RetrogeneDB ID: retro_btau_1485

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:22671302..22671686(-)
• Located in intron of: ENSBTAG00000016247

Retrocopy information

• Ensembl ID: ENSBTAG00000046850
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YWHAE
• Ensembl ID: ENSBTAG00000005664
• Aliases: None
• Description: 14-3-3 protein epsilon [Source:UniProtKB/Swiss-Prot;Acc:P62261]

Sequence

>retro_btau_1485
CACCTCATTCCAGCAGCTAACACTGGTGAGTCCAAGGTTTTCTATTATAAAATGAAAGGGGACTACCACAGGTGTCAGGC
TGAATTTGCCACAGGAAATGACAGGAAGGAGGCTGCAGAGAACAGCCTAGTGGCTTATAAAGCTGCTAGTGATATTGCAA
TGACAGAACTTCCACCAAAACATCCCATTTGCTTAGGTCTTGCTCTCAATTTTTCTGTATTCTACTATGATATTCTTAAT
TCCCCTGACTGTGCCTGCAGGTTGGCAAAAGCAGCTTTTGATGATGTAATTGCAGAACTGGACATGCTGAGTGAAGAAAG
CTATAAGGACTCTACATTTATCATGCAGTTACTACGTGATAATCTGACACTATGTACTTCAGAA

Alignment

ORF - retro_btau_1485 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.41 %
• Parental protein coverage: 50.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALN
          HLIPAANTGESKVFYYKMKGDYHR..AEFATGNDRKEAAENSLVAYKAASDIAMTELPP.HPI.LGLALN
Retrocopy HLIPAANTGESKVFYYKMKGDYHRCQAEFATGNDRKEAAENSLVAYKAASDIAMTELPPKHPICLGLALN

Parental  FSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSD
          FSVFYY.ILNSPD.ACRLAKAAFDD.IAELD.LSEESYKDST.IMQLLRDNLTL.TS.
Retrocopy FSVFYYDILNSPDCACRLAKAAFDDVIAELDMLSEESYKDSTFIMQLLRDNLTLCTSE

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	230.27 RPM
ERP005899_muscle	0.00 RPM	301.95 RPM
SRP017611_brain	0.05 RPM	572.86 RPM
SRP017611_kidney	0.06 RPM	411.05 RPM
SRP017611_liver	0.00 RPM	177.29 RPM
SRP030211_testis	0.02 RPM	287.69 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1485 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1485 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1485 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000236	4 retrocopies	retro_btau_1482, retro_btau_635, retro_btau_68, retro_btau_910,
Bos taurus	ENSBTAG00000002108	2 retrocopies	retro_btau_1180, retro_btau_86,
Bos taurus	ENSBTAG00000005664	3 retrocopies	retro_btau_1485 , retro_btau_372, retro_btau_954,
Choloepus hoffmanni	ENSCHOG00000010861	2 retrocopies	retro_chof_1912, retro_chof_905,
Ciona intestinalis	ENSCING00000023856	1 retrocopy	retro_cint_15,
Ciona savignyi	ENSCSAVG00000011723	2 retrocopies	retro_csav_13, retro_csav_9,
Echinops telfairi	ENSETEG00000012056	2 retrocopies	retro_etel_1762, retro_etel_738,
Homo sapiens	ENSG00000108953	4 retrocopies	retro_hsap_2324, retro_hsap_3739, retro_hsap_3851, retro_hsap_4703,
Gorilla gorilla	ENSGGOG00000016840	1 retrocopy	retro_ggor_2596,
Monodelphis domestica	ENSMODG00000010174	2 retrocopies	retro_mdom_1567, retro_mdom_744,
Nomascus leucogenys	ENSNLEG00000000656	2 retrocopies	retro_nleu_2067, retro_nleu_2868,
Otolemur garnettii	ENSOGAG00000006155	2 retrocopies	retro_ogar_1003, retro_ogar_2144,
Pongo abelii	ENSPPYG00000007769	4 retrocopies	retro_pabe_1644, retro_pabe_1646, retro_pabe_2107, retro_pabe_3219,
Pan troglodytes	ENSPTRG00000008521	5 retrocopies	retro_ptro_1697, retro_ptro_2538, retro_ptro_2624, retro_ptro_2626, retro_ptro_2993,
Ictidomys tridecemlineatus	ENSSTOG00000005084	1 retrocopy	retro_itri_1175,
Vicugna pacos	ENSVPAG00000010288	3 retrocopies	retro_vpac_230, retro_vpac_411, retro_vpac_559,