RetrogeneDB ID: retro_hsap_3809

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:150446823..150447144(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000241134
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BET1
• Ensembl ID: ENSG00000105829
• Aliases: BET1, HBET1
• Description: Bet1 golgi vesicular membrane trafficking protein [Source:HGNC Symbol;Acc:14562]

Sequence

>retro_hsap_3809
ATGAAGCATGCAGGCCTGGGTGAAGGAATACCTCCTGACAACTCCGGGAATGATGGCTATGCTAATAATGGGTATAGTGC
CCGTGAAGAAGAAAATGAGACACTCACTGAAAATCTGAGAAGCAAAGTAACTGCTATAAAATCTTTTTCCATTGAAATAG
GCCATGAAGTTAAAACCCAAAATAAATTATTAGCTGTAATGGATTCACAATTTGATTCTACAACTGGATTTCTAGGTAAA
ACTATGGGCAAACTGGAGATTTTATCCATAAGGAGCCAAACAAAGCTGCTGTGCTCTGCAATGCTGTTTCATTTATTTGT
C

Alignment

ORF - retro_hsap_3809 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.18 %
• Parental protein coverage: 90.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRRAGLGEGVPPGNYGNYGYANSGYSACEEENERLTESLRSKVTAIKSLSIEIGHEVKTQNKLLAEMDSQ
          M..AGLGEG.PP.N.GN.GYAN.GYSA.EEENE.LTE.LRSKVTAIKS.SIEIGHEVKTQNKLLA.MDSQ
Retrocopy MKHAGLGEGIPPDNSGNDGYANNGYSAREEENETLTENLRSKVTAIKSFSIEIGHEVKTQNKLLAVMDSQ

Parental  FDSTTGFLGKTMGKLKILSRGSQTKLLCYMMLFSLFV
          FDSTTGFLGKTMGKL.ILS..SQTKLLC..MLF.LFV
Retrocopy FDSTTGFLGKTMGKLEILSIRSQTKLLCSAMLFHLFV

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	0.32 RPM	12.42 RPM
bodymap2_adrenal	0.31 RPM	13.94 RPM
bodymap2_brain	0.21 RPM	9.07 RPM
bodymap2_breast	0.29 RPM	22.37 RPM
bodymap2_colon	0.00 RPM	17.09 RPM
bodymap2_heart	0.15 RPM	9.16 RPM
bodymap2_kidney	0.23 RPM	32.88 RPM
bodymap2_liver	0.04 RPM	15.27 RPM
bodymap2_lung	1.11 RPM	17.91 RPM
bodymap2_lymph_node	2.19 RPM	25.46 RPM
bodymap2_ovary	0.04 RPM	31.69 RPM
bodymap2_prostate	0.26 RPM	29.03 RPM
bodymap2_skeletal_muscle	0.00 RPM	2.42 RPM
bodymap2_testis	0.25 RPM	21.64 RPM
bodymap2_thyroid	0.15 RPM	14.65 RPM
bodymap2_white_blood_cells	0.85 RPM	21.54 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3809 was not detected

EST

No EST(s) were mapped for retro_hsap_3809 retrocopy.

TSS

No TSS is located nearby retro_hsap_3809 retrocopy 5' end.

Lab

retro_hsap_3809 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3809 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2584
Gorilla gorilla	retro_ggor_2560

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003424	1 retrocopy	retro_btau_1054,
Choloepus hoffmanni	ENSCHOG00000001276	1 retrocopy	retro_chof_2211,
Callithrix jacchus	ENSCJAG00000013720	3 retrocopies	retro_cjac_1411, retro_cjac_2019, retro_cjac_3155,
Dasypus novemcinctus	ENSDNOG00000001012	3 retrocopies	retro_dnov_1683, retro_dnov_393, retro_dnov_60,
Homo sapiens	ENSG00000105829	1 retrocopy	retro_hsap_3809 ,
Gorilla gorilla	ENSGGOG00000002176	1 retrocopy	retro_ggor_2560,
Loxodonta africana	ENSLAFG00000000587	1 retrocopy	retro_lafr_1023,
Macaca mulatta	ENSMMUG00000000007	1 retrocopy	retro_mmul_1656,
Nomascus leucogenys	ENSNLEG00000015441	1 retrocopy	retro_nleu_2151,
Oryctolagus cuniculus	ENSOCUG00000017029	2 retrocopies	retro_ocun_1116, retro_ocun_355,
Ochotona princeps	ENSOPRG00000004536	4 retrocopies	retro_opri_201, retro_opri_249, retro_opri_388, retro_opri_880,
Pan troglodytes	ENSPTRG00000019408	1 retrocopy	retro_ptro_2584,
Rattus norvegicus	ENSRNOG00000011008	2 retrocopies	retro_rnor_2195, retro_rnor_2196,
Sus scrofa	ENSSSCG00000015325	2 retrocopies	retro_sscr_455, retro_sscr_516,
Tupaia belangeri	ENSTBEG00000000765	2 retrocopies	retro_tbel_3115, retro_tbel_4272,
Tarsius syrichta	ENSTSYG00000009729	2 retrocopies	retro_tsyr_136, retro_tsyr_1843,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.04 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.14 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.13 RPM
FIN_HG00183	0.08 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.12 RPM
FIN_HG00338	0.09 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.09 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.06 RPM
TSI_NA20513	0.10 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.27 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.17 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.08 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.08 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

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