RetrogeneDB ID: retro_btau_1409

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:17207298..17208346(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000020784
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTGR2
• Ensembl ID: ENSBTAG00000003747
• Aliases: PTGR2, ZADH1
• Description: Prostaglandin reductase 2 [Source:UniProtKB/Swiss-Prot;Acc:Q32L99]

Sequence

>retro_btau_1409
ATGATTGTATAAAGAGTGGTATTGAATTCCAGACCTGGAAAAAATGGTCATCCGGTGGCAGAAAATTTCCAAGTAGAAGA
AGTAAACTTACCAGATTGTGTCAATGAAAGACAAGTACAAGTCAGAACTCTTTATCTTTCCATGGATCCTTACATGCGTT
GTAGAATGAATGAAGACACTGGCAGTGACTATATAACACCTTGGCAGCTGTCTCAGGTGGTTGATGCTGGAGGTGTTGGG
ATTATAGAAGAAAGAAAACACAAATTTTACAAAAGGCGATTTTGTGACTTCCTTCTATTGGCCCTGGCAAACCACGGTTA
TTCTGGATGGAAATATCCTTGAAAAGGTAGACCCACAACTTGTGGATGGACACCTTTCATACTTTCTTGAAGCTATAGGG
ATGCCTGGTTTGACTTACTTGATTGGGGTACAGGAAAAAAGTCATATAACTGCTGGATCTAATCAAACAATGGTTGTTAG
TGGGGCTGCTGGTGCTTGTGGATCCTTGGCTGGGCAGATTGGCCGTTTGCTGGGCTGTTCCAAAGTCGTGGGAATTTGTG
GAACACCTGAGAAGTGCCTCTTTTTGACCTCAGAATTGGGCTTCAATGCTGCAATTAATTATAAAGAGGGGAATGTTGCA
GAACAACTCCATAAATTATGCCCAGCTGGAGTGGATGTTTACTTGAACAATGTTGGCGGTGACATCAGTGATACAGTGAT
AAGTCAGATGAATCAGAACAGCCACATCATCCTCTGTGGTCAAATTTCTCAGTACAACAAAGATGTGCCTTATCCTCCAC
TACACCCTGCTATAGAAGCAATCCAGAAAGAAAGAAACATCACAAGAGAAAGATTTCTGGTGTTAAATTATAAGGATAAA
TTTGAGTTTGGTATTCTCCAACTGAGCCAATGGTTTAAAGAAGGAAAGCTAAAGATCAAAGAGACTAGAATAAATGGATT
GGAAAACATGGGAGCTGCATTCCAGTCCATGATGACAGGAGGTAACATTGGAAAGCAGATAGTTTGCATTTCAGGAGATA
CCTCTTTG

Alignment

ORF - retro_btau_1409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIVQRVVLNSRPGKNGHPVAENFRVEEVNLPDCVNEGQVQVRTLYLSVDPYMRCRMNEDTGSDYITPWQL
          MIV.RVVLNSRPGKNGHPVAENF.VEEVNLPDCVNE.QVQVRTLYLS.DPYMRCRMNEDTGSDYITPWQL
Retrocopy MIV*RVVLNSRPGKNGHPVAENFQVEEVNLPDCVNERQVQVRTLYLSMDPYMRCRMNEDTGSDYITPWQL

Parental  SQVVDGGGVGIIEESKHTNFMK-GDFVTSFYWPWQTKVILDGNILEKVDPQLVDGHLSYFLGAIGMPGLT
          SQVVD.GGVGIIEE.KH..F.K.GDFVTSFYWPWQT.VILDGNILEKVDPQLVDGHLSYFL.AIGMPGLT
Retrocopy SQVVDAGGVGIIEERKH-KFYK>GDFVTSFYWPWQTTVILDGNILEKVDPQLVDGHLSYFLEAIGMPGLT

Parental  SLIGVQEKGHITAGSNQTMVVSGAAGACGSLAGQIGRLLGCSRVVGICGTPEKCLFLTSELGFDAAINYK
          .LIGVQEK.HITAGSNQTMVVSGAAGACGSLAGQIGRLLGCS.VVGICGTPEKCLFLTSELGF.AAINYK
Retrocopy YLIGVQEKSHITAGSNQTMVVSGAAGACGSLAGQIGRLLGCSKVVGICGTPEKCLFLTSELGFNAAINYK

Parental  EGNVAEQLHKLCPAGVDVYFDNVGGDISDTVISQMNQNSHIILCGQISQYNKDVPYPPPLPPAIEAIQKE
          EGNVAEQLHKLCPAGVDVY..NVGGDISDTVISQMNQNSHIILCGQISQYNKDVPY.PPL.PAIEAIQKE
Retrocopy EGNVAEQLHKLCPAGVDVYLNNVGGDISDTVISQMNQNSHIILCGQISQYNKDVPY-PPLHPAIEAIQKE

Parental  RNITRERFLVLNYKDKFEFGILQLSQWFKEGKLKIKETMINGLENMGAAFQSMMTGGNIGKQIVCISGDT
          RNITRERFLVLNYKDKFEFGILQLSQWFKEGKLKIKET.INGLENMGAAFQSMMTGGNIGKQIVCISGDT
Retrocopy RNITRERFLVLNYKDKFEFGILQLSQWFKEGKLKIKETRINGLENMGAAFQSMMTGGNIGKQIVCISGDT

Parental  SL
          SL
Retrocopy SL

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	0.00 RPM	82.41 RPM
ERP005899_muscle	0.11 RPM	14.78 RPM
SRP017611_brain	0.05 RPM	16.90 RPM
SRP017611_kidney	0.00 RPM	73.85 RPM
SRP017611_liver	0.00 RPM	60.10 RPM
SRP030211_testis	0.07 RPM	19.70 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1409 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1409 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1409 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003747	1 retrocopy	retro_btau_1409 ,
Echinops telfairi	ENSETEG00000005782	1 retrocopy	retro_etel_216,
Otolemur garnettii	ENSOGAG00000014524	1 retrocopy	retro_ogar_3340,