RetrogeneDB ID: retro_hsap_2399

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:234651892..234652562(-)
• Located in intron of: ENSG00000167165

Retrocopy information

• Ensembl ID: ENSG00000227802
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAJB6
• Ensembl ID: ENSG00000105993
• Aliases: DNAJB6, DJ4, DnaJ, HHDJ1, HSJ-2, HSJ2, LGMD1D, LGMD1E, MRJ, MSJ-1
• Description: DnaJ (Hsp40) homolog, subfamily B, member 6 [Source:HGNC Symbol;Acc:14888]

Sequence

>retro_hsap_2399
ATGGTGGACTACTACGAGGTGCTGGACGTGCCCCGGCAGGCCTCATCCGAGGCCATCAAGAAGGCGTACCGCAAGCTGGC
GCTCAAGTGGCACCCCGACAAAAACCCTGAGAACAAGGAGGAAGCGGAGAGGAGATTCAAGCAGGTGGCCGAGGCCTACG
AGGTGTTGTCGGACGCCAAGAAACGCGATATCTATGACCGCTATGGCGAGGCGGGGGCGGAGGGCGGCTGCACAGGCGGC
AGGCCCTTCGAGGACCCCTTCGAGTACGTCTTCAGCTTCCGCGACCCAGCCGACGTCTTCAGGGAGTTCTTCGGCGGCCA
GGACCCATTCTCCTTTGACCTCTTGGGAAACCCGCTGGAGAATATTTTGGGGGGGTCAGAGGAACTGCTGGGGAAGCAGA
AGCAGAGCGTCTGCACCCCTTTTCTCTGCCTTCAGTGAATTTCCAGCTTTTGGGGGTGTTTTTTCTTCTTTTGATACAGG
ATTTCGTTCCTTTGGCTCCCTGGGAAGTGGGGGCCTTTCTTCCTTCTGCATGTCCTACGGTAGTGATGGGACAGGCAGCT
TCAAGTCCATGTCGACTTCCACTGAAATAGTTGATGGTAAAAAAATCACCACCAAGAGAATCATTGAGAATGGCCAAGAA
AGGGTGGAAGTGGAGGAAGATGGAGAGTTG

Alignment

ORF - retro_hsap_2399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.0 %
• Parental protein coverage: 68.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVDYYEVLGVQRHASPEDIKKAYRKLALKWHPDKNPENKEEAERKFKQVAEAYEVLSDAKKRDIYDKYGK
          MVDYYEVL.V.R.AS.E.IKKAYRKLALKWHPDKNPENKEEAER.FKQVAEAYEVLSDAKKRDIYD.YG.
Retrocopy MVDYYEVLDVPRQASSEAIKKAYRKLALKWHPDKNPENKEEAERRFKQVAEAYEVLSDAKKRDIYDRYGE

Parental  EGLNGGGGGGSHFDSPFEFGFTFRNPDDVFREFFGGRDPFSFDFFEDPFED-FFGNRRGPRGSRSRGTGS
          .G..GG..GG..F..PFE..F.FR.P.DVFREFFGG.DPFSFD....P.E..F.G..R...GSRSR....
Retrocopy AGAEGGCTGGRPFEDPFEYVFSFRDPADVFREFFGGQDPFSFDLLGNPLEN>FWGGQRNCWGSRSRASAP

Parental  FFSAFSGFPSFGSGFSSFDTGFTSFGSLGHGGLTSFSSTSFGGSGMGNFKSISTSTKMVNGRKITTKRIV
          .FSAFS.FP.FG..FSSFDTGF.SFGSLG.GGL.SF...S.G..G.G.FKS.STST..V.G.KITTKRI.
Retrocopy LFSAFSEFPAFGGVFSSFDTGFRSFGSLGSGGLSSF-CMSYGSDGTGSFKSMSTSTEIVDGKKITTKRII

Parental  ENGQERVEVEEDGQL
          ENGQERVEVEEDG.L
Retrocopy ENGQERVEVEEDGEL

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	81.30 RPM
bodymap2_adrenal	0.00 RPM	80.67 RPM
bodymap2_brain	0.00 RPM	114.06 RPM
bodymap2_breast	0.00 RPM	99.30 RPM
bodymap2_colon	0.00 RPM	180.15 RPM
bodymap2_heart	0.00 RPM	132.94 RPM
bodymap2_kidney	0.15 RPM	90.02 RPM
bodymap2_liver	0.04 RPM	26.47 RPM
bodymap2_lung	0.00 RPM	117.26 RPM
bodymap2_lymph_node	0.00 RPM	182.88 RPM
bodymap2_ovary	0.00 RPM	78.07 RPM
bodymap2_prostate	0.05 RPM	151.57 RPM
bodymap2_skeletal_muscle	0.00 RPM	278.60 RPM
bodymap2_testis	6.45 RPM	194.62 RPM
bodymap2_thyroid	0.00 RPM	122.59 RPM
bodymap2_white_blood_cells	0.00 RPM	92.61 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2399 was not detected

EST

No EST(s) were mapped for retro_hsap_2399 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_120374	1826 libraries	0 libraries	0 libraries	1 library	2 libraries
TSS #2	TSS_120375	1825 libraries	1 library	3 libraries	0 libraries	0 libraries

The graphical summary, for retro_hsap_2399 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_2399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2399 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 27 parental genes, and 122 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001332	3 retrocopies	retro_amel_127, retro_amel_685, retro_amel_95,
Bos taurus	ENSBTAG00000000771	3 retrocopies	retro_btau_163, retro_btau_222, retro_btau_248,
Canis familiaris	ENSCAFG00000005174	6 retrocopies	retro_cfam_155, retro_cfam_201, retro_cfam_2085, retro_cfam_2131, retro_cfam_527, retro_cfam_8,
Callithrix jacchus	ENSCJAG00000005288	7 retrocopies	retro_cjac_104, retro_cjac_1455, retro_cjac_1648, retro_cjac_1692, retro_cjac_2922, retro_cjac_3880, retro_cjac_948,
Cavia porcellus	ENSCPOG00000013953	17 retrocopies	retro_cpor_1035, retro_cpor_1074, retro_cpor_1147, retro_cpor_1352, retro_cpor_1360, retro_cpor_1364, retro_cpor_259, retro_cpor_325, retro_cpor_38, retro_cpor_40, retro_cpor_538, retro_cpor_610, retro_cpor_720, retro_cpor_793, retro_cpor_814, retro_cpor_840, retro_cpor_952,
Equus caballus	ENSECAG00000009005	2 retrocopies	retro_ecab_105, retro_ecab_22,
Felis catus	ENSFCAG00000015654	2 retrocopies	retro_fcat_1072, retro_fcat_91,
Homo sapiens	ENSG00000101152	1 retrocopy	retro_hsap_4028,
Homo sapiens	ENSG00000105993	9 retrocopies	retro_hsap_103, retro_hsap_166, retro_hsap_2399 , retro_hsap_2400, retro_hsap_4031, retro_hsap_519, retro_hsap_54, retro_hsap_889, retro_hsap_939,
Gorilla gorilla	ENSGGOG00000004703	6 retrocopies	retro_ggor_1819, retro_ggor_201, retro_ggor_210, retro_ggor_251, retro_ggor_478, retro_ggor_719,
Loxodonta africana	ENSLAFG00000013384	4 retrocopies	retro_lafr_105, retro_lafr_107, retro_lafr_260, retro_lafr_468,
Microcebus murinus	ENSMICG00000009760	1 retrocopy	retro_mmur_474,
Myotis lucifugus	ENSMLUG00000009123	4 retrocopies	retro_mluc_1371, retro_mluc_147, retro_mluc_304, retro_mluc_333,
Macaca mulatta	ENSMMUG00000003176	6 retrocopies	retro_mmul_1050, retro_mmul_165, retro_mmul_2326, retro_mmul_243, retro_mmul_379, retro_mmul_970,
Mustela putorius furo	ENSMPUG00000009797	4 retrocopies	retro_mputfur_1084, retro_mputfur_11, retro_mputfur_1199, retro_mputfur_70,
Mus musculus	ENSMUSG00000029131	6 retrocopies	retro_mmus_113, retro_mmus_171, retro_mmus_2023, retro_mmus_3273, retro_mmus_435, retro_mmus_870,
Nomascus leucogenys	ENSNLEG00000001380	5 retrocopies	retro_nleu_1524, retro_nleu_2, retro_nleu_2063, retro_nleu_2820, retro_nleu_52,
Oryctolagus cuniculus	ENSOCUG00000000064	2 retrocopies	retro_ocun_240, retro_ocun_83,
Otolemur garnettii	ENSOGAG00000010640	2 retrocopies	retro_ogar_248, retro_ogar_3412,
Pongo abelii	ENSPPYG00000018228	4 retrocopies	retro_pabe_100, retro_pabe_2165, retro_pabe_226, retro_pabe_669,
Pelodiscus sinensis	ENSPSIG00000018102	1 retrocopy	retro_psin_19,
Pteropus vampyrus	ENSPVAG00000000155	1 retrocopy	retro_pvam_24,
Rattus norvegicus	ENSRNOG00000010353	6 retrocopies	retro_rnor_1680, retro_rnor_1930, retro_rnor_212, retro_rnor_2673, retro_rnor_60, retro_rnor_641,
Ictidomys tridecemlineatus	ENSSTOG00000002964	7 retrocopies	retro_itri_1090, retro_itri_1143, retro_itri_169, retro_itri_54, retro_itri_74, retro_itri_832, retro_itri_85,
Tupaia belangeri	ENSTBEG00000009586	7 retrocopies	retro_tbel_1521, retro_tbel_1533, retro_tbel_1571, retro_tbel_1978, retro_tbel_3918, retro_tbel_4142, retro_tbel_67,
Tarsius syrichta	ENSTSYG00000005448	4 retrocopies	retro_tsyr_1358, retro_tsyr_297, retro_tsyr_360, retro_tsyr_491,
Tursiops truncatus	ENSTTRG00000013929	2 retrocopies	retro_ttru_1864, retro_ttru_637,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 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	0.03 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 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	0.04 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

---

Indel association:

The presence of retro_hsap_2399 across human populations is associated with 2 indels. The percentage values indicate the frequencies of retro_hsap_2399 presence in various populations. Based on Kabza et al. 2015 (PubMed).

#	Indel coordinates	AFR, African			AMR, Ad Mixed American			EUR, European					EAS, East Asian
		ASW	YRI	LWK	MXL	PUR	CLM	CEU	IBS	GBR	FIN	TSI	JPT	CHB	CHS
1.	2:234648330..234660000	99.18	96.59	96.39	100	100	99.17	100	100	100	100	100	100	100	100
2.	2:234650078..234662000	99.18	97.16	96.39	100	100	99.17	100	100	100	100	100	100	100	100

---

Indel #1, located at the genomic coordinates 2:234648330..234660000.

Indel #2, located at the genomic coordinates 2:234650078..234662000.