RetrogeneDB ID: retro_btau_1431

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:66263039..66263723(-)
• Located in intron of: ENSBTAG00000000022

Retrocopy information

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

Parental gene information

• Parental gene symbol: FNTA
• Ensembl ID: ENSBTAG00000003201
• Aliases: None
• Description: protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha [Source:RefSeq peptide;Acc:NP_803464]

Sequence

>retro_btau_1431
ATGGCGGCCACCACCGGGTCGGGGAGGCCGCAGGGGGTGGGGAACCAGGTCAGCGGAAGCTGCTGCCGCCGCCTCCTCAG
CCCCATACTCCTCCACCGCCTCCCCAGCCGCTGCAGAAAGAGGCGGCAGCCCCTATGGATGATGGGTTCCTGAGCCTGGA
CTCGCCCACCTATGTCCTGTACAGGGACAGAGCAGAATGGCCTGATATAGATCCAGTGTCACAGAATGATGGCCCCAATC
CAGTGGTCCAGATCATTTATAGTGAGAAATTTCAGGACGTCTGTGATTATTTCTGGGCTGTCCTGCAGCGGGACGAGAGA
AGTGAGCAGGCTTTTAAATTAATCAGAGATGCTATTGAGTTAAATGCAGCCAGTTACATAGTGTGGCATTTCCAGAGTGT
TCTCTCAAAGTCACTTCAGAAGGATCTACATGAGGAAATGAACTACACGTCTCGGCAATAATTGAGCAGCGGCCCAAAAA
CTATCAAGTTTGGCATCATAGGTGAGTGCTGGTGGAATGGCTGAGAGACCCATCTCAGGAGCTTGAGTTTATTGCGGATA
TTCTTACTCAGGGTGCAAAGAATTACCATGCCTGGCAACACCGACAGGTTATTCAGGAATTTAAACTTTGGATAATGAGT
TGCAGTATGTAGACCAACTTCTCAAAGAGGATGTGAGAAATAAC

Alignment

ORF - retro_btau_1431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.68 %
• Parental protein coverage: 61.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAADG-VGEAAQGGDPGQPEP-PPPPQPHPPPPPPQPPQEEAAAASPMDDGFLSLDSPTYVLYRDRPEW
          MAA..G.VGEAA.GG.PGQ....PPPPQPH.PPPPPQP.Q.EAAA..PMDDGFLSLDSPTYVLYRDR.EW
Retrocopy MAATTG<VGEAAGGGEPGQRKLLPPPPQPHTPPPPPQPLQKEAAA--PMDDGFLSLDSPTYVLYRDRAEW

Parental  ADIDPVPQNDGPNPVVQIIYSEKFQDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLK
          .DIDPV.QNDGPNPVVQIIYSEKFQDV.DYF.AVLQRDERSE.AFKL.RDAIELNAA.Y.VWHF..VL.K
Retrocopy PDIDPVSQNDGPNPVVQIIYSEKFQDVCDYFWAVLQRDERSEQAFKLIRDAIELNAASYIVWHFQSVLSK

Parental  SLQKDLHEEMNYIS-AIIEEQ-PKNYQVWHHRRVLVEWLRDPSQELEFIADILTQDAKNYHAWQHRQWVI
          SLQKDLHEEMNY.S...I.EQ.PKNYQVWHHR.VLVEWLRDPSQELEFIADILTQ.AKNYHAWQHRQ.VI
Retrocopy SLQKDLHEEMNYTS<SAIIEQRPKNYQVWHHR*VLVEWLRDPSQELEFIADILTQGAKNYHAWQHRQ-VI

Parental  QEFKLW-DNELQYVDQLLKEDVRNN
          QEFKLW.DNELQYVDQLLKEDVRNN
Retrocopy QEFKLW<DNELQYVDQLLKEDVRNN

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	45.56 RPM
ERP005899_muscle	0.05 RPM	34.79 RPM
SRP017611_brain	0.05 RPM	75.87 RPM
SRP017611_kidney	0.06 RPM	39.53 RPM
SRP017611_liver	0.00 RPM	21.29 RPM
SRP030211_testis	0.09 RPM	280.98 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1431 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1431 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1431 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003201	2 retrocopies	retro_btau_1431 , retro_btau_1768,
Canis familiaris	ENSCAFG00000005385	1 retrocopy	retro_cfam_941,
Homo sapiens	ENSG00000168522	1 retrocopy	retro_hsap_805,
Macaca mulatta	ENSMMUG00000017158	1 retrocopy	retro_mmul_1078,
Monodelphis domestica	ENSMODG00000010003	1 retrocopy	retro_mdom_1656,
Nomascus leucogenys	ENSNLEG00000012979	1 retrocopy	retro_nleu_2408,
Pteropus vampyrus	ENSPVAG00000013502	2 retrocopies	retro_pvam_1157, retro_pvam_1433,
Tursiops truncatus	ENSTTRG00000008870	1 retrocopy	retro_ttru_579,