RetrogeneDB ID: retro_btau_539

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 14:27854000..27855851(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF2
• Ensembl ID: ENSBTAG00000004258
• Aliases: EEF2, EF-2
• Description: Elongation factor 2 [Source:UniProtKB/Swiss-Prot;Acc:Q3SYU2]

Sequence

>retro_btau_539
ATGGTGAACTTCACAGTAAACCAGATCCAGCCCATCATGGACAAGAAGGCCAACATCAGGAACATGGCCTTCATCACCCA
CGTGAACCATGCCAAGTCCACTCTGACGGACTTCCTGATGTGCAAGGCGGGTGTCATCGCCTCTGCCCGGTCTGGGGAGA
CCTGTTTCACTAACACCCGGAAGGATGAGCAGGAGCGTTGCATCAGCATCAAGTCAATGGCCATCTTCCTTTTCTACAAG
CCTTCAGAGAACAACTTGAATTTCATCAAGCAGAGCAGGGATGGCTCTGGCTTCCTCATTAACCTCATCAACTCCCCTGG
GCATGTAGACTTCTCCTCAGAGGTGACAGCTGCGCTCCATGTCACCGACAGCACCTTGGTGATGGTGGACTGCATGTCGG
GCATGTGTGTGCAAACACAGATGGTGCTGTGCCAGGCTGTCACCAAGGGCGTCAAGCCAGTGCTGATGATGAACAAGATG
GACTCGGCCCTGCTGAACTGCAGCAGGAGCCCAAGGAGCTCTACAAGCCCTTCCAGCACATTGCGGAGAACATCAACGTC
ATTGTCTCCACCTATGGCAAGGGCGAGAGTGGCCCCATGGGCAGTGTCATAATCAACCCTGTCCTCAGTACTGTTGGCTT
CGGGTCTGGTCTCCACAGTTGGGCCTTTACCCTGAAGTAGTTTGCAGAGTTGTATGTGGCCAAGTTTGTTGCCAAGGGCA
AAGGCCAGCTGGGGCCTGCTGAGTGGGCCAAGAAAGTGGAGGACATAATGAAAAAGCTGTGGGGAGACCGGTACTTTGAT
CCACCCACCAGCAAGTTCAGCAAGTCAGCCAACAACCCAATGACAAGAAGCTGCTGCTAACATTCTACCAGCTCATCCTG
GACCCCATCTTCAAGGTGTCTGATGCAATCATGAACTTCAAGAAAGAGGAGACGGCAAAACTAATTGAAAAACTGGACAT
CAAGTGGGACAGTGAAGATAAGGATAAGGAGGGCAAATCACTTCTGAAGGCTGTGATGCGCCGCTGGCTGTCTGCTGGGG
ACACCCTGCTGCAAATGATCACCATCCATCTGCCCTCCCCTGTGATGGCCCAGAAGTACCACTGTGAGCTCCTGTATGAG
GGGCCCCCAGGTGAGGAGGCAGCCATGGGCACTAAAAGCTGTGATCCCAAAGGCCCTCTCATGATATACCTTCCAAAATG
GTGTCAACCTCTGACAAAGGTCAGTTCTATGCCTTTGGCCAGGTCTTCTCAGGGGTGGTGTACACTGGCCTGACGGTCTG
CATCATGGGACCCAACTCCATGGAGAAGGAGGACCTGTACCTGAAGCCAATCCAGAGGACAATCCTGATGATGGGCTGTT
ATGTGGAGCCCGTTGAGGATGTGCCTTGTGGTAACATCATGGGCCTGGTGGGCGTGGATCAGTTCCTGGTGAAGACCAAC
ACCATCACCACCTTTGAGCATAGCCACAACACACGGGCAATGAAGTTCAGTGTGAGCCCTGTTGTCAGGGTCATTGTGGA
GGCAAAGAACCCAGCAGACCTGCCCAAGCTGGTGGAGGGCCTGAAGCAGCTGGCCAAGTCGGACCCCATGATGCAGTGTA
TCATTGAGGAGTCCAGGGAGCACATCATCATTGGGGGCTGGGGAATTGCACTTGGAAATCTGCCTCAAGGATGGGGAGGA
GGATCATGCCTGCATCCCCATCAAGAGAAATCTGACCCAGTTGTCTCGTACTAGGAGACTGTCAGCAAGGAGTCAAACGT
GCTCTGCCTGTCCAAGGTCCCCAACAAGCACAATAGGCTTTATATGAAGGCACAGCCCTTCCCTGATGGCCTAGCCGAGG
ACATCGACAAG

Alignment

ORF - retro_btau_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.2 %
• Parental protein coverage: 72.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MVNFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAGIIASARAGETRFTDTRKDEQERCITI
          MVNFTV.QI..IMDKKANIRNM..I.HV.H.KSTLTD.L.CKAG.IASAR.GET.FT.TRKDEQERCI.I
Retrocopy MVNFTVNQIQPIMDKKANIRNMAFITHVNHAKSTLTDFLMCKAGVIASARSGETCFTNTRKDEQERCISI

Parental  KSTAISLFYELSENDLNFIKQSKDGSGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQTE
          KS.AI.LFY..SEN.LNFIKQS.DGSGFLINLI.SPGHVDFSSEVTAAL.VTD..LV.VDC.SG.CVQT.
Retrocopy KSMAIFLFYKPSENNLNFIKQSRDGSGFLINLINSPGHVDFSSEVTAALHVTDSTLVMVDCMSGMCVQTQ

Parental  TVLRQAIAERIKPVLMMNKMDRALL-ELQLEPEELYQTFQRIVENVNVIISTYGEGESGPMGNIMIDPVL
          .VL.QA.....KPVLMMNKMD.ALL.ELQ.EP.ELY..FQ.I.EN.NVI.STYG.GESGPMG...I.PVL
Retrocopy MVLCQAVTKGVKPVLMMNKMDSALL<ELQQEPKELYKPFQHIAENINVIVSTYGKGESGPMGSVIINPVL

Parental  GTVGFGSGLHGWAFTLKQFAEMYVAKFAAKGEGQLGPAERAKKVEDMMKKLWGDRYFDPATGKFSKSANS
          .TVGFGSGLH.WAFTLK.FAE.YVAKF.AKG.GQLGPAE.AKKVED.MKKLWGDRYFDP.T.KFSKSAN.
Retrocopy STVGFGSGLHSWAFTLK*FAELYVAKFVAKGKGQLGPAEWAKKVEDIMKKLWGDRYFDPPTSKFSKSANN

Parental  -PDGKKLPRTFCQLILDPIFKVFDAIMNFKKEETAKLIEKLDIKLDSEDKDKEGKPLLKAVMRRWLPAGD
          .P..KKL..TF.QLILDPIFKV.DAIMNFKKEETAKLIEKLDIK.DSEDKDKEGK.LLKAVMRRWL.AGD
Retrocopy <PNDKKLLLTFYQLILDPIFKVSDAIMNFKKEETAKLIEKLDIKWDSEDKDKEGKSLLKAVMRRWLSAGD

Parental  ALLQMITIHLPSPVTAQKYRCELLYEGPPDDEAAMGIKSCDPKGPLMMYI-SKMVPTSDKGRFYAFGRVF
          .LLQMITIHLPSPV.AQKY.CELLYEGPP..EAAMG.KSCDPKGPLM.Y..SKMV.TSDKG.FYAFG.VF
Retrocopy TLLQMITIHLPSPVMAQKYHCELLYEGPPGEEAAMGTKSCDPKGPLMIYL<SKMVSTSDKGQFYAFGQVF

Parental  SGLVSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCGNIVGLVGVDQFLVKTGTITT
          SG.V.TGL.V.IMGPN.....KEDLYLKPIQRTILMMG.YVEP.EDVPCGNI.GLVGVDQFLVKT.TITT
Retrocopy SGVVYTGLTVCIMGPNSM--EKEDLYLKPIQRTILMMGCYVEPVEDVPCGNIMGLVGVDQFLVKTNTITT

Parental  FEHAHNMRVMKFSVSPVVRVAVEAKNPADLPKLVEGLKRLAKSDPMVQCIIEESGEHII-AGAGELHLEI
          FEH.HN.R.MKFSVSPVVRV.VEAKNPADLPKLVEGLK.LAKSDPM.QCIIEES.EHII..GAGELHLEI
Retrocopy FEHSHNTRAMKFSVSPVVRVIVEAKNPADLPKLVEGLKQLAKSDPMMQCIIEESREHII>LGAGELHLEI

Parental  CLKDLEEDHACIPIKKSDPVVSYRETVSEESNVL-CLSKSP-NKHNRLYMKARPFPDGLAEDIDK
          CLKD.EEDHACIPIK......S.....S..S........SP.NKHNRLYMKA.PFPDGLAEDIDK
Retrocopy CLKDGEEDHACIPIKRNLTQLSRTRRLSARSQTCSACPRSP<NKHNRLYMKAQPFPDGLAEDIDK

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	319.39 RPM
ERP005899_muscle	0.00 RPM	3452.20 RPM
SRP017611_brain	0.00 RPM	801.63 RPM
SRP017611_kidney	0.00 RPM	1021.25 RPM
SRP017611_liver	0.00 RPM	831.73 RPM
SRP030211_testis	0.05 RPM	590.80 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_539 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_539 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004258	2 retrocopies	retro_btau_1809, retro_btau_539 ,
Canis familiaris	ENSCAFG00000019158	1 retrocopy	retro_cfam_1503,
Latimeria chalumnae	ENSLACG00000011124	1 retrocopy	retro_lcha_83,
Macaca mulatta	ENSMMUG00000022767	1 retrocopy	retro_mmul_2026,
Monodelphis domestica	ENSMODG00000000750	1 retrocopy	retro_mdom_223,
Mus musculus	ENSMUSG00000034994	1 retrocopy	retro_mmus_2521,