RetrogeneDB ID: retro_btau_1076

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 25:36105613..36106149(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C13H20ORF43
• Ensembl ID: ENSBTAG00000027390
• Aliases: RTFDC1, C13H20orf43
• Description: UPF0549 protein C20orf43 homolog [Source:RefSeq peptide;Acc:NP_001069093]

Sequence

>retro_btau_1076
GGGTTGCAACAGGGAACAGTCCCTAAGAGTCATAAACCGGTGAAGGGGCCAAAGAAGGTTGAGAAGGTCAACAAGGATGC
TGAATTAGTGGCCAAGTGGAACTGCTATACTCTAAGTCAGGAAATGTTAAGATGACCAGTAGTTGCCTGTGAACTTGGCA
GACTTTACAACAAAGATGCCGTCACTGAGTTTTTACTGGCCAAATCTTCTGTAAAGGCTCTTGGGAAGGCAGCCTCTCAC
ATTAAAAGCATTAAGAATGTGACAGAACTGAGGCTCTCGGACAACCCCACCTGGGAAGGCGATCAAGGAAACCCTAAAGG
TGCCAAGCATGACGACCTCCAGCGGGCACATTTCATCTGCCCCCTCGTGGGCTTGGAGATGAACAGCCAACACAGCTATT
GCTTCTTCCGGTGCTTTGATTGTGTGTTTTCCGGGTAAGCCCTCAAAGAGATCGAAGCAGAAGTTTGTCACACGTGCAGG
GCTGCCTTCCAGGAGGGGACGAGGTCATCGGGCTCAACAGCACCAAGGAAGGCGTG

Alignment

ORF - retro_btau_1076 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.67 %
• Parental protein coverage: 59.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GCDGGTIPKRHELVKGPKKVEKVDKDAELVAQWNYCTLSQEILRRPIVACELGRLYNKDAVIEFLLDKSS
          G...GT.PK.H..VKGPKKVEKV.KDAELVA.WN..TLSQE.LR.P.VACELGRLYNKDAV.EFLL.KSS
Retrocopy GLQQGTVPKSHKPVKGPKKVEKVNKDAELVAKWNCYTLSQEMLR*PVVACELGRLYNKDAVTEFLLAKSS

Parental  EKALGKAASHIKSIKNVTELRLSDNPAWEGDKGNTKGDKHDDLQRARFICPVVGLEMNGRHRFCFLRCCG
          .KALGKAASHIKSIKNVTELRLSDNP.WEGD.GN.KG.KHDDLQRA.FICP.VGLEMN..H..CF.RC..
Retrocopy VKALGKAASHIKSIKNVTELRLSDNPTWEGDQGNPKGAKHDDLQRAHFICPLVGLEMNSQHSYCFFRCFD

Parental  CVFSERALKEIKAEVCHTCGAAFQE-DDVIV-LNGTKEDV
          CVFS..ALKEI.AEVCHTC.AAFQE..D....LN.TKE.V
Retrocopy CVFSG*ALKEIEAEVCHTCRAAFQE<GDEVIGLNSTKEGV

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	6.92 RPM
ERP005899_muscle	0.00 RPM	23.02 RPM
SRP017611_brain	0.00 RPM	31.34 RPM
SRP017611_kidney	0.00 RPM	29.99 RPM
SRP017611_liver	0.00 RPM	9.59 RPM
SRP030211_testis	0.04 RPM	59.12 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1076 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1076 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1076 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	ENSBTAG00000027390	1 retrocopy	retro_btau_1076 ,
Echinops telfairi	ENSETEG00000003143	1 retrocopy	retro_etel_2095,
Mus musculus	ENSMUSG00000027502	1 retrocopy	retro_mmus_339,
Ornithorhynchus anatinus	ENSOANG00000009249	1 retrocopy	retro_oana_124,
Otolemur garnettii	ENSOGAG00000004444	1 retrocopy	retro_ogar_3150,