RetrogeneDB ID: retro_btau_262

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:78593636..78594303(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.62601
• Ensembl ID: ENSBTAG00000030930
• Aliases: None
• Description: UPF0361 protein C3orf37 homolog [Source:RefSeq peptide;Acc:NP_001069402]

Sequence

>retro_btau_262
TCCTGCCACCTGCTCAGGGACACCCTCACTTGAGGTTGCACCCTACAGGACCAGCAAGGGCACTGGTGGCTATTGGAGTG
TGGGAACCCAGACCAGTACTGCCCCTCAGACAACAGCCTGCAGTCCCCCAGCTGGGTACTCTTGTCCCAGCTGCACTTGG
AGAAGAGTGCAGATTCATCTGAGTGTATCATTGCTCCCATGCAAGGCGGCTTTTACTGACTTGGTTTAAAGAAGCTGATT
CTTCCAAGCTGCAATTCAACACCACCAGCTGAAGAGACCATAATGGAGAAACTGTCCTTTAAGCTGCTTCTGGGAAAAGA
AAGATGCTATGTTGTTTTAGCAGATGGATTCCCCAAGTGGCAGCAATGTCAGGGAACACCCAGAGGCAGCCCTACTTCTT
CTTATTCCCCCAAATCAAAACATAAAAGTCAGAGAGTGAGTGCTGTAGACAGCCCTGAGAACTAGGAGGAAGTCTGGGAC
AACTGGAGGCCACTAACAATGGCCAGGATCTTTGGCTGCTGGGAGCTTCCAGAGGAAAAAGACAGCCTGTGTTCCAAAAC
CGTTATCACAAGAGATTCCTTCAAAGGCTTAAATGAAATCCCCCAACACGATGCCTGCCACATTAGATGGACAGGAGGCA
GTCTCTAAGTGACTGGACTTTGGTAAG

Alignment

ORF - retro_btau_262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.33 %
• Parental protein coverage: 63.84 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SCHLPREVLARACAYRDRQGHQRLPEWRDPDRYCPSYNKSPRSSSPVLLSRLHLEKDADSSERIIAPMRW
          SCHL.R..L...C...D.QGH..L.E...PD.YCPS.N.S..S.S.VLLS.LHLEK.ADSSE.IIAPM..
Retrocopy SCHLLRDTLT*GCTLQDQQGHWWLLECGNPDQYCPSDN-SLQSPSWVLLSQLHLEKSADSSECIIAPMQG

Parental  GLVPYWFKEADLSKLQINTSNCRSDTIMEKRSFKVPLVKGRRCVVLADGFYEWQRRQAT-SHRQPYFIYF
          G......K...L.....N.......TIMEK.SFK..L.K.R..VVLADGF..WQ..Q.T...RQPYF..F
Retrocopy GFY*LGLKKLILPSC--NSTPPAEETIMEKLSFKLLLGKERCYVVLADGFPKWQQCQGT<TQRQPYFFLF

Parental  -PQVKPEKSEQVGAVASPEDWEKVWDNWRPLTMAGIFDCWEPPAGGDCLYSYSIITVDSCKVLNDI-HNR
          .P..K..KS..V.AV.SPE..E.VWDNWRPLTMA.IF.CWE.P...D.L.S...IT.DS.K.LN.I..N.
Retrocopy >PKSK-HKSQRVSAVDSPEN*EEVWDNWRPLTMARIFGCWELPEEKDSLCSKTVITRDSFKGLNEI>PNT

Parental  MPAILDGEEAVSKWLDFGE
          MPA.LDG.EAVSK.LDFG.
Retrocopy MPATLDGQEAVSK*LDFGK

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	3.39 RPM
ERP005899_muscle	0.00 RPM	18.85 RPM
SRP017611_brain	0.00 RPM	9.55 RPM
SRP017611_kidney	0.00 RPM	15.83 RPM
SRP017611_liver	0.08 RPM	4.23 RPM
SRP030211_testis	0.01 RPM	59.09 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_262 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_262 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_262 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	ENSBTAG00000030930	1 retrocopy	retro_btau_262 ,
Myotis lucifugus	ENSMLUG00000010630	1 retrocopy	retro_mluc_2331,