RetrogeneDB ID: retro_btau_291

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:34585232..34585958(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3E
• Ensembl ID: ENSBTAG00000006702
• Aliases: EIF3E, EIF3S6
• Description: Eukaryotic translation initiation factor 3 subunit E [Source:UniProtKB/Swiss-Prot;Acc:Q3T102]

Sequence

>retro_btau_291
ATAGATAATAATTCTGTGAATTCTCCACTTCAATCTCTTCAGCAGTGAATATGGTTCACTCATTGGTCTCTGTTTTCTTC
TATCACCCCAAAGCACAATAACATTAAGGATCAATTCCTTTACCAGCCACAGTATCTTAGTGCAGTTCCAATGATGCGCC
CACATATTCTCTACTATTTAACCACAGCAGTCATAACAAACAAAGATGTTCGAAAACACGGGCAAGTGCTAAAAGATCTG
GTCAAATTTATTCAGTAGGAACCTTGCACATATTTATATAAAGACCCAATTTTAGAATTTGTTAAATGCTTATATGTTAA
CTTCCATGGGGCTCACATAAAGCTGAAGAAATGTGGATCAATGCAAGTGAATGACTTCTTCTTGGTGGCTTATCTTGAGG
ATTTCACTGAAGATACCTATTTCCGTATTTGAGACTTGTGTCACATCCATCAGTGTATCAGCATTAACATGTTGGCAGTT
AAACTAAGCATGACTCCAGAATAAGTTCAAAAGTAGATTATAAATTTGGTTACAAATGCAAGACTGAGTATCAAGACTGA
TTCTAAATTAGGTCATGAGGTTATGAGTAACAATACCATCTCACAAGTGATGAAACCATGCAAGTGATTGAAAAGACCAA
AAGCCTTTTATTTAAGAAGCCAAATACTGACCATGAATACTGAGAAGAAATTTAATCAGAATAGTAAGTAAGTAGAGGCT
CCTAAT

Alignment

ORF - retro_btau_291 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.35 %
• Parental protein coverage: 54.16 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IDNNSVSSPLQSLQQRTWLIHWSLFVFFNHPKGRDNIIDLFLYQPQYLNAIQTMCPHILRYLTTAVITNK
          IDNNSV.SPLQSLQQ..W..HWSLF.....PK...NI.D.FLYQPQYL.A...M.PHIL.YLTTAVITNK
Retrocopy IDNNSVNSPLQSLQQ*IWFTHWSLFSSIT-PK-HNNIKDQFLYQPQYLSAVPMMRPHILYYLTTAVITNK

Parental  DVRKRRQVLKDLVKVIQQE--SYTYKDPITEFVECLYVNFDFDGAQKKLRECESVLVNDFFLVACLEDFI
          DVRK..QVLKDLVK.IQ.E...Y.YKDPI.EFV.CLYVN..F.GA..KL..C.S..VNDFFLVA.LEDF.
Retrocopy DVRKHGQVLKDLVKFIQ*EPCTYLYKDPILEFVKCLYVN--FHGAHIKLKKCGSMQVNDFFLVAYLEDFT

Parental  ENARLFIFETFCRIHQCISINMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPYQQ
          E....F.....C.IHQCISINMLA.KL.MTPE.....I.NL..NARL..K.DSKLGH.VM.NN..S....
Retrocopy EDT-YFRI*DLCHIHQCISINMLAVKLSMTPE*VQK*IINLVTNARLSIKTDSKLGHEVMSNNTISQVMK

Parental  V---IEKTKSLSFRSQMLAMNIEKKLNQNSR-SEAPN
          ........K....RSQ.L.MN.EKK.NQNS...EAPN
Retrocopy PCK*LKRPKAFYLRSQILTMNTEKKFNQNSK*VEAPN

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	208.21 RPM
ERP005899_muscle	0.00 RPM	321.27 RPM
SRP017611_brain	0.00 RPM	63.72 RPM
SRP017611_kidney	0.00 RPM	129.92 RPM
SRP017611_liver	0.00 RPM	61.61 RPM
SRP030211_testis	0.00 RPM	170.86 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_291 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_291 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_291 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006702	1 retrocopy	retro_btau_291 ,
Canis familiaris	ENSCAFG00000000702	1 retrocopy	retro_cfam_1127,
Callithrix jacchus	ENSCJAG00000006458	3 retrocopies	retro_cjac_2333, retro_cjac_2686, retro_cjac_701,
Equus caballus	ENSECAG00000000236	1 retrocopy	retro_ecab_860,
Echinops telfairi	ENSETEG00000013105	1 retrocopy	retro_etel_2048,
Felis catus	ENSFCAG00000003665	1 retrocopy	retro_fcat_231,
Homo sapiens	ENSG00000104408	1 retrocopy	retro_hsap_3489,
Gorilla gorilla	ENSGGOG00000022955	2 retrocopies	retro_ggor_2354, retro_ggor_2355,
Myotis lucifugus	ENSMLUG00000007269	1 retrocopy	retro_mluc_1796,
Macaca mulatta	ENSMMUG00000011359	1 retrocopy	retro_mmul_2585,
Mustela putorius furo	ENSMPUG00000005924	2 retrocopies	retro_mputfur_193, retro_mputfur_736,
Mus musculus	ENSMUSG00000022336	2 retrocopies	retro_mmus_1801, retro_mmus_2807,
Nomascus leucogenys	ENSNLEG00000004120	1 retrocopy	retro_nleu_333,
Oryctolagus cuniculus	ENSOCUG00000008050	1 retrocopy	retro_ocun_1399,
Pan troglodytes	ENSPTRG00000020505	1 retrocopy	retro_ptro_2362,
Rattus norvegicus	ENSRNOG00000027690	4 retrocopies	retro_rnor_1133, retro_rnor_2879, retro_rnor_583, retro_rnor_584,
Ictidomys tridecemlineatus	ENSSTOG00000008976	1 retrocopy	retro_itri_545,
Tursiops truncatus	ENSTTRG00000011025	2 retrocopies	retro_ttru_1602, retro_ttru_1794,