RetrogeneDB ID: retro_btau_1463

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:87555287..87556151(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000007816
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PNP
• Ensembl ID: ENSBTAG00000012317
• Aliases: PNP, NP
• Description: Purine nucleoside phosphorylase [Source:UniProtKB/Swiss-Prot;Acc:P55859]

Sequence

>retro_btau_1463
ATGGAGAATGGATTTACATATGAAGATTATCAAGACACTGCAAAATGGCTTTTGTCTCATACCGAACAGCAACCTCGAGT
GGCAATGATCTGTGGTTCTGGGTTAGGAGGTCTGATTAACAGATTGACTCAAGCCCAGACCTTTGACTACAGTGAAATAC
CAAACTTTCCCAAAAGTACAGTGCCAGGTCATGCTGGTCGACTGGTGTTTGGGATCTTGAATGGCAGAGCCTGTGTGATG
ATGCAGGGCAGGTTCCACATGTATGAAGGCTACCCGTTCTGGAAGGTGACGTTCCCAGTGAGGGTTTTCCGGCTTCTGGG
TGTGGAGATCCTAGTGGTCACCAACGCAGCTGGAGGGCTGAACCCCAACTTTGAGGTTGGCGATATCATGCTGATCCGTG
ATCACATCAACCTACCTGGTTTCAGTGGTGAGAACCCTCTCAGAGGGCCCAATGAGGAAAGGTTTGGAGTTCGTTTCCCT
GCCATGTCTGATGCCTACGACCGGGATATGAGGCAGAAAGCTCACAGTACCTGGAAACAAATGGGGGAGCAAAGAGAGTT
ACAGGAAGGCACCTATGTGATGTTGGGGGGCCCCAATTATGAGACTGTGGCAGAGTGTCGCCTGCTGCGGAATCTAGGGG
CAGATGCTGTTGGCATGAGCACAGTACCAGAAGTTATAGTCGCAAGACACTGTGGACTTCGAGTCTTTGGCTTCTCACTC
ATCACAAACAAGGTCATCATGGATTATGAAAGCCAGGGGAAGGCCGATCACAAGGAAGTACTAGAGGCTGGGAAGCAAGC
TGCACAGAAATTAGAGCAGTTTGTCTCCCTTCTTATGGCTAGCATTCCACTGCCAGGGCACACC

Alignment

ORF - retro_btau_1463 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.14 %
• Parental protein coverage: 99.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MANGYTYEDYQDTAKWLLSHTEQRPQVAVICGSGLGGLVNKLTQAQTFDYSEIPNFPESTVPGHAGRLVF
          M.NG.TYEDYQDTAKWLLSHTEQ.P.VA.ICGSGLGGL.N.LTQAQTFDYSEIPNFP.STVPGHAGRLVF
Retrocopy MENGFTYEDYQDTAKWLLSHTEQQPRVAMICGSGLGGLINRLTQAQTFDYSEIPNFPKSTVPGHAGRLVF

Parental  GILNGRACVMMQGRFHMYEGYPFWKVTFPVRVFRLLGVETLVVTNAAGGLNPNFEVGDIMLIRDHINLPG
          GILNGRACVMMQGRFHMYEGYPFWKVTFPVRVFRLLGVE.LVVTNAAGGLNPNFEVGDIMLIRDHINLPG
Retrocopy GILNGRACVMMQGRFHMYEGYPFWKVTFPVRVFRLLGVEILVVTNAAGGLNPNFEVGDIMLIRDHINLPG

Parental  FSGENPLRGPNEERFGVRFPAMSDAYDRDMRQKAHSTWKQMGEQRELQEGTYVMLGGPNFETVAECRLLR
          FSGENPLRGPNEERFGVRFPAMSDAYDRDMRQKAHSTWKQMGEQRELQEGTYVMLGGPN.ETVAECRLLR
Retrocopy FSGENPLRGPNEERFGVRFPAMSDAYDRDMRQKAHSTWKQMGEQRELQEGTYVMLGGPNYETVAECRLLR

Parental  NLGADAVGMSTVPEVIVARHCGLRVFGFSLITNKVIMDYESQGKANHEEVLEAGKQAAQKLEQFVSLLMA
          NLGADAVGMSTVPEVIVARHCGLRVFGFSLITNKVIMDYESQGKA.H.EVLEAGKQAAQKLEQFVSLLMA
Retrocopy NLGADAVGMSTVPEVIVARHCGLRVFGFSLITNKVIMDYESQGKADHKEVLEAGKQAAQKLEQFVSLLMA

Parental  SIPVSGHT
          SIP..GHT
Retrocopy SIPLPGHT

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
ERP005899_liver	0.65 RPM	244.91 RPM
ERP005899_muscle	0.00 RPM	60.71 RPM
SRP017611_brain	0.09 RPM	21.15 RPM
SRP017611_kidney	0.53 RPM	91.81 RPM
SRP017611_liver	0.68 RPM	109.26 RPM
SRP030211_testis	0.80 RPM	14.90 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1463 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1463 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1463 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005373	1 retrocopy	retro_amel_1666,
Bos taurus	ENSBTAG00000012317	1 retrocopy	retro_btau_1463 ,
Choloepus hoffmanni	ENSCHOG00000009274	5 retrocopies	retro_chof_1328, retro_chof_1595, retro_chof_1827, retro_chof_1933, retro_chof_348,
Callithrix jacchus	ENSCJAG00000009676	2 retrocopies	retro_cjac_1195, retro_cjac_1511,
Dasypus novemcinctus	ENSDNOG00000011630	1 retrocopy	retro_dnov_322,
Erinaceus europaeus	ENSEEUG00000002411	1 retrocopy	retro_eeur_541,
Felis catus	ENSFCAG00000006934	1 retrocopy	retro_fcat_1368,
Homo sapiens	ENSG00000198805	1 retrocopy	retro_hsap_2282,
Gorilla gorilla	ENSGGOG00000002126	1 retrocopy	retro_ggor_1695,
Macropus eugenii	ENSMEUG00000014512	3 retrocopies	retro_meug_1282, retro_meug_1560, retro_meug_211,
Macaca mulatta	ENSMMUG00000019126	1 retrocopy	retro_mmul_287,
Mustela putorius furo	ENSMPUG00000018119	2 retrocopies	retro_mputfur_420, retro_mputfur_822,
Nomascus leucogenys	ENSNLEG00000010969	1 retrocopy	retro_nleu_1964,
Otolemur garnettii	ENSOGAG00000013344	4 retrocopies	retro_ogar_1631, retro_ogar_2141, retro_ogar_3083, retro_ogar_594,
Pongo abelii	ENSPPYG00000005567	1 retrocopy	retro_pabe_1938,
Pan troglodytes	ENSPTRG00000006095	1 retrocopy	retro_ptro_1616,
Pteropus vampyrus	ENSPVAG00000010734	1 retrocopy	retro_pvam_1302,
Rattus norvegicus	ENSRNOG00000009982	1 retrocopy	retro_rnor_891,
Tupaia belangeri	ENSTBEG00000016378	1 retrocopy	retro_tbel_4632,
Tarsius syrichta	ENSTSYG00000000748	3 retrocopies	retro_tsyr_2057, retro_tsyr_2127, retro_tsyr_235,