RetrogeneDB ID: retro_sscr_1068

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:96258776..96259730(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000015366
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRPS1
• Ensembl ID: ENSSSCG00000012560
• Aliases: None
• Description: phosphoribosyl pyrophosphate synthetase 1 [Source:HGNC Symbol;Acc:9462]

Sequence

>retro_sscr_1068
ATGCCAAATATCAAAATCTTCAGCGGCAGCTCCCACCAGGATTTATCCCAGAAAATTGCTGGCCGTCTGGGTTTGAAGCT
AGGCAAGGTGGTGACGAAGAAATTCAGCAACCAGGAGACCTGTGTGGAAATTGGTGAGAGTGTGCGAGGAGAAGATGTCT
ACATAATGCAGAGTGGTTGTGGTGAAATCAACGACAATCTGATGGAGCTTTTGATCATGATTAATGCCTGCAAGACTGCT
TCAGCCAGTCGGGTAACTGCAGTCATCCCCTGCTTCCCGTATGCCCGGCAGGATAAGAAGGATAAGAACCAGGCGCCAAT
CTCTGCCAAGCTTGTTGCAAATATGCTGTCTGTAGCAGGAGCAGATCACATCATCACCATGGATTTACATGCTTCTCAAA
TTCAGGGCTTTTTTGATATCCCAGTAGACAATTTGTATGCAGAGCCAGCTGTCCTGAAGTGGATAAAGGAGAATATCTCT
GAGTGGAGGAATTGCACAATTGTCTCCCCAGATGCTGATGGAGCTAAGAGAGTGACTTCCATTGCAGACAGATTGAATGT
GGACTTTGCCTTGATTCACAAAGAAAAAAAGAAGGCCAATGAAGTAAACCGAATGGTGCTAGTGGGAGATGTGAAAGATC
GTGTGGCTATCCTTGTGGATGACATAGCTGACACTTGTGGCACAATCTGCCATGCAGCTGACAAACTTCTCTCAGCTGGA
GCCATCAGAGTTTATGCAATCTTGTCTCATGGAATCTTTTCTGGTCCAGCCATTACTCACATCAACAGTGCATGCTTTGA
AGCAGTAGTAGTCACCAACACCATACCTCAGGAAGATAAGATGAAGCGTTGCTCCAAAATACAGGTTATCGACATCTCCA
TGATCCTTGCAGAAGCCATCAGAAGAACTCACAATGGGGAATCTGTCTCCTACCTGTTCAGCCATGTCCCATTA

Alignment

ORF - retro_sscr_1068 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.65 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMEL
          MPNIKIFSGSSHQDLSQKIA.RLGL.LGKVVTKKFSNQETCVEIGESVRGEDVYI.QSGCGEINDNLMEL
Retrocopy MPNIKIFSGSSHQDLSQKIAGRLGLKLGKVVTKKFSNQETCVEIGESVRGEDVYIMQSGCGEINDNLMEL

Parental  LIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDI
          LIMINACK.ASASRVTAVIPCFPYARQDKKDK..APISAKLVANMLSVAGADHIITMDLHASQIQGFFDI
Retrocopy LIMINACKTASASRVTAVIPCFPYARQDKKDKNQAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDI

Parental  PVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKERKKANEVDRMVLVGD
          PVDNLYAEPAVLKWI.ENISEWRNCTIVSPDA.GAKRVTSIADRLNVDFALIHKE.KKANEV.RMVLVGD
Retrocopy PVDNLYAEPAVLKWIKENISEWRNCTIVSPDADGAKRVTSIADRLNVDFALIHKEKKKANEVNRMVLVGD

Parental  VKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDK
          VKDRVAILVDD.ADTCGTICHAADKLLSAGA.RVYAIL.HGIFSGPAI..IN.ACFEAVVVTNTIPQEDK
Retrocopy VKDRVAILVDDIADTCGTICHAADKLLSAGAIRVYAILSHGIFSGPAITHINSACFEAVVVTNTIPQEDK

Parental  MKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
          MK.CSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
Retrocopy MKRCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL

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
SRP014902_placenta	0.00 RPM	13.14 RPM
SRP014902_testis	0.00 RPM	40.74 RPM
SRP018288_heart	0.03 RPM	23.10 RPM
SRP018288_kidney	0.00 RPM	35.86 RPM
SRP018288_liver	0.00 RPM	30.54 RPM
SRP018288_lung	0.00 RPM	27.49 RPM
SRP018856_adipose	0.00 RPM	47.60 RPM
SRP035408_brain	0.06 RPM	63.58 RPM
SRP035408_liver	0.00 RPM	57.80 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1068 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1068 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1068 has 0 orthologous retrocopies within eutheria group .

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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,