RetrogeneDB ID: retro_btau_812

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:25026046..25026738(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3M
• Ensembl ID: ENSBTAG00000005338
• Aliases: EIF3M, HFL-B5
• Description: eukaryotic translation initiation factor 3 subunit M [Source:RefSeq peptide;Acc:NP_001030389]

Sequence

>retro_btau_812
AGCCTCACTATAGTTGCAGGCTCTTGCGGGGCCATCCAGTATATTCCAACTGAGCTGGATCAAGTTAGAAAATGGATTTC
TGACTGGAACCTCACCACTTAAAAGAAAAAAACAAAACACACTCTTTTAAGACTACATCATGAGGCACTTGTGGCTTGTA
AGAAAAGTGATGCCGCATCAAAAGTTATGGTGGAATTGTTAGGCAGTTACATGGAGGACAATGCTTCCCAGGCTCGAGTT
GATGCCCACAGGTATATTGTGCAAGCATTTAAGATCCAAATGCATTCCTTTCTGATCATCTTCTTACTTTAAAACCAGTC
AAATTTTTGAAAGGCGAGCTTATGCATGATCTTTTAACCATTTTTTGTGAGTGCTAAATTAGCATCATATGTCATTTCAT
CAGAATGATACAGACTTCATTGATTCAGTTGGCCTACTACATGAACAGAATATGGCAAAAATGAGACTGCTTATTTTATG
GGAATGGCAGTGGAAAATAAAGAAATTTCTTTTGACACAATGCAACAAGATCTTCAAATTGGAGCTGATGATGTTGAAGC
ATTTGTTACTGATGTGGTAAGAACTAAAATGGTCTTCTACAAAAGTGATCAAACCCAGAGAAAAGTAGTTGTCAGCATAG
CACACATCGGACATTTGGAAAACAACAATGCCAACAACTCTATGACACAATG

Alignment

ORF - retro_btau_812 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.08 %
• Parental protein coverage: 61.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SLIKVAASCGAIQYIPTELDQVRKWISDWNLTTEKK---HTLLRLLYEALVDCKKSDAASKVMVELLGSY
          SL..VA.SCGAIQYIPTELDQVRKWISDWNLTT......HTLLRL..EALV.CKKSDAASKVMVELLGSY
Retrocopy SLTIVAGSCGAIQYIPTELDQVRKWISDWNLTTXXXXXXHTLLRLHHEALVACKKSDAASKVMVELLGSY

Parental  TEDNASQARVDAHRCIVRALK-DPNAFLFDHLLTLKPVKFLEGELIHDLLTIFVSAKLA-SYVKFYQNNK
          .EDNASQARVDAHR.IV.A.K.DPNAFL.DHLLTLKPVKFL.GEL.HDLLTIF...........F.QN..
Retrocopy MEDNASQARVDAHRYIVQAFK<DPNAFLSDHLLTLKPVKFLKGELMHDLLTIFCEC*IS<HHMSFHQNDT

Parental  DFIDSLGLLHEQNMAKMRLLT-FMGMAVENKEISFDTMQQELHIGADDVEAFVIDAVRTKMVYCKIDQTQ
          DFIDS.GLLHEQNMAKMRLL..FMGMAVENKEISFDTMQQ.L.IGADDVEAFV.D.VRTKMV..K.DQTQ
Retrocopy DFIDSVGLLHEQNMAKMRLLI<FMGMAVENKEISFDTMQQDLQIGADDVEAFVTDVVRTKMVFYKSDQTQ

Parental  RKVVVS-HSTHRTFGKQQWQQLYDTL
          RKVVVS.HSTHRTFGKQQ.QQLYDT.
Retrocopy RKVVVS<HSTHRTFGKQQCQQLYDTM

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	40.45 RPM
ERP005899_muscle	0.00 RPM	184.71 RPM
SRP017611_brain	0.00 RPM	9.36 RPM
SRP017611_kidney	0.06 RPM	36.27 RPM
SRP017611_liver	0.00 RPM	15.25 RPM
SRP030211_testis	0.09 RPM	111.39 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_812 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_812 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_812 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005338	2 retrocopies	retro_btau_1736, retro_btau_812 ,
Echinops telfairi	ENSETEG00000013437	1 retrocopy	retro_etel_120,
Myotis lucifugus	ENSMLUG00000014727	2 retrocopies	retro_mluc_1982, retro_mluc_431,
Mus musculus	ENSMUSG00000027170	1 retrocopy	retro_mmus_421,
Oryctolagus cuniculus	ENSOCUG00000004483	1 retrocopy	retro_ocun_282,
Otolemur garnettii	ENSOGAG00000015913	1 retrocopy	retro_ogar_1783,
Pteropus vampyrus	ENSPVAG00000015083	1 retrocopy	retro_pvam_1134,
Vicugna pacos	ENSVPAG00000007791	1 retrocopy	retro_vpac_342,