RetrogeneDB ID: retro_btau_1232

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:80686160..80686572(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSBTAG00000010598
• Aliases: None
• Description: eukaryotic translation initiation factor 4E type 2 isoform 1 [Source:RefSeq peptide;Acc:NP_001069263]

Sequence

>retro_btau_1232
GAACATCCCTTGCGGCCCAGCTCCGCTTTCTGGTACTCCAGGAGGATCCCTGGCCATCCCACCCACTCACAAGGCTCTGA
ACAGAGTATCAATGCCTTTGCCTGTATAGAGCAGTCCTGAAGGTTTTACAGCAGCATGGTAGCTCCCTGGAATCTGACAG
GCCACAGTAACTTTCTCAAAGAAGGAGTTAGTCGTATCTGGAGGATGATGCAGATAAAAATGGTGGCAAGTGAATTATTT
TGTTATGGAAGGGTATGGCATCCTGTTGCTGGCAGAATCTCATCCTGGCTTTGCTAGGGGACTAGTTCACGGTTGTGGAG
GAACTCTGTGGGCGCCTGCACTCTCTGTGTGGTTTCAGAAAGACATTATTTCAATGTAGAATAAGACTGCAAGTGACCTA
GCATCCACAGCC

Alignment

ORF - retro_btau_1232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.38 %
• Parental protein coverage: 60.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EHPLQYNYTFWYSRRTPGRPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKP
          EHPL.....FWYSRR.PG.PT.SQ..EQ....I..FA..EQ..RFYS.MV.P..LTGHS.F...KEG...
Retrocopy EHPLRPSSAFWYSRRIPGHPTHSQGSEQS---INAFACIEQS*RFYSSMVAPWNLTGHSNF--LKEGVSR

Parental  MW-EDDANKNGGKWIIRLRKGLASRCWENLILAMLGEQFMVGEEIC-GA-VVSVRFQEDIISIWNKTASD
          .W.EDDA.KNGGK.II.L.KG.AS.CW.NLILA.LG..F.V.EE.C.GA...SV.FQ.DIIS..NKTASD
Retrocopy IW<EDDADKNGGK*IILLWKGMASCCWQNLILALLGD*FTVVEELC>GA>ALSVWFQKDIISM*NKTASD

Parental  QATTA
          .A.TA
Retrocopy LASTA

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	2.23 RPM
ERP005899_muscle	0.00 RPM	10.08 RPM
SRP017611_brain	0.00 RPM	6.53 RPM
SRP017611_kidney	0.12 RPM	9.25 RPM
SRP017611_liver	0.00 RPM	2.64 RPM
SRP030211_testis	0.02 RPM	17.01 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1232 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1232 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1232 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_847

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016456	1 retrocopy	retro_amel_1304,
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	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Callithrix jacchus	ENSCJAG00000013786	2 retrocopies	retro_cjac_1061, retro_cjac_2717,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Mustela putorius furo	ENSMPUG00000005206	2 retrocopies	retro_mputfur_110, retro_mputfur_1554,
Otolemur garnettii	ENSOGAG00000009155	1 retrocopy	retro_ogar_104,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101,