RetrogeneDB ID: retro_btau_1094

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 26:11110370..11110748(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000007883
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF4E
• Ensembl ID: ENSBTAG00000009522
• Aliases: None
• Description: Eukaryotic translation initiation factor 4E [Source:UniProtKB/Swiss-Prot;Acc:Q9N0T5]

Sequence

>retro_btau_1094
AAACACCCTTTACAGAACAGATGGGCACTCTGGTTTTTTAAAAATGATAAAGGCAAAACTTGGCAAGCAAACCTTCGATT
GACCTCTAAGTTTGATACTATTGAAGACTTCTGGGCTCTGTACAACCATATCCAGTTATCTAGTAATTTAATGACTGGCT
GTGACTACTCACTTTTTAAGGATGGTATTGAGCCTATGTGGGAAGATGAGAAAAACAAACGAGGACAATGGCTAATTACA
CTGAACAAACAGCAGAGACGAAGTGACCTCGATGTTTTTTGGCTAGAGACACTGCTGTGCCTTATTGGAGAATCTTTTGA
TGACTACAGTGATGATGTATGTGGAGTTGTTGTTAATATTAGAGCTAACGGTGATAAG

Alignment

ORF - retro_btau_1094 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.34 %
• Parental protein coverage: 58.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDE
          KHPLQNRWALWFFKNDK.KTWQANLRL.SKFDT.EDFWALYNHIQLSSNLM.GCDYSLFKDGIEPMWEDE
Retrocopy KHPLQNRWALWFFKNDKGKTWQANLRLTSKFDTIEDFWALYNHIQLSSNLMTGCDYSLFKDGIEPMWEDE

Parental  KNKRGGRWLITLNKQQRRSDLDRFWLETVLCLIGESFDDYSDDVCGAVVNVRAKGDK
          KNKRG..WLITLNKQQRRSDLD.FWLET.LCLIGESFDDYSDDVCG.VVN.RA.GDK
Retrocopy KNKRG-QWLITLNKQQRRSDLDVFWLETLLCLIGESFDDYSDDVCGVVVNIRANGDK

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	2.45 RPM	41.38 RPM
ERP005899_muscle	5.54 RPM	40.59 RPM
SRP017611_brain	0.82 RPM	33.44 RPM
SRP017611_kidney	0.41 RPM	48.31 RPM
SRP017611_liver	0.45 RPM	21.07 RPM
SRP030211_testis	0.30 RPM	96.42 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1094 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1094 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1094 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003103	1 retrocopy	retro_btau_1679,
Bos taurus	ENSBTAG00000009522	3 retrocopies	retro_btau_1094 , retro_btau_1702, retro_btau_944,
Bos taurus	ENSBTAG00000010598	2 retrocopies	retro_btau_1232, retro_btau_1498,
Canis familiaris	ENSCAFG00000010307	1 retrocopy	retro_cfam_1276,
Choloepus hoffmanni	ENSCHOG00000009450	9 retrocopies	retro_chof_1177, retro_chof_1219, retro_chof_124, retro_chof_1319, retro_chof_1551, retro_chof_200, retro_chof_604, retro_chof_918, retro_chof_992,
Dasypus novemcinctus	ENSDNOG00000013712	5 retrocopies	retro_dnov_1722, retro_dnov_2378, retro_dnov_2570, retro_dnov_353, retro_dnov_638,
Echinops telfairi	ENSETEG00000007347	3 retrocopies	retro_etel_1285, retro_etel_1449, retro_etel_499,
Macropus eugenii	ENSMEUG00000011104	3 retrocopies	retro_meug_2087, retro_meug_2114, retro_meug_428,
Myotis lucifugus	ENSMLUG00000005035	3 retrocopies	retro_mluc_1519, retro_mluc_24, retro_mluc_474,
Monodelphis domestica	ENSMODG00000020716	1 retrocopy	retro_mdom_701,
Mustela putorius furo	ENSMPUG00000002041	1 retrocopy	retro_mputfur_37,
Otolemur garnettii	ENSOGAG00000001131	1 retrocopy	retro_ogar_259,
Tursiops truncatus	ENSTTRG00000004206	2 retrocopies	retro_ttru_1591, retro_ttru_592,
Vicugna pacos	ENSVPAG00000006072	3 retrocopies	retro_vpac_238, retro_vpac_444, retro_vpac_93,
Drosophila melanogaster	FBgn0035709	1 retrocopy	retro_dmel_68,