RetrogeneDB ID: retro_btau_1467

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:92136099..92136495(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000046788
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FABP3
• Ensembl ID: ENSBTAG00000016819
• Aliases: FABP3, FABP, FABP-3, H-FABP
• Description: Fatty acid-binding protein, heart [Source:UniProtKB/Swiss-Prot;Acc:P10790]

Sequence

>retro_btau_1467
GTGGACACCTTCATGGGTACCTGGAAGTTAGTGGATAGCAGGAATTTCGATGACTACATGAAGTCTCTTGGTGTGGGTTT
TGCTACCAAACAGGCGGCCAATATTACCAAGCCTATCACAGTCATCGAAGTGAATGTGGACACAATCACCATAAAAACAC
AAAGCGTCTTCCAGAATAGGGAGGTTAGCTTCGAGCTGGGAGTGAATTTCAATGAGACAACAGCAGATGACAGGAAAGTC
AAGTCCATCGTGATGCTGGATGGAGGCAAATTTGTCCACGTGCAGAATTGGAATGGACAAGAGACAACACTTGTACGGGA
AATAGTTGATGAGAAACTCATCCTGCCGCTCACCCACTGCAGTGCGGTTTGCAATCGTACTTACAAGGAAGAGGCA

Alignment

ORF - retro_btau_1467 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.76 %
• Parental protein coverage: 99.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDAFVGTWKLVDSKNFDDYMKSLGVGFATRQVGNMTKPTTIIEVNGDTVIIKTQSTFKNTEISFKLGVEF
          VD.F.GTWKLVDS.NFDDYMKSLGVGFAT.Q..N.TKP.T.IEVN.DT..IKTQS.F.N.E.SF.LGV.F
Retrocopy VDTFMGTWKLVDSRNFDDYMKSLGVGFATKQAANITKPITVIEVNVDTITIKTQSVFQNREVSFELGVNF

Parental  DETTADDRKVKSIVTLDGGKLVHVQKWNGQETSLVREMVDGKLILTLTHGTAVCTRTYEKQA
          .ETTADDRKVKSIV.LDGGK.VHVQ.WNGQET.LVRE.VD.KLIL.LTH..AVC.RTY...A
Retrocopy NETTADDRKVKSIVMLDGGKFVHVQNWNGQETTLVREIVDEKLILPLTHCSAVCNRTYKEEA

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	0.79 RPM
ERP005899_muscle	0.00 RPM	36.42 RPM
SRP017611_brain	0.00 RPM	21.83 RPM
SRP017611_kidney	0.06 RPM	80.31 RPM
SRP017611_liver	0.00 RPM	0.60 RPM
SRP030211_testis	0.02 RPM	9.30 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1467 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1467 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1467 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016819	2 retrocopies	retro_btau_1467 , retro_btau_295,
Bos taurus	ENSBTAG00000020028	1 retrocopy	retro_btau_1290,
Bos taurus	ENSBTAG00000047330	3 retrocopies	retro_btau_1312, retro_btau_1828, retro_btau_886,
Danio rerio	ENSDARG00000023290	1 retrocopy	retro_drer_33,
Dasypus novemcinctus	ENSDNOG00000000511	2 retrocopies	retro_dnov_1510, retro_dnov_2482,
Equus caballus	ENSECAG00000024852	1 retrocopy	retro_ecab_519,
Homo sapiens	ENSG00000121769	1 retrocopy	retro_hsap_1258,
Gorilla gorilla	ENSGGOG00000014432	1 retrocopy	retro_ggor_990,
Macropus eugenii	ENSMEUG00000012501	6 retrocopies	retro_meug_1037, retro_meug_148, retro_meug_1660, retro_meug_273, retro_meug_563, retro_meug_819,
Microcebus murinus	ENSMICG00000009359	4 retrocopies	retro_mmur_1490, retro_mmur_203, retro_mmur_621, retro_mmur_734,
Myotis lucifugus	ENSMLUG00000013609	2 retrocopies	retro_mluc_1144, retro_mluc_1717,
Mus musculus	ENSMUSG00000028773	3 retrocopies	retro_mmus_2804, retro_mmus_3204, retro_mmus_65,
Nomascus leucogenys	ENSNLEG00000001586	1 retrocopy	retro_nleu_2097,
Otolemur garnettii	ENSOGAG00000013757	4 retrocopies	retro_ogar_1148, retro_ogar_1312, retro_ogar_1873, retro_ogar_959,
Pongo abelii	ENSPPYG00000001616	1 retrocopy	retro_pabe_1048,
Pan troglodytes	ENSPTRG00000000457	1 retrocopy	retro_ptro_3047,
Rattus norvegicus	ENSRNOG00000012879	1 retrocopy	retro_rnor_2199,
Ictidomys tridecemlineatus	ENSSTOG00000003842	3 retrocopies	retro_itri_1544, retro_itri_640, retro_itri_641,