RetrogeneDB ID: retro_hsap_3499

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:99622619..99623354(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000232699
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BDH2
• Ensembl ID: ENSG00000164039
• Aliases: None
• Description: 3-hydroxybutyrate dehydrogenase, type 2 [Source:HGNC Symbol;Acc:32389]

Sequence

>retro_hsap_3499
ATGGGTCAACTTGATGGGAAAGTCATCATCCTGACAGCCGCTGCTCAGGGGATTGGCCAAGCAGCTGCCTTAGCTTTTGT
AAGAGAAGGTGCCAAAGTCATAGCCACAGACATTAATGTGTCCAAACTTCAGGAACTGGAAAAGTACCTGGGTATTCAAA
CTCGTGTCCTTGATGTCACAAAGAAGAAACAAATTGATCAGTTCGCCAATGAAGTTGAGAGACTTGATGTTCTCTTTAAT
GTTGCTGGTTTTGTCCATCATGGAACTGTCCTGGATTGTGAGGAGAAAGACTGGGACTTCTCGATGAATCTCAATGTGCG
CAGCACGTACCTGATGATCAAGGCATTCCTTCCTAAAATGCTTGCTCAAAAATCTGGCAATATTATCACCATGTTTTCTG
TGGTTTCCAGCATCAAAGGAGTTGTGAACAGATGTGTGTACAGCACAACCAAGGCAGCCGTGATTGGCCTCACAAAATCT
GTGGCTGCAGATTTCATCCAGCAGGGCATCAGGTGCAACTGTGTGTGCCCAGGAACGGTTGATACGCCATCTCTACAAGA
AAGAATACAAGCCAGAGGAAATCCTGAAGAGGCACGGAATGATTTCCTGAAGAGACAAAAGATGGGACGATTTGCAACTG
CAGAAGAAATAGCCATGCTCTGCGTGTATGTGGCTTCTGATGAATCTGCTTATGTAACTGGTAACCCTGTCATCATTGAT
GGAGGATGGAGCTTG

Alignment

ORF - retro_hsap_3499 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRLDGKVIILTAAAQGIGQAAALAFAREGAKVIATDINESKLQELEKYPGIQTRVLDVTKKKQIDQFAN
          MG.LDGKVIILTAAAQGIGQAAALAF.REGAKVIATDIN.SKLQELEKY.GIQTRVLDVTKKKQIDQFAN
Retrocopy MGQLDGKVIILTAAAQGIGQAAALAFVREGAKVIATDINVSKLQELEKYLGIQTRVLDVTKKKQIDQFAN

Parental  EVERLDVLFNVAGFVHHGTVLDCEEKDWDFSMNLNVRSMYLMIKAFLPKMLAQKSGNIINMSSVASSVKG
          EVERLDVLFNVAGFVHHGTVLDCEEKDWDFSMNLNVRS.YLMIKAFLPKMLAQKSGNII.M.SV.SS.KG
Retrocopy EVERLDVLFNVAGFVHHGTVLDCEEKDWDFSMNLNVRSTYLMIKAFLPKMLAQKSGNIITMFSVVSSIKG

Parental  VVNRCVYSTTKAAVIGLTKSVAADFIQQGIRCNCVCPGTVDTPSLQERIQARGNPEEARNDFLKRQKTGR
          VVNRCVYSTTKAAVIGLTKSVAADFIQQGIRCNCVCPGTVDTPSLQERIQARGNPEEARNDFLKRQK.GR
Retrocopy VVNRCVYSTTKAAVIGLTKSVAADFIQQGIRCNCVCPGTVDTPSLQERIQARGNPEEARNDFLKRQKMGR

Parental  FATAEEIAMLCVYLASDESAYVTGNPVIIDGGWSL
          FATAEEIAMLCVY.ASDESAYVTGNPVIIDGGWSL
Retrocopy FATAEEIAMLCVYVASDESAYVTGNPVIIDGGWSL

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	0.02 RPM	11.69 RPM
bodymap2_adrenal	0.00 RPM	14.64 RPM
bodymap2_brain	0.02 RPM	27.17 RPM
bodymap2_breast	0.02 RPM	19.88 RPM
bodymap2_colon	0.02 RPM	22.47 RPM
bodymap2_heart	0.00 RPM	13.50 RPM
bodymap2_kidney	0.06 RPM	94.90 RPM
bodymap2_liver	0.00 RPM	28.26 RPM
bodymap2_lung	0.00 RPM	23.77 RPM
bodymap2_lymph_node	0.00 RPM	14.25 RPM
bodymap2_ovary	0.00 RPM	31.88 RPM
bodymap2_prostate	0.03 RPM	23.12 RPM
bodymap2_skeletal_muscle	0.31 RPM	4.69 RPM
bodymap2_testis	0.00 RPM	24.00 RPM
bodymap2_thyroid	0.09 RPM	43.26 RPM
bodymap2_white_blood_cells	0.00 RPM	5.61 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3499 was not detected

EST

No EST(s) were mapped for retro_hsap_3499 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_168572	1054 libraries	530 libraries	238 libraries	7 libraries	0 libraries

The graphical summary, for retro_hsap_3499 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_3499 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3499 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_199
Pongo abelii	retro_pabe_2891

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000164039	1 retrocopy	retro_hsap_3499 ,
Gorilla gorilla	ENSGGOG00000006381	1 retrocopy	retro_ggor_199,
Pongo abelii	ENSPPYG00000025868	1 retrocopy	retro_pabe_2891,
Xenopus tropicalis	ENSXETG00000021320	2 retrocopies	retro_xtro_35, retro_xtro_37,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.07 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.00 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	0.06 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 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).