RetrogeneDB ID: retro_btau_1736

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:36171713..36172835(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000047051
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1736
ATGAGTGTCCCGGCGTTCATCGACATCAGCGAGGAAGATCAGGCTGCTGAACTTCGCGCTTATTTGAAGTCTAAAGGAGC
TGAAATTTCAGAAGAGAATTCAGAAGGTGGACTTCATGTAGATTTAGCTCAGATTATTGAAGCCTGCGATGTATGTCTGA
AGGAAGATGATAAAGATGTTGAAAGTGTGATGAACAGCGTGGTATCCCTCCTGTTGATCCTGGAACCAGATAAGCAAGAA
GCTCTGATTGAAAGCCTATGTGAGAAACTGGTCAAATTTCGGGAAGGTGAACGTCCGTCTCTGAGACTGCAGTTGCTAAG
CAACCTTTTCCATGGGATGGATAAGAATACTCCTGTAAGATATACAGTGTATTGCAGCCTCATTAAAGTGGCAGCATCTT
GTGGGGCCATCCAGTATATTCCAACTGAGCTGGATCAAGTTAGAAAATGGATTTCTGACTGGAACCTCACCACTGAAAAA
AAACACACCCTTTTAAGACTACTTTATGAGGCACTTGTGGATTGTAAGAAAAGTGATGCCGCATCAAAAGTTATGGTGGA
ATTGTTAGGCAGTTACACGGAGGACAATGCTTCCCAGGCTCGAGTTGATGCCCACAGGTGTATTGTGCGAGCATTGAAAG
ATCCAAATGCATTCCTTTTTGACCATCTTCTTACGTTAAAACCAGTCAAGTTTTTGGAAGGCGAGCTTATTCATGATCTT
TTAACCATTTTTGTGAGTGCTAAATTGGCATCATATGTCAAGTTTTATCAGAATAATAAAGACTTCATTGATTCACTTGG
CCTACTGCATGAACAGAATATGGCAAAAATGAGACTGCTTACTTTTATGGGAATGGCCGTGGAAAATAAAGAAATTTCTT
TTGACACAATGCAACAAGAACTTCAGATTGGAGCTGATGATGTTGAAGCATTTGTTATTGATGCTGTAAGAACTAAAATG
GTCTACTGCAAAATTGATCAAACCCAGAGAAAAGTTGTTGTCAGCCATAGCACACATCGGACATTTGGAAAACAGCAGTG
GCAGCAACTCTATGACACACTTAATGCCTGGAAACAAAATTTGAACAAAGTGAAAAACAGCCTTTTGAGTCTTTCTGACA
CC

Alignment

ORF - retro_btau_1736 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVPAFIDISEEDQAAELRAYLKSKGAEISEENSEGGLHVDLAQIIEACDVCLKEDDKDVESVMNSVVSL
          MSVPAFIDISEEDQAAELRAYLKSKGAEISEENSEGGLHVDLAQIIEACDVCLKEDDKDVESVMNSVVSL
Retrocopy MSVPAFIDISEEDQAAELRAYLKSKGAEISEENSEGGLHVDLAQIIEACDVCLKEDDKDVESVMNSVVSL

Parental  LLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVRYTVYCSLIKVAASCGAIQYI
          LLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVRYTVYCSLIKVAASCGAIQYI
Retrocopy LLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVRYTVYCSLIKVAASCGAIQYI

Parental  PTELDQVRKWISDWNLTTEKKHTLLRLLYEALVDCKKSDAASKVMVELLGSYTEDNASQARVDAHRCIVR
          PTELDQVRKWISDWNLTT...HTLLRLLYEALVDCKKSDAASKVMVELLGSYTEDNASQARVDAHRCIVR
Retrocopy PTELDQVRKWISDWNLTTXXXHTLLRLLYEALVDCKKSDAASKVMVELLGSYTEDNASQARVDAHRCIVR

Parental  ALKDPNAFLFDHLLTLKPVKFLEGELIHDLLTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMRLL
          ALKDPNAFLFDHLLTLKPVKFLEGELIHDLLTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMRLL
Retrocopy ALKDPNAFLFDHLLTLKPVKFLEGELIHDLLTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMRLL

Parental  TFMGMAVENKEISFDTMQQELHIGADDVEAFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQL
          TFMGMAVENKEISFDTMQQEL.IGADDVEAFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQL
Retrocopy TFMGMAVENKEISFDTMQQELQIGADDVEAFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQL

Parental  YDTLNAWKQNLNKVKNSLLSLSDT
          YDTLNAWKQNLNKVKNSLLSLSDT
Retrocopy YDTLNAWKQNLNKVKNSLLSLSDT

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	20.40 RPM	40.45 RPM
ERP005899_muscle	14.31 RPM	184.71 RPM
SRP017611_brain	1.28 RPM	9.36 RPM
SRP017611_kidney	6.82 RPM	36.27 RPM
SRP017611_liver	1.51 RPM	15.25 RPM
SRP030211_testis	1.00 RPM	111.39 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

7 EST(s) were mapped to retro_btau_1736 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AJ693001	36171953	36172424	99.6	469	2	467
AV608557	36171883	36172386	100	503	0	503
CX735035	36171685	36172296	99.9	610	1	609
DT888619	36171740	36172313	100	573	0	573
DY040496	36171723	36172321	99.7	596	2	594
DY046635	36171958	36172385	100	427	0	427
DY059756	36171701	36172321	99.9	619	1	618

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1736 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1736 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,