RetrogeneDB ID: retro_btau_390

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:14689853..14690257(+)
• Located in intron of: ENSBTAG00000009246

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM33
• Ensembl ID: ENSBTAG00000043958
• Aliases: None
• Description: None

Sequence

>retro_btau_390
GCTTTGCTGGCAAGTGCTCTGGCCAGTGCTCTGAGGCTGTACCAAAGATGACTTCGCTTCCAGTTAAGCAGAGCATTTCT
GGCCTGAGCTTTGTTAGGGGACTGCTGGCACTACCTGTTATATTCATTCATCTTTGTCAACTCTTCCAGTTACAATGAAT
ATTCTCCCAGTCTTGTTATTTTCTTGGCTTCATGCTGCCACATACTGGAAAAAGGCACTTAGTGCAAAGGGTTCAAATAG
TTTATCTCTACTGGGACCTCTCGTCCATAAATTAAACACTAATCAACAGAATATTCTGAAATTCAATACTTATCATTAAA
TAATCTTGATGGCTGCTACAGTTTTTATGCTTTTTTAGTGGCCAAGAAAGTTTGCTCCAGCTTTTTATATACTATAGATT
CCTC

Alignment

ORF - retro_btau_390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.42 %
• Parental protein coverage: 54.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ALLANALTSALRLHQRLPHFQLSRAFLAQALLEDSCHYLL-YSLIFVNSYPVTMSIFPVLLFSLLHAATY
          ALLA.AL.SALRL.QR...FQLSRAFLA.ALL.D.C...L.Y........PVTM.I.PVLLFS.LHAATY
Retrocopy ALLASALASALRLYQR*LRFQLSRAFLA*ALLGD-CWHYL>YIHSSLSTLPVTMNILPVLLFSWLHAATY

Parental  TKKILDAKDSNSLPLLRSLLDKLSANQQNILKFIACNEIFLMPATVFML-FSGQGSLFQPFIYYRFL
          .KK.L.AK.SNSL.LL..L..KL..NQQNILKF.....I.LM.ATVFML.FSGQ.SL.Q.FIYYRFL
Retrocopy WKKALSAKGSNSLSLLGPLVHKLNTNQQNILKFNTYH*IILMAATVFML>FSGQESLLQLFIYYRFL

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	0.07 RPM	6.85 RPM
ERP005899_muscle	0.05 RPM	18.90 RPM
SRP017611_brain	0.09 RPM	18.68 RPM
SRP017611_kidney	0.71 RPM	32.84 RPM
SRP017611_liver	0.00 RPM	16.31 RPM
SRP030211_testis	0.26 RPM	4.62 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_390 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_390 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_390 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000043958	1 retrocopy	retro_btau_390 ,
Choloepus hoffmanni	ENSCHOG00000007675	1 retrocopy	retro_chof_1766,
Tursiops truncatus	ENSTTRG00000003870	1 retrocopy	retro_ttru_673,