RetrogeneDB ID: retro_btau_1809

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:40175482..40177110(-)
• Located in intron of: ENSBTAG00000047855

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_1809
GTGGTGAACTTCACAGTAGACCAGATCCGGGCCATCATGGACAAGAAGGCCAACATCTGGAACATGTCTGTCATTGGCCG
CGTGGACCATGGCAAGTCCACTCTGACGGACTCCCTGGTGTGCAAGGCAGGTGTCATCGCCTCTGCCCGGACTAGGGAGA
CCCGCTTCACTGACACCCGGAAAGACGAGCAGGAGCATTGCATCACCATCAAGTCAACGGCCATCTCCCTTTTCTATGAG
CTTTCAGAGGACGATTTGAATTTCATCAAGCAGAGCAAGGATGGCTCTGGCTTCCTCATCAACCTCATCAGCTCCCCTGG
GCACGTCAACTTTTCCTCAGAGGTGACAGCCGTGCTCCGTGTCACTGACGGTGCCTTGGTGGTGGTGGACTGCGTGTCGG
GTATGTGTGTGCAGACAGAGACAGTGCTGTGCCAGGCCATTGCCGAGCGCATCAAGCCAGTGCTGACGATGAACAAGATG
GACCGGGCCCTGCCTGAGCTGCAGCTGGAGCCTGAGGAGCTCTACCAAACCTTCCAGCGCATCGTGGAGAACGTCAACAT
CATTATCTCTACCTATGGTGAGGGCGAGAGTGGCCCCTTGGGCAACATCATGATCGACCCCGTCCTTGGTACTGTTGGCT
TCAGGTCTGGTCTGCACGGTTGGGCCTTTACCCTGAAGCAGTTTGCAGAGATGTATGTGGCCAAGTTTGCCACCAAGGGC
GAGGGACAGCTAGGGCCTGCTGAGCGGGCCAAGAAGGTGGAGGACATGATGAAAAAGCTGTGGGGAGACCGGTACTTTGA
TCCAGCCACCGGCAAGTTCAGCAAGTCAGCCAACAGCCCTGATGGCAAGAAGCTGCCACGGACATTCTACCAGCTTATCC
TGGACCCAGTCTTCAAGGTGTTTGATGCAATCATGAACTTCAAGAAAGAGGAGATGGCAAAACTAATTGAAAAACTGGAC
ATCAAGTTGGACAGTAAAGATAAGGACAAGGAGGGTAAACCACTTCTGAAAGCTGTGATGTGCCGCTGGCTGCCTCCTGG
GGATGCCCTGCTGTAGATGATCACCATCCACTGTCTTCCCCTGTGACGGCCCAGAAGTACTGCAGTGAGCTCCTGTACGA
GGGGCCCCCAGACGATGAGGCAGCCATGGGCATTAAAAGCTGTGATCCCAAAGGCCCTCTCATGATGTACATTTCCAAAA
TGGTGCCGACCTCTGCCAAAGGTCGGTTCTGTGCCTTTGGCCTGGTCTTCTCAGAGCTGGTGTCTACTGGCCTGAAGGTG
CGCATCATGGGACCCAACTATACTCCTGGGAAGAAGGAGGACCTGTACCTGAAGCTGATCCAGAGGACAATCCTGATGAT
GGGCCATTACATGGAGCCTATCAAGGATGTGCCTTGTGGCAACATTGTGGGCCTGGTGGGCGTGGACCAGTTCCTGGTGA
AGACTGGCACCATCACCACCTTTGAGCATGCCCACAACGTGCGGGTGATGAAGTTCAGTGTGAGCCCTGTTGTCAGGATC
GCTGTGGAGGCCAAGAACCCGGCCAACCTGCCCAAGCTGGTGGAAGGTCTGAAGCGGCTGGCCAAGTCGGACCCCATGGT
GCAGTACATCATCGAGGAGTCTGGGGAG

Alignment

ORF - retro_btau_1809 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.1 %
• Parental protein coverage: 63.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVNFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAGIIASARAGETRFTDTRKDEQERCITI
          .VNFTVDQIRAIMDKKANI.NMSVI..VDHGKSTLTDSLVCKAG.IASAR..ETRFTDTRKDEQE.CITI
Retrocopy VVNFTVDQIRAIMDKKANIWNMSVIGRVDHGKSTLTDSLVCKAGVIASARTRETRFTDTRKDEQEHCITI

Parental  KSTAISLFYELSENDLNFIKQSKDGSGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQTE
          KSTAISLFYELSE.DLNFIKQSKDGSGFLINLI.SPGHV.FSSEVTA.LRVTDGALVVVDCVSG.CVQTE
Retrocopy KSTAISLFYELSEDDLNFIKQSKDGSGFLINLISSPGHVNFSSEVTAVLRVTDGALVVVDCVSGMCVQTE

Parental  TVLRQAIAERIKPVLMMNKMDRALLELQLEPEELYQTFQRIVENVNVIISTYGEGESGPMGNIMIDPVLG
          TVL.QAIAERIKPVL.MNKMDRAL.ELQLEPEELYQTFQRIVENVN.IISTYGEGESGP.GNIMIDPVLG
Retrocopy TVLCQAIAERIKPVLTMNKMDRALPELQLEPEELYQTFQRIVENVNIIISTYGEGESGPLGNIMIDPVLG

Parental  TVGFGSGLHGWAFTLKQFAEMYVAKFAAKGEGQLGPAERAKKVEDMMKKLWGDRYFDPATGKFSKSANSP
          TVGF.SGLHGWAFTLKQFAEMYVAKFA.KGEGQLGPAERAKKVEDMMKKLWGDRYFDPATGKFSKSANSP
Retrocopy TVGFRSGLHGWAFTLKQFAEMYVAKFATKGEGQLGPAERAKKVEDMMKKLWGDRYFDPATGKFSKSANSP

Parental  DGKKLPRTFCQLILDPIFKVFDAIMNFKKEETAKLIEKLDIKLDSEDKDKEGKPLLKAVMRRWLPAGDAL
          DGKKLPRTF.QLILDP.FKVFDAIMNFKKEE.AKLIEKLDIKLDS.DKDKEGKPLLKAVM.RWLP.GDAL
Retrocopy DGKKLPRTFYQLILDPVFKVFDAIMNFKKEEMAKLIEKLDIKLDSKDKDKEGKPLLKAVMCRWLPPGDAL

Parental  LQMITIH-LPSPVTAQKYRCELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYAFGRVFSG
          L.MITIH.L.SPVTAQKY..ELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTS.KGRF.AFG.VFS.
Retrocopy L*MITIH<LSSPVTAQKYCSELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSAKGRFCAFGLVFSE

Parental  LVSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCGNIVGLVGVDQFLVKTGTITTFE
          LVSTGLKVRIMGPNYTPGKKEDLYLK.IQRTILMMG.Y.EPI.DVPCGNIVGLVGVDQFLVKTGTITTFE
Retrocopy LVSTGLKVRIMGPNYTPGKKEDLYLKLIQRTILMMGHYMEPIKDVPCGNIVGLVGVDQFLVKTGTITTFE

Parental  HAHNMRVMKFSVSPVVRVAVEAKNPADLPKLVEGLKRLAKSDPMVQCIIEESGE
          HAHN.RVMKFSVSPVVR.AVEAKNPA.LPKLVEGLKRLAKSDPMVQ.IIEESGE
Retrocopy HAHNVRVMKFSVSPVVRIAVEAKNPANLPKLVEGLKRLAKSDPMVQYIIEESGE

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	0.36 RPM	319.39 RPM
ERP005899_muscle	1.79 RPM	3452.20 RPM
SRP017611_brain	0.37 RPM	801.63 RPM
SRP017611_kidney	1.01 RPM	1021.25 RPM
SRP017611_liver	0.08 RPM	831.73 RPM
SRP030211_testis	0.99 RPM	590.80 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1809 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1809 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1809 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,