RetrogeneDB ID: retro_mmus_33

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:57238425..57239382(+)
• Located in intron of: ENSMUSG00000047022

Retrocopy information

• Ensembl ID: ENSMUSG00000079104
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Prps1
• Ensembl ID: ENSMUSG00000031432
• Aliases: Prps1, 2310010D17Rik, C76571, C76678, PRS-I, Prps-1
• Description: phosphoribosyl pyrophosphate synthetase 1 [Source:MGI Symbol;Acc:MGI:97775]

Sequence

>retro_mmus_33
ATGTCGAATATCAAAATCTTCAGCGGGAGCTCGCACCAGGACTTATCCCAGAAAATAGCTGACCGCCTGGGCTTGGAGCT
AGGCAAGGTGGTGACTAAGAAATTCAGCAACCAGGAGACCTGTGTGGAAATTGGAGAAAGCGTTCGTGGAGAGGATGTCT
ACATTGTTCAGAGTGGATGTGGTGAGATAAATGACAATCTAATGGAGCTTTTGATCATGATTAATGCTTGCAAGATTGCT
TCAGCCAGCAGGGTTACTGCAGTCATCCCATGCTTCCCTTATGCCCGCCAAGATAAGAAGGATAAGAGCCGGGCTCCAAT
CTCAGCTAAGCTTGTTGCAAATATGCTATCTGTAGCAGGTGCGGATCATATTATCACCATGGATCTACATGCATCTCAAA
TTCAGGGTTTCTTTGATATCCCGGTGGACAATTTATATGCAGAGCCAGCTGTCCTAAAGTGGATACGGGAGAATATATCT
GAGTGGAGAAACTGTACTATTGTCTCACCTGATGCTGGTGGAGCCAAGAGAGTGACCTCCATTGCAGACCGGTTGAATGT
GGATTTTGCTTTGATTCACAAGGAACGGAAGAAGGCCAATGAAGTAGACCGCATGGTACTAGTAGGAGATGTGAAGGATC
GTGTGGCTATACTTGTGGATGACATGGCTGACACTTGCGGTACAATTTGTCATGCTGCTGACAAACTTCTCTCAGCTGGA
GCTACCAGAGTTTATGCTATCTTGACGCATGGAATCTTCTCTGGCCCTGCCATTTCTCGCATCAACAATGCATGCTTTGA
AGCAGTAGTAGTTACCAATACCATACCTCAGGAAGACAAGATGAAACACTGCTCCAAAATACAGGTGATTGACATCTCTA
TGATCCTTGCAGAAGCCATCAGGAGAACCCACAATGGAGAATCTGTCTCCTACCTGTTCAGCCATGTTCCTTTGTAA

Alignment

ORF - retro_mmus_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.69 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMEL
          M.NIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMEL
Retrocopy MSNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMEL

Parental  LIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDI
          LIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDI
Retrocopy LIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDI

Parental  PVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKERKKANEVDRMVLVGD
          PVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKERKKANEVDRMVLVGD
Retrocopy PVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKERKKANEVDRMVLVGD

Parental  VKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDK
          VKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDK
Retrocopy VKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDK

Parental  MKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
          MKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
Retrocopy MKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL

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
SRP007412_brain	5.33 RPM	56.84 RPM
SRP007412_cerebellum	10.77 RPM	49.59 RPM
SRP007412_heart	10.18 RPM	22.07 RPM
SRP007412_kidney	23.00 RPM	25.56 RPM
SRP007412_liver	26.57 RPM	27.17 RPM
SRP007412_testis	24.15 RPM	11.11 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_33 was not detected

EST

5 EST(s) were mapped to retro_mmus_33 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BY071381	57238359	57238711	100	352	0	352
BY138474	57238359	57238698	99.8	338	1	337
BY138752	57238359	57238717	98.7	356	2	353
CF165524	57238400	57238870	100	470	0	470
CJ169212	57238359	57238770	100	411	0	411

TSS

No TSS is located nearby retro_mmus_33 retrocopy 5' end.

Lab

retro_mmus_33 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_33 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_249

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 48 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	ENSMUSG00000020528	2 retrocopies	retro_mmus_1937, retro_mmus_3515,
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,