RetrogeneDB ID: retro_btau_1400

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:101838613..101840386(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000040450
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TH1L
• Ensembl ID: ENSBTAG00000018783
• Aliases: LOC514958, TH1L
• Description: None

Sequence

>retro_btau_1400
CGGAAGAGTCCAGTGGGGGCCATGCCTGGTGCCACCATGGACATGGACCAGGATGACTTCGGGAGCCCTGCCGAGTGGGG
TGACCAGCAGCCAGAAGATGGTGTGCTGGGAGAAGAAGATGCCCAGGTCCAGCAAGAATGCCTGCAGAAATTTTCTACCC
CAGATTATATCATGGAGCCCTCTGTCTTCAACACTTTGATGAGATATTTCCAGGCAGGAAGGTCTCCAGAGGAGGTGATC
CGCCTCTTATCAGACAACTACACAGCTGTGGCCCAGACCATCAACCTGCTGGCCCAGTGGCTCATTCAGACCGGGGTGGA
ACCAGTGCAGATTCAGGAAACAGTGGAAAACCACTTGAAGGACTTAGTGATGCAACACTTCGACCCCCGCAAAGCAGATT
CTATCTTTACAAACGAAAGGGCAACCCCCGCCTGGCTGGAACAAATGATTGCACATCCCACCTGGAGGGATCTTGTTTAC
CAGCTGATGGAAGTGCACCCAGACTGTCTGATGCTGAAATTCACGGTCAAGCTCATTTCCGATGCAGGATACCAAGGCGA
GATCACTGGCGTGGTGGCAGCCTGCCAGCAGCTCGAAGTGTTCTCTAGAGTTCTCGGGAGCTCTCTAGCTACCATTTTGG
ATGGAGGAGAAGCCAACCTTGCAGAAAACCTGCCTCAGTTTGCTAAGATGGTGTGCCACGGCGAGCATACGTACCTGCTG
GCTCAGGTCCTGATGGCCGTGCTGGCCCAGGAAGGCCAGCGGGGCGGGGCAGTGCGCAGGGTCGCACAGGAGGTCCAGCG
CTTCGCCCAGGAGAGTGGCCACGATGCCAGTCGCATCCCGCTTGCCCTGGGCAGAGCTGCCTCCTACCCCCGGCTGTGCC
AGGCCCTGGGGGCCATGCTGTCCAAGGAGGCCCTGAATCCAGCCGACATCACCGTCCTCTACAACCTGTTTGTTACCAGC
AGGGACCCGCCTCCTGTCGAGCTCATCCGGGTGCCAGCCTTCCTGGACCTGTTCATGCAATCGCTCTTTAAACCTGGGGC
CAGGATCAACCCAGACCACAAGCACAAGTATATCCATCTCTTAGCCTACGCGGCCAGCGTGGTGGAGATCTGGAAGAAGA
ACAAACGCCTGAGCATCAATCAAGATGAGCTGAAGGCAACAGCGAAGGCTATTGAAACTGTTCACAATTTGTGCTGTGCT
GAGAACACAGGGGCAAGCGAGCTCCTGGCCGAGCTGAGCACCCTCTATAGGTGCATCAGATTTCCAGTGGTGGCAGTGGG
TGTGCTGACGTGGGTGAACGGGACCGTGTCAAAGCCCAAGTTCTTCGAGCAGCACACCCACCCCACTCCAGTGCCCCTGG
CCCTGCTAGACGAGGTCAGCACCTACCATCCCCTCCTGCACCCCCACGTCTTGCAGCTACTGATCAAGCTCTTGGAGACT
GAATACCCCGAGCTAGATGCCATGAAGCAGCTCAAGGTGAAGAAGACCCTCCTGAACAGGATGGTGCACCTGCTGAGTTG
CGGCCATGTGCTCCCCGTGGTCGCCTACATCCGCAGGTGTCTGGAGAAGCTGGACACCGACCTGTCTCTCATCCGCTACT
TTGTGTCCGAGGTGCTGGATATGATCATCCCTCCCTACACCTCTGACTTTGTGCGGCTTTTCCTGCCCATCCTGGAAAAC
GACAGCATTGCCAGCACCCTGAAAAGGGCGGGTGAACATGACCCTGTGACAGAGTTCATAGCTCACTGCCAGTCTAACTT
CATGTTGCTGGAC

Alignment

ORF - retro_btau_1400 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.55 %
• Parental protein coverage: 99. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RERMAGAAPGAIMD--EDYFGNAAEWGDEAEGGQPQEDDYGEGEDDAEVQQECLHKFSTRDYIMEPSIFN
          R....GA.PGA.MD...D.FG..AEWGD.....QP.....G..E.DA.VQQECL.KFST.DYIMEPS.FN
Retrocopy RKSPVGAMPGATMDMDQDDFGSPAEWGDQ----QPEDGVLG--EEDAQVQQECLQKFSTPDYIMEPSVFN

Parental  TLKRYFQAGGSPENVIQLLSENYTAVAQTVNLLAEWLIQTGVEPVQVQETVENHLKSLLIKHFDPRKADS
          TL.RYFQAG.SPE.VI.LLS.NYTAVAQT.NLLA.WLIQTGVEPVQ.QETVENHLK.L...HFDPRKADS
Retrocopy TLMRYFQAGRSPEEVIRLLSDNYTAVAQTINLLAQWLIQTGVEPVQIQETVENHLKDLVMQHFDPRKADS

Parental  IFTEEGETPAWLEQMIAHTTWRDLFYKLAEAHPDCLMLNFTVKLISDAGYQGEITSVSTACQQLEVFSRV
          IFT.E..TPAWLEQMIAH.TWRDL.Y.L.E.HPDCLML.FTVKLISDAGYQGEIT.V..ACQQLEVFSRV
Retrocopy IFTNERATPAWLEQMIAHPTWRDLVYQLMEVHPDCLMLKFTVKLISDAGYQGEITGVVAACQQLEVFSRV

Parental  LRTSLATILDGGEENLEKNLPEFAKMVCHGEHTYLFAQALMSVLAQEEQGGSAVRRIAQEVQRFAQERGH
          L..SLATILDGGE.NL..NLP.FAKMVCHGEHTYL.AQ.LM.VLAQE.Q.G.AVRR.AQEVQRFAQE.GH
Retrocopy LGSSLATILDGGEANLAENLPQFAKMVCHGEHTYLLAQVLMAVLAQEGQRGGAVRRVAQEVQRFAQESGH

Parental  DASQITLALGTAASYPRACQALGAMLSKGALNPADITVLFKMF-TSMDPPPVELIRVPAFLDLFMQSLFK
          DAS.I.LALG.AASYPR.CQALGAMLSK.ALNPADITVL...F.TS.DPPPVELIRVPAFLDLFMQSLFK
Retrocopy DASRIPLALGRAASYPRLCQALGAMLSKEALNPADITVLYNLFVTSRDPPPVELIRVPAFLDLFMQSLFK

Parental  PGARINQDHKHKYIHILAYAASVVETWKKNKRVSINKDELKSTSKAVETVHNLCCNENKGASELVAELST
          PGARIN.DHKHKYIH.LAYAASVVE.WKKNKR.SIN.DELK.T.KA.ETVHNLCC.EN.GASEL.AELST
Retrocopy PGARINPDHKHKYIHLLAYAASVVEIWKKNKRLSINQDELKATAKAIETVHNLCCAENTGASELLAELST

Parental  LYQCIRFPVVAMGVLKWVDWTVSEPRYFQLQTDHTPVHLALLDEISTCHQLLHPQVLQLLVKLFETEHSQ
          LY.CIRFPVVA.GVL.WV..TVS.P..F...T..TPV.LALLDE.ST.H.LLHP.VLQLL.KL.ETE...
Retrocopy LYRCIRFPVVAVGVLTWVNGTVSKPKFFEQHTHPTPVPLALLDEVSTYHPLLHPHVLQLLIKLLETEYPE

Parental  LDVMEQLELKKTLLDRMVHLLSRGYVLPVVSYIRKCLEKLDTDISLIRHFVTEVLDVIAPPYTSDFVQLF
          LD.M.QL..KKTLL.RMVHLLS.G.VLPVV.YIR.CLEKLDTD.SLIR.FV.EVLD.I.PPYTSDFV.LF
Retrocopy LDAMKQLKVKKTLLNRMVHLLSCGHVLPVVAYIRRCLEKLDTDLSLIRYFVSEVLDMIIPPYTSDFVRLF

Parental  LPILENDSIAGTIKTEGEHDPVTEFIAHCKSNFILVN
          LPILENDSIA.T.K..GEHDPVTEFIAHC.SNF.L..
Retrocopy LPILENDSIASTLKRAGEHDPVTEFIAHCQSNFMLLD

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	31.22 RPM
ERP005899_muscle	0.05 RPM	58.65 RPM
SRP017611_brain	0.00 RPM	50.80 RPM
SRP017611_kidney	0.00 RPM	108.88 RPM
SRP017611_liver	0.00 RPM	39.87 RPM
SRP030211_testis	0.01 RPM	53.16 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1400 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1400 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1400 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018783	1 retrocopy	retro_btau_1400 ,
Tursiops truncatus	ENSTTRG00000008389	1 retrocopy	retro_ttru_11,