RetrogeneDB ID: retro_btau_1478

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:12235315..12235627(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBD1
• Ensembl ID: ENSBTAG00000011866
• Aliases: PCBD1, DCoH, PCD, PHS
• Description: Pterin-4-alpha-carbinolamine dehydratase [Source:UniProtKB/Swiss-Prot;Acc:Q3ZBD3]

Sequence

>retro_btau_1478
ATGACTGGCTAAGCCCACAAACTAAGTGCTCAGGAGGAGGACCAGCTGCTGCCAAACCCACCTGCCATGAGGTGGAGGGA
GCCAGATGGGCAGGAATGCCATCTGCAGGCAGCTCCATTTCAAAGACTTCAGTAGGGCTCTTGGCCTCCGGATGACAGTG
GCCTGCAGACTGAAAAACTGGACCAGCATCCTGAATGGTTTAACCTGTGCACCAAGGCCCACACCATCCTGAGTACCCCC
AAGTGTGCGGGCTTTTCAGAAAGGGACATAAACACGGCCAGCTTCAGGGAGCAAGTGGCAGGGTCCGTGACA

Alignment

ORF - retro_btau_1478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGKAHRLSAEERDQLLPNLRAVGWNELE-GRDAIFKQFHFKDFNRAFGFMTRVA-LQAEKLDHHPEWFN
          M.G.AH.LSA.E.DQLLPN..A..W.E...GR.AI..Q.HFKDF.RA.G....VA.LQ.EKLD.HPEWFN
Retrocopy MTG*AHKLSAQEEDQLLPNPPAMRWREPD>GRNAICRQLHFKDFSRALGLRMTVA<LQTEKLDQHPEWFN

Parental  VYNKVHITLSTHECAGLSERDVNLASFIEQVAVSMT
          ...K.H..LST..CAG.SERD.N.ASF.EQVA.S.T
Retrocopy LCTKAHTILSTPKCAGFSERDINTASFREQVAGSVT

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	240.15 RPM
ERP005899_muscle	0.00 RPM	43.29 RPM
SRP017611_brain	0.00 RPM	38.69 RPM
SRP017611_kidney	0.00 RPM	83.10 RPM
SRP017611_liver	0.00 RPM	107.60 RPM
SRP030211_testis	0.00 RPM	1.09 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1478 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1478 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1478 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011866	1 retrocopy	retro_btau_1478 ,
Cavia porcellus	ENSCPOG00000012703	1 retrocopy	retro_cpor_61,
Felis catus	ENSFCAG00000001235	1 retrocopy	retro_fcat_1478,
Loxodonta africana	ENSLAFG00000001397	1 retrocopy	retro_lafr_1028,
Myotis lucifugus	ENSMLUG00000016074	3 retrocopies	retro_mluc_1534, retro_mluc_2459, retro_mluc_462,
Procavia capensis	ENSPCAG00000007201	1 retrocopy	retro_pcap_46,
Sus scrofa	ENSSSCG00000010275	1 retrocopy	retro_sscr_744,
Takifugu rubripes	ENSTRUG00000017869	1 retrocopy	retro_trub_26,
Tursiops truncatus	ENSTTRG00000005775	1 retrocopy	retro_ttru_1541,
Vicugna pacos	ENSVPAG00000004496	1 retrocopy	retro_vpac_69,