RetrogeneDB ID: retro_hsap_10

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:18066448..18067405(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000229937
• Aliases: PRPS1L1, PRPS1, PRPS3, PRPSL, PRS-III
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PRPS1
• Ensembl ID: ENSG00000147224
• Aliases: PRPS1, ARTS, CMTX5, DFN2, DFNX1, PPRibP, PRS-I, PRSI
• Description: phosphoribosyl pyrophosphate synthetase 1 [Source:HGNC Symbol;Acc:9462]

Sequence

>retro_hsap_10
ACGCCGAATATCAAAATCTTCAGCGGCAGCTCCCACCAGGACTTATCCCAGAAAATTGCTGACCGCCTGGGCCTGGAGCT
AGGCAAGGTGGTGACTAAGAAATTCAGCAACCAGGAGACCTGCGTGGAAATTGATGAGAGTGTGCGTGGAGAGGATGTCT
ACATCGTTCAGAGTGGTTGTGGCGAAATCAACGACAGTCTAATGGAGCTTTTGATCATGATTAATGCCTGCAAGATTGCT
TCAGCTAGCCGAGTTACTGCAGTCATCCCATGCTTCCCTTATGCCCGACAGGATAAGAAGGATAAGAGCCGGTCCCCAAT
CTCTGCCAAGCTTGTTGCAAATATGCTCTCTATAGCAGGTGCGGATCATATCATCACCATGGACCTACATGCTTCTCAAA
TTCAGGGCTTTTTTGATATCCCAGTAGACAACTTGTATGCAGAGCCAACTGTCCTGAAGTGGATAAGGGAGAATATCCCT
GAGTGGAAGAACTGCATTATTGTCTCGCCAGATGCTGGTGGAGCTAAAAGAGTGACCTCCATTGCAGACCAGTTGAATGT
GGACTTTGCTTTGATTCATAAAGAACGGAAGAAGGCCAATGAAGTGGACTGCATAGTGCTAGTGGGAGATGTGAATGATC
GTGTGGCTATCCTTGTAGATGACATGGCAGACACTTGTGTTACAATCTGCCTCGCAGCTGACAAACTTCTCTCAGCTGGA
GCAACCAGAGTTTATGCTATCTTGACTCATGGAATCTTTTCTGGCCCAGCCATTTCTCGCATCAACACTGCATGCTTTGA
AGCAGTGGTAGTCACCAATACCATACCTCAAGATGAGAAGATGAAGCATTGCTCCAAAATACGAGTAATTGACATCTCCA
TGATCCTTGCAGAAGCCATAAGGAGAACTCATAATGGGGAATCTGTTTCCTACCTGTTCAGCCATGTTCCTTTATAA

Alignment

ORF - retro_hsap_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.32 %
• Parental protein coverage: 99.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMELL
          PNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEI.ESVRGEDVYIVQSGCGEIND.LMELL
Retrocopy PNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIDESVRGEDVYIVQSGCGEINDSLMELL

Parental  IMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDIP
          IMINACKIASASRVTAVIPCFPYARQDKKDKSR.PISAKLVANMLS.AGADHIITMDLHASQIQGFFDIP
Retrocopy IMINACKIASASRVTAVIPCFPYARQDKKDKSRSPISAKLVANMLSIAGADHIITMDLHASQIQGFFDIP

Parental  VDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKERKKANEVDRMVLVGDV
          VDNLYAEP.VLKWIRENI.EW.NC.IVSPDAGGAKRVTSIAD.LNVDFALIHKERKKANEVD..VLVGDV
Retrocopy VDNLYAEPTVLKWIRENIPEWKNCIIVSPDAGGAKRVTSIADQLNVDFALIHKERKKANEVDCIVLVGDV

Parental  KDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDKM
          .DRVAILVDDMADTC.TIC.AADKLLSAGATRVYAILTHGIFSGPAISRIN.ACFEAVVVTNTIPQ..KM
Retrocopy NDRVAILVDDMADTCVTICLAADKLLSAGATRVYAILTHGIFSGPAISRINTACFEAVVVTNTIPQDEKM

Parental  KHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
          KHCSKI.VIDISMILAEAIRRTHNGESVSYLFSHVPL
Retrocopy KHCSKIRVIDISMILAEAIRRTHNGESVSYLFSHVPL

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	0.06 RPM	28.62 RPM
bodymap2_adrenal	0.00 RPM	39.94 RPM
bodymap2_brain	0.00 RPM	43.43 RPM
bodymap2_breast	0.00 RPM	22.08 RPM
bodymap2_colon	0.00 RPM	28.04 RPM
bodymap2_heart	0.00 RPM	16.50 RPM
bodymap2_kidney	0.00 RPM	25.91 RPM
bodymap2_liver	0.00 RPM	33.63 RPM
bodymap2_lung	0.00 RPM	49.95 RPM
bodymap2_lymph_node	0.00 RPM	32.14 RPM
bodymap2_ovary	0.00 RPM	41.73 RPM
bodymap2_prostate	0.00 RPM	34.64 RPM
bodymap2_skeletal_muscle	0.00 RPM	30.17 RPM
bodymap2_testis	21.08 RPM	23.11 RPM
bodymap2_thyroid	0.00 RPM	46.19 RPM
bodymap2_white_blood_cells	0.00 RPM	47.17 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_10 was not detected

EST

5 EST(s) were mapped to retro_hsap_10 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
HY190258	18066404	18066889	99	482	2	479
HY218972	18066404	18066837	100	433	0	433
HY220926	18066404	18066850	99.8	445	1	444
HY237766	18066404	18066845	99.8	440	1	439
HY243946	18066404	18066836	100	432	0	432

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_173439	1823 libraries	3 libraries	1 library	2 libraries	0 libraries
TSS #2	TSS_173440	1822 libraries	4 libraries	0 libraries	1 library	2 libraries
TSS #3	TSS_173441	1825 libraries	1 library	1 library	1 library	1 library

The graphical summary, for retro_hsap_10 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_10 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_10 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2600
Pongo abelii	retro_pabe_46
Macaca mulatta	retro_mmul_305
Mus musculus	retro_mmus_19
Oryctolagus cuniculus	retro_ocun_430
Equus caballus	retro_ecab_73

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002784	1 retrocopy	retro_amel_22,
Bos taurus	ENSBTAG00000019703	3 retrocopies	retro_btau_157, retro_btau_1686, retro_btau_914,
Canis familiaris	ENSCAFG00000017976	1 retrocopy	retro_cfam_1443,
Equus caballus	ENSECAG00000024711	2 retrocopies	retro_ecab_433, retro_ecab_73,
Felis catus	ENSFCAG00000012286	1 retrocopy	retro_fcat_394,
Homo sapiens	ENSG00000147224	1 retrocopy	retro_hsap_10 ,
Gorilla gorilla	ENSGGOG00000012418	1 retrocopy	retro_ggor_2583,
Macropus eugenii	ENSMEUG00000010071	2 retrocopies	retro_meug_1612, retro_meug_443,
Microcebus murinus	ENSMICG00000001929	5 retrocopies	retro_mmur_1223, retro_mmur_1422, retro_mmur_514, retro_mmur_810, retro_mmur_90,
Myotis lucifugus	ENSMLUG00000015498	2 retrocopies	retro_mluc_107, retro_mluc_356,
Macaca mulatta	ENSMMUG00000004674	3 retrocopies	retro_mmul_1204, retro_mmul_1619, retro_mmul_305,
Mustela putorius furo	ENSMPUG00000003793	2 retrocopies	retro_mputfur_183, retro_mputfur_430,
Mus musculus	ENSMUSG00000031432	2 retrocopies	retro_mmus_19, retro_mmus_33,
Nomascus leucogenys	ENSNLEG00000013911	2 retrocopies	retro_nleu_1456, retro_nleu_217,
Oryctolagus cuniculus	ENSOCUG00000012391	3 retrocopies	retro_ocun_430, retro_ocun_867, retro_ocun_912,
Ochotona princeps	ENSOPRG00000013140	1 retrocopy	retro_opri_704,
Pongo abelii	ENSPPYG00000020612	2 retrocopies	retro_pabe_3061, retro_pabe_46,
Pan troglodytes	ENSPTRG00000022163	2 retrocopies	retro_ptro_2600, retro_ptro_2612,
Rattus norvegicus	ENSRNOG00000025166	2 retrocopies	retro_rnor_249, retro_rnor_341,
Sus scrofa	ENSSSCG00000012560	1 retrocopy	retro_sscr_1068,
Ictidomys tridecemlineatus	ENSSTOG00000007638	2 retrocopies	retro_itri_11, retro_itri_173,
Tarsius syrichta	ENSTSYG00000013556	2 retrocopies	retro_tsyr_1063, retro_tsyr_1567,
Tursiops truncatus	ENSTTRG00000003835	2 retrocopies	retro_ttru_307, retro_ttru_485,
Vicugna pacos	ENSVPAG00000000255	1 retrocopy	retro_vpac_274,