RetrogeneDB ID: retro_btau_1356

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:81908122..81908662(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PSMA7
• Ensembl ID: ENSBTAG00000005127
• Aliases: None
• Description: Proteasome subunit alpha type-7 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZBG0]

Sequence

>retro_btau_1356
ATGAGCTGTAACCGCTCCATCACCGTCTTCTCTCCCAACGGCCACCTCTTCCCAGTGGAGTACTTGCAGGAGGCCATGAA
GAAGGGCTGGACCATGGTCAGTGTTCGAGGAAAAGACATTGTTGTTCTTGGTGTGGAGAAGTCAGTGGCCAAACTGCAGG
ATGAAAGGACAGGGCGGAAGGTCTGTGCTCTGGATGATAATGTCTGCATGGCATTCGCCGACTCACTGCTAACGCAAGGA
TAGTCACCAACAGGGCCCGGGTGGAATGCCAGAGCCACCGGCTGACTGTGGAGGACCTAGTCACCATGGAGTACATCACC
CGTTATATCGCCAGTCTGAAGCAGCGCTACACACAGAGCAAGGAGCGCTGGGGGTTTGGCATCTCTGCCCTCCTTGTGGG
TTTTGACTTTGATGGCACCCCCGACTCTATCAGACTGACCTCCCAGCACATACCATGCCTGGAAAGCCAATGCTGTAGGC
CAGGTTGCCAAGTCAGTGCGTGAATTCCTAGAGAATTATACTGAGGAAGCCATTGAAACC

Alignment

ORF - retro_btau_1356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.26 %
• Parental protein coverage: 73.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGKDIVVLGVEKKSVAKLQDERTVRKICALDDNVC
          MS..R.ITVFSP.GHLF.VEY.QEA.KKG.T.V.VRGKDIVVLGVEK.SVAKLQDERT.RK.CALDDNVC
Retrocopy MSCNRSITVFSPNGHLFPVEYLQEAMKKGWTMVSVRGKDIVVLGVEK-SVAKLQDERTGRKVCALDDNVC

Parental  MAFAG-LTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDFD
          MAFA..LTA.ARIV.NRARVECQSHRLTVED.VT.EYITRYIASLKQRYTQS..R..FGISAL.VGFDFD
Retrocopy MAFAD<LTANARIVTNRARVECQSHRLTVEDLVTMEYITRYIASLKQRYTQSKERWGFGISALLVGFDFD

Parental  GT-PRLYQTD-PSGTYHAWKANAIGRGAKSVREFLEKNYTDEAIET
          GT.PRLYQTD.P..TYHAWKANA.G..AKSVREFLE.NYT.EAIET
Retrocopy GT<PRLYQTD<PPSTYHAWKANAVGQVAKSVREFLE-NYTEEAIET

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	88.82 RPM
ERP005899_muscle	0.00 RPM	130.13 RPM
SRP017611_brain	0.00 RPM	44.31 RPM
SRP017611_kidney	0.00 RPM	96.44 RPM
SRP017611_liver	0.00 RPM	66.98 RPM
SRP030211_testis	0.88 RPM	21.49 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1356 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1356 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1356 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005127	1 retrocopy	retro_btau_1356 ,
Felis catus	ENSFCAG00000003249	1 retrocopy	retro_fcat_1621,
Tupaia belangeri	ENSTBEG00000012281	2 retrocopies	retro_tbel_1048, retro_tbel_2392,
Drosophila melanogaster	FBgn0004066	1 retrocopy	retro_dmel_63,