2370 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNSKGQYPTQPTYPVQPPGNPVYPQTLHLPQAPPYTDAPPAYSELYRPSFVHP-GAATVPTMSAAF-PGA
          MNSKGQYPTQPT.PVQPPGNPVYPQTLHL.QA.PYTDAP.AYSELY.PSFVHP.GAATVPTMSAAF.PGA
Retrocopy MNSKGQYPTQPT*PVQPPGNPVYPQTLHLSQALPYTDAPTAYSELYHPSFVHP>GAATVPTMSAAF<PGA

Parental  SLYLPMAQSVAVGPLGSTIPMAYYPVGPIYPPGSTVLVEGGYDAGARFGAGATAGNIPPPPPGCPPNAAQ
          SLYLPMAQSVAVG.LGSTIPMAYYPVGPIYPPGSTVLVEGGYDAGARFGAGATAGNI.PPPPGCPP.AAQ
Retrocopy SLYLPMAQSVAVGSLGSTIPMAYYPVGPIYPPGSTVLVEGGYDAGARFGAGATAGNILPPPPGCPPSAAQ

Parental  LAVMQGANVLVTQRKGNFFMGGSDGGYTIW
          LAVMQ.ANVLVTQ.KGNFFMG.SDGGYTIW
Retrocopy LAVMQAANVLVTQWKGNFFMGESDGGYTIW

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	0.28 RPM	217.96 RPM
bodymap2_adrenal	0.59 RPM	303.38 RPM
bodymap2_brain	0.45 RPM	214.64 RPM
bodymap2_breast	0.19 RPM	153.11 RPM
bodymap2_colon	0.27 RPM	166.29 RPM
bodymap2_heart	0.00 RPM	168.29 RPM
bodymap2_kidney	1.90 RPM	315.21 RPM
bodymap2_liver	0.08 RPM	119.96 RPM
bodymap2_lung	0.14 RPM	333.56 RPM
bodymap2_lymph_node	0.18 RPM	213.11 RPM
bodymap2_ovary	0.23 RPM	161.69 RPM
bodymap2_prostate	0.50 RPM	240.47 RPM
bodymap2_skeletal_muscle	0.13 RPM	103.23 RPM
bodymap2_testis	0.51 RPM	155.12 RPM
bodymap2_thyroid	0.17 RPM	299.06 RPM
bodymap2_white_blood_cells	0.95 RPM	879.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2370 was not detected

EST

No EST(s) were mapped for retro_hsap_2370 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_117410	436 libraries	660 libraries	682 libraries	38 libraries	13 libraries

The graphical summary, for retro_hsap_2370 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_2370 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2370 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1800
Pongo abelii	retro_pabe_2140
Macaca mulatta	retro_mmul_958

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017661	2 retrocopies	retro_cjac_636, retro_cjac_793,
Homo sapiens	ENSG00000183283	1 retrocopy	retro_hsap_2370 ,
Gorilla gorilla	ENSGGOG00000026861	1 retrocopy	retro_ggor_1800,
Myotis lucifugus	ENSMLUG00000009959	1 retrocopy	retro_mluc_351,
Macaca mulatta	ENSMMUG00000001884	1 retrocopy	retro_mmul_958,
Nomascus leucogenys	ENSNLEG00000017776	1 retrocopy	retro_nleu_360,
Otolemur garnettii	ENSOGAG00000007977	3 retrocopies	retro_ogar_2109, retro_ogar_2139, retro_ogar_3130,
Pongo abelii	ENSPPYG00000004524	1 retrocopy	retro_pabe_2140,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.06 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.08 RPM
GBR_HG00099	0.15 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.05 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.07 RPM
GBR_HG00134	0.13 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.06 RPM
YRI_NA19213	0.10 RPM
YRI_NA19214	0.12 RPM
YRI_NA19223	0.08 RPM

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Indel association:

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