RetrogeneDB ID: retro_btau_52

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:70697539..70698145(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000003383
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TMED2
• Ensembl ID: ENSBTAG00000039630
• Aliases: None
• Description: transmembrane emp24 domain-containing protein 2 precursor [Source:RefSeq peptide;Acc:NP_001153290]

Sequence

>retro_btau_52
ATGGTGACGCTTGCTGAGCTGCTGGTGCTCCTGGCCACCCTCCTGGCCACGGCCTTGGGCTACTTCATCAGCATTGACGC
ACATGCAGAGGAGTGCTTCTTCGAGTGGGTCACCTTGGGCACCAAGATGGGCCTCATCTTCGAGGTGGCCGAGGACGGCT
TCCTGGACATCAACATGGAGATTACAGGACCTGATAATAAAGGAATTTATAAAGGAGACCGGGAGTCCAGTGGGAAATAC
ACATTTGCTGCTCACATGGATGGAACATATAAGTTTTGTTTTAGCAACAGGATGTATACCATGACTCCAAAGATAGTGAT
GTTCACCATTGATATTGGGGAAGTCCCCAAAGGACAAGACATGGAAACAGAAGCTCACCAGAACAAGCTAGAAGAAATGA
TTAATGAGCTCACAGTGGTGATGACAGCTGTGAAGCATGAACAGGAATACATGGAAGTTCAAGAGAGAATACACAGAGCA
ATCAATGACAACACAAACAGCAGAGTGGTCCTTTGGTCCTTCTTTGAAGCTCTTGTTCTAGTTGCCATGACACTGGGACA
AATCTACTACCTGAAGAGATTCTTCGAAGTCCGGAGGGTTGTTTAA

Alignment

ORF - retro_btau_52 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVTLAELLVLLAALLATASGYFVSIDAHAEECFFERVTSGTKMGLIFEVAEGGFLDIDVEITGPDNKGIY
          MVTLAELLVLLA.LLATA.GYF.SIDAHAEECFFE.VT.GTKMGLIFEVAE.GFLDI..EITGPDNKGIY
Retrocopy MVTLAELLVLLATLLATALGYFISIDAHAEECFFEWVTLGTKMGLIFEVAEDGFLDINMEITGPDNKGIY

Parental  KGDRESSGKYTFAAHMDGTYKFCFSNRMSTMTPKIVMFTIDIGEAPKGQDMETEAHQNKLEEMINELAVA
          KGDRESSGKYTFAAHMDGTYKFCFSNRM.TMTPKIVMFTIDIGE.PKGQDMETEAHQNKLEEMINEL.V.
Retrocopy KGDRESSGKYTFAAHMDGTYKFCFSNRMYTMTPKIVMFTIDIGEVPKGQDMETEAHQNKLEEMINELTVV

Parental  MTAVKHEQEYMEVRERIHRAINDNTNSRVVLWSFFEALVLVAMTLGQIYYLKRFFEVRRVV
          MTAVKHEQEYMEV.ERIHRAINDNTNSRVVLWSFFEALVLVAMTLGQIYYLKRFFEVRRVV
Retrocopy MTAVKHEQEYMEVQERIHRAINDNTNSRVVLWSFFEALVLVAMTLGQIYYLKRFFEVRRVV

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	46.93 RPM
ERP005899_muscle	0.26 RPM	119.88 RPM
SRP017611_brain	0.09 RPM	28.50 RPM
SRP017611_kidney	0.18 RPM	58.26 RPM
SRP017611_liver	0.30 RPM	160.46 RPM
SRP030211_testis	0.14 RPM	53.13 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_52 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_52 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_52 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015262	2 retrocopies	retro_amel_1923, retro_amel_337,
Bos taurus	ENSBTAG00000039630	2 retrocopies	retro_btau_52 , retro_btau_819,
Choloepus hoffmanni	ENSCHOG00000012728	6 retrocopies	retro_chof_104, retro_chof_1277, retro_chof_2323, retro_chof_2601, retro_chof_2709, retro_chof_981,
Callithrix jacchus	ENSCJAG00000020466	1 retrocopy	retro_cjac_1392,
Echinops telfairi	ENSETEG00000000556	2 retrocopies	retro_etel_2109, retro_etel_2154,
Homo sapiens	ENSG00000086598	1 retrocopy	retro_hsap_2793,
Gorilla gorilla	ENSGGOG00000028536	1 retrocopy	retro_ggor_1943,
Macropus eugenii	ENSMEUG00000006459	2 retrocopies	retro_meug_1478, retro_meug_745,
Macaca mulatta	ENSMMUG00000031491	2 retrocopies	retro_mmul_1439, retro_mmul_613,
Mustela putorius furo	ENSMPUG00000001598	1 retrocopy	retro_mputfur_1241,
Mus musculus	ENSMUSG00000029390	2 retrocopies	retro_mmus_1361, retro_mmus_3262,
Nomascus leucogenys	ENSNLEG00000001652	2 retrocopies	retro_nleu_2454, retro_nleu_2794,
Oryctolagus cuniculus	ENSOCUG00000003453	1 retrocopy	retro_ocun_576,
Otolemur garnettii	ENSOGAG00000009192	1 retrocopy	retro_ogar_2548,
Pongo abelii	ENSPPYG00000005090	3 retrocopies	retro_pabe_1919, retro_pabe_2227, retro_pabe_3597,
Tursiops truncatus	ENSTTRG00000007249	7 retrocopies	retro_ttru_1369, retro_ttru_1592, retro_ttru_1750, retro_ttru_1815, retro_ttru_216, retro_ttru_43, retro_ttru_615,