RetrogeneDB ID: retro_btau_1432

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:66479849..66481135(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.68634
• Ensembl ID: ENSBTAG00000017889
• Aliases: None
• Description: T-complex protein 1 subunit epsilon [Source:RefSeq peptide;Acc:NP_001029767]

Sequence

>retro_btau_1432
AGTGGTTGTCCTTTGGAAAAGGCTGAGCAGCTGCTGGACCTCCGTATTCACCCAATCAGGATCACCGACGGCCAAGAGCA
GGTCACCCGCATCACTATTGAACACCTGGACAAGATCAGCAACAGTGTCCTCGACAACATGAAGAACACCAAGCCCCTGA
TCCAGACAGTGAAGACCACGCTGGGCTCCAAAGTAATTAACAGCTGTCACTGACAAATGGCCTAGATCACTGTGAATGCC
GTTCTCACCGTGGCCAACATGCAGCACAGAGACATTGACTTCCAGCTCATCAAGGTAGAAGGCAAGGTGGGTGGGTGGCT
GAAGGACACCAAGCTGATCAAGGGCTTTATCATGGACAAGGACTTCAGTCACCCGCAGAAGACCAGGCAAGTGGAAGATG
CTAAGGTTGCAATCCTCACATGTTCATTTGAGCCACCGAAACCAAAGATGAAGTATAAGGTGGATGTGACATCTGTAGAA
GATTTTAAAGCCCTTCAGAAGTACGAAAAGGAGAAGTTTGAAGAGATGATCCAGCACATTAAAGAAACTGGTGCTAACCT
AGCTATTTGCCAGTGGGGCTTTGATGATGAAGCCAATCATTTACTTCTCCAGAATAATCTGTCAGCGGTTCACTAGGTTG
GAGGATCTGAAACTGAGTTGATCGCCATTGCCACAGGTGGCCACATCATCCCTAGGTTCTCAGAGCTCATAGCTGAGAAG
CTGGGCTTTGCAGATCCTGTGAAAGAGATCTCGTTTGGGACCACCAAAGACAAGATGCTGGTCATTGAGCAGTGTAAGAA
CTTCAGAGCCGTCACCATTTTCATCAGAGGAGGAAATAAGATGATCATCAAGGAGGCCAAGCGTTCCCGTCATGACGCTC
TGTGTGTAATCTGCAACCTCATTGGGACAACCGCATGGTATATTGCAGGGGTGCTACCGAGATCGCTTGCGCCCTGGTGG
TGAGCCAGGAGGCCGACCAGTGCCCGGCCCTGGAGCAGTACCCATGCACGCCTTTGCCGAGGGACTGGTGGGCATCCCCA
TGGAGCTCATGGAGAACAGAGGCATGAAGCCCATCCAGACCATGACTGAGGTCCGAACCAGACACGTGAAGGAGGTGAAC
CCCGCCCTCGGGGATTGGCTGTCTGCACAAGGGAACCAATAATATGAAACATCAACATGTCATAGAAACCTTGATTGGCA
AAAAGCAGCAGATCTCTCTTGTAACACAAATGGTTAGAATGACTTTGAAGATTGACAACATCCATAAGCCTGGAGAATCT
GAACAG

Alignment

ORF - retro_btau_1432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.56 %
• Parental protein coverage: 79.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AGALLEEAEQLLDRGIHPIRIADGYEQAARIAIEHLDKISDSVLVDMKNTEPLIQTAKTTLGSKVVNSCH
          .G..LE.AEQLLD..IHPIRI.DG.EQ..RI.IEHLDKIS.SVL..MKNT.PLIQT.KTTLGSKV.NSCH
Retrocopy SGCPLEKAEQLLDLRIHPIRITDGQEQVTRITIEHLDKISNSVLDNMKNTKPLIQTVKTTLGSKVINSCH

Parental  RQMAEIAVNAVLTVADMQRRDVDFELIKVEGKVGGRLEDTKLIKGVIVDKDFSHPQMPKQVEDAKIAILT
          .QMA.I.VNAVLTVA.MQ.RD.DF.LIKVEGKVGG.L.DTKLIKG.I.DKDFSHPQ...QVEDAK.AILT
Retrocopy *QMA*ITVNAVLTVANMQHRDIDFQLIKVEGKVGGWLKDTKLIKGFIMDKDFSHPQKTRQVEDAKVAILT

Parental  CPFEPPKPKTKHKLDVTSVEDFKALQKYEKEKFEEMIRQIKETGANLAICQWGFDDEANHLLLQNDLPAV
          C.FEPPKPK.K.K.DVTSVEDFKALQKYEKEKFEEMI..IKETGANLAICQWGFDDEANHLLLQN.L.AV
Retrocopy CSFEPPKPKMKYKVDVTSVEDFKALQKYEKEKFEEMIQHIKETGANLAICQWGFDDEANHLLLQNNLSAV

Parental  RWVGGPEIELIAIATGGRIVPRFSELTAEKLGFAGLVKEISFGTTKDKMLVIEQCKNSRAVTIFIRGGNK
          ..VGG.E.ELIAIATGG.I.PRFSEL.AEKLGFA..VKEISFGTTKDKMLVIEQCKN.RAVTIFIRGGNK
Retrocopy H*VGGSETELIAIATGGHIIPRFSELIAEKLGFADPVKEISFGTTKDKMLVIEQCKNFRAVTIFIRGGNK

Parental  MIIEEAKRSLHDALCVIRNLIR-DNRVVYGGGAAEISCALAVSQEADKCPTLEQY-AMRAFADALEVIPM
          MII.EAKRS.HDALCVI.NLI..DNR.VY..GA.EI.CAL.VSQEAD.CP.LEQY..M.AFA..L..IPM
Retrocopy MIIKEAKRSRHDALCVICNLIG<DNRMVYCRGATEIACALVVSQEADQCPALEQY<PMHAFAEGLVGIPM

Parental  ALAENSGMNPIQTMTEVRARQVKEVNPAL-GIDCLHKGTNDMKHQHVIETLIGKKQQISLATQMVRMILK
          .L.EN.GM.PIQTMTEVR.R.VKEVNPAL.GI.CLHKGTN.MKHQHVIETLIGKKQQISL.TQMVRM.LK
Retrocopy ELMENRGMKPIQTMTEVRTRHVKEVNPAL>GIGCLHKGTNNMKHQHVIETLIGKKQQISLVTQMVRMTLK

Parental  IDDIRKPGESEE
          ID.I.KPGESE.
Retrocopy IDNIHKPGESEQ

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	23.86 RPM
ERP005899_muscle	0.00 RPM	121.41 RPM
SRP017611_brain	0.00 RPM	66.05 RPM
SRP017611_kidney	0.00 RPM	83.22 RPM
SRP017611_liver	0.00 RPM	65.47 RPM
SRP030211_testis	0.13 RPM	282.40 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1432 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1432 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1432 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017889	1 retrocopy	retro_btau_1432 ,
Callithrix jacchus	ENSCJAG00000008977	1 retrocopy	retro_cjac_516,
Gorilla gorilla	ENSGGOG00000024064	1 retrocopy	retro_ggor_2197,
Myotis lucifugus	ENSMLUG00000007977	1 retrocopy	retro_mluc_1735,
Monodelphis domestica	ENSMODG00000002356	1 retrocopy	retro_mdom_861,