RetrogeneDB ID: retro_btau_563

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 14:59706796..59708766(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBC1D1
• Ensembl ID: ENSBTAG00000013699
• Aliases: None
• Description: TBC1 domain family member 1 [Source:UniProtKB/Swiss-Prot;Acc:O97790]

Sequence

>retro_btau_563
ATGATGACCCTGAAGCAGGCCTTCATGGTGGTCTCAGTGCAGCAGACAGAGAAGGCGCTGGTCCAGCTATGTGAGGGCTG
CCCCTGCAGGGCCTGCACAAGCTCTGTGAGCAGATAGAGGGAAGGAATTCTTCCAAAACCAAACTAGAGCTCCAGAAGCA
CCTGACAACATTAACTAATCAGGAGCAAGCAACTATTTTTGAGGAGGTTCAGAAACTGAGATCAAGGAATGAGCAGTGAG
AGAATGAATTGGTTATTTCTTTCCTGAGATGTTTACATGAAGAGAAGCTAAAAGTTCACGTCCATATTGGGGAGATAAAA
AAAGATGTCACAGATTGCAGTGGAGAATATTGGAAATGAGTTACCATCAAGTACCACTTGATTTAGGCTGGATATGCTGA
AAAATAAAGCGAAGAGGTCTTTAACAGAATCTTTAGAAAGTATTTTGCCCTGGGATAATAAAGCCAGAGGCCTCCAGGAG
CACTCGGCCAGTCTGGGTCTGGACAGCTCTGTGTCTGGAACATTCAGTAACACCAGCAAAGAGCTGTCTGGCTGTGAAAA
GGAGGCTTTTCCCATCTCCAAGAGCTGCTTCAGGCTCCTCAGCTCCTTGGAGGACCTGTCCAGTGACTCGGAGAGCCAAC
CCACGGAAGAGCCAGCCCTGCCCTCACCCAAGCAGGGCTTCCAAAGGCACGCCAACACCTGAGTCATGTCCTCATGGAAT
GCCAGAAATCCTCCGCAGCTGGCATGGGGGTCCCCAGGGGTCTCACAAAGGAAGCTTGTGAGGTATCACTCAGTGAGCAC
AGAGCCCACCTCATGAATCAAAGAACTTTGAGTCCAAAGCTGACCACATGGGTGACCCCAGCAGGACCTCCATAAAGACA
CAGAGACCGTGGAGGCAGCAGATCTTCCTTCGAGTGGCCACCCCACCGAAAGCCTGCGATTCTCTCAGCAGATACGAAGA
TTATTCAGAGCTGGGAGAGCTTTCCCCACGATCTCCTCTAGAACCAGTTTATGAAGATGGACCCTTCGGCCCTATCCCAG
AGGGAAAAAAAAGGACATCTTGTGAACTCCGAGAGCTATGGCAAAAAGCCATTCTACAACAGATACTGCTGTTCAGGATG
GAGAAGGAAAAACAAAAGCTGCAAGCCTCTGAGAATGATTTGCTGAACAAGTGCCTAAACCTTGATTATGAAGAAATCAC
TCCTTGTCTTAAAGAAGTGACTACAGTGTGGGAAAAGATGCTAAGCACTCCAGGAAGATCAAAAACTAAGTTTGACATGG
AAAAAATGCACTTGGCTGTTGGCCAAGGTGTGCCATGACATCACCAGGGCAAAATCTGGAAATTCTTGGTGGAGCAGTGC
CATGAAGCACCTGTTCCTCATCAAACAGCAGCCCAAGGAGATTCCCTACAAAGAGCACTTAAAGCAGCTCATCTCCCAGC
AGCACACCATTCTCATCTACCTCGGGAGAACCTTTCCAACACATCGGTACTACTCTGCTCAGCTAGGAGCAGGGCAGCTG
TCACTTTACAACATCCTGAAGGCCTGCTCGCTTCCAGACGAAGAAGTGGGCTATTGCCAAGGCCTCAGCTTTGTAGCAGG
CATCCTCCTGCTTCACATGGGTGAATAAGAGGCGTTTAACATGCTTAAGGTTCTGATGTTTGACATGGGACTGTGGAAAC
AGTATTGAATGGACATGATTATTTTACAGATCCAGATGTACCAAATCTCAAGGCTGTTCCATGATTACCACAGGGACCTA
TCCAACCACCTGGAGGGACATGAGATCAGCCCCAGCCTCTATGCCGTGTCCTGGTTCCTCACTGTGTTTGCCTTGCAGTT
CCCCCTGGGCTTTGTCACCGGAGTCTTTGATATGATCTTTCTTCAGGGATCAGAGGTCATATTTAAAGTGGCTTTAAGTC
TGCTGGGATACCATAAGCCCTTGATTCTGCAGCATGAAAACCCAGAAACC

Alignment

ORF - retro_btau_563 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.68 %
• Parental protein coverage: 56.48 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MMTLKQAFTVAAVQQTAKAPAQLCEGCP-LQGLHKLCERIEGMNSSKTKLELQKHLTTLTNQEQATIFEE
          MMTLKQAF.V..VQQT.KA..QLCEGCP.LQGLHKLCE.IEG.NSSKTKLELQKHLTTLTNQEQATIFEE
Retrocopy MMTLKQAFMVVSVQQTEKALVQLCEGCP<LQGLHKLCEQIEGRNSSKTKLELQKHLTTLTNQEQATIFEE

Parental  VQKLRPRNEQRENELIISFLRCLYEEKQKVHIHIGEIKQT-SQIAAENIGSELPSSATRFRLDMLKNKAK
          VQKLR.RNEQ.ENEL.ISFLRCL.EEK.KVH.HIGEIK...SQIA.ENIG.ELPSS.T.FRLDMLKNKAK
Retrocopy VQKLRSRNEQ*ENELVISFLRCLHEEKLKVHVHIGEIKKD>SQIAVENIGNELPSSTT*FRLDMLKNKAK

Parental  RSLTESLESILSRGNKARGLQEHSASLDLDSSVSSMFSNTSKEPSGYEKEALPISESCFRLLGSSDDLSS
          RSLTESLESIL...NKARGLQEHSASL.LDSSVS..FSNTSKE.SG.EKEA.PIS.SCFRLL.S..DLSS
Retrocopy RSLTESLESILPWDNKARGLQEHSASLGLDSSVSGTFSNTSKELSGCEKEAFPISKSCFRLLSSLEDLSS

Parental  DSESQLTEEPALLSPKQGFRRRANT-LSHVPVECQE-PPQLVRGSPGVSQRKLVRYHSVSTET-PHERKD
          DSESQ.TEEPAL.SPKQGF.R.ANT.LSHV..ECQ..PPQL..GSPGVSQRKLVRYHSVSTE..PHE.K.
Retrocopy DSESQPTEEPALPSPKQGFQRHANT<LSHVLMECQK>PPQLAWGSPGVSQRKLVRYHSVSTEP>PHESKN

Parental  FESKADHISDASRTPVKTRRHSWRQQIFLRVATPQKACESPKRYEDYSELGELPPRSPLEPVCEDGPFGP
          FESKADH..D.SRT..KT.R..WRQQIFLRVATP.KAC.S..RYEDYSELGEL.PRSPLEPV.EDGPFGP
Retrocopy FESKADHMGDPSRTSIKTQR-PWRQQIFLRVATPPKACDSLSRYEDYSELGELSPRSPLEPVYEDGPFGP

Parental  VPEEKKRTSHELRELWQKAILQQILLLRMEKENQKLQASENDLLNKRLKLDYEEITPCLKEVTTVWEKIL
          .PE....TS.ELRELWQKAILQQILL.RMEKE.QKLQASENDLLNK.L.LDYEEITPCLKEVTTVWEK.L
Retrocopy IPEXXXXTSCELRELWQKAILQQILLFRMEKEKQKLQASENDLLNKCLNLDYEEITPCLKEVTTVWEKML

Parental  STPGRSKIKFDMEKMHSAVGQGVPRHHRGEIWKFLAEQYHLKHPFP-CKQQPKDTPYKELLKQLTSQQHA
          STPGRSK.KFDMEKMH.AVGQGVP.HH.G.IWKFL.EQ.H...P.P..KQQPK..PYKE.LKQL.SQQH.
Retrocopy STPGRSKTKFDMEKMHLAVGQGVP*HHQGKIWKFLVEQCH-EAPVP>IKQQPKEIPYKEHLKQLISQQHT

Parental  ILIDLGRTFPTHPYYSAQLGAGQLSLYNILKAYSLLDQEVGYCQGLSFVAGILLLHMGEEEAFNMLKFLM
          ILI.LGRTFPTH.YYSAQLGAGQLSLYNILKA.SL.D.EVGYCQGLSFVAGILLLHMGE.EAFNMLK.LM
Retrocopy ILIYLGRTFPTHRYYSAQLGAGQLSLYNILKACSLPDEEVGYCQGLSFVAGILLLHMGE*EAFNMLKVLM

Parental  FDMGLRKQYRPDMIILQIQMYQLSRLLHDYHRDLYNHLEEHEIGPSLYAAPWFLTVFASQFPLGFVARVF
          FDMGL.KQY..DMIILQIQMYQ.SRL.HDYHRDL.NHLE.HEI.PSLYA..WFLTVFA.QFPLGFV..VF
Retrocopy FDMGLWKQY*MDMIILQIQMYQISRLFHDYHRDLSNHLEGHEISPSLYAVSWFLTVFALQFPLGFVTGVF

Parental  DMIFLQGSEVIFKVALSLLGSHKPLILQHENLET
          DMIFLQGSEVIFKVALSLLG.HKPLILQHEN.ET
Retrocopy DMIFLQGSEVIFKVALSLLGYHKPLILQHENPET

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	6.06 RPM
ERP005899_muscle	0.00 RPM	26.61 RPM
SRP017611_brain	0.00 RPM	49.29 RPM
SRP017611_kidney	0.00 RPM	86.42 RPM
SRP017611_liver	0.00 RPM	7.55 RPM
SRP030211_testis	0.30 RPM	209.25 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_563 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_563 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_563 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013699	1 retrocopy	retro_btau_563 ,