RetrogeneDB ID: retro_ecab_860

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:50543917..50544694(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3E
• Ensembl ID: ENSECAG00000000236
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit E [Source:HGNC Symbol;Acc:3277]

Sequence

>retro_ecab_860
GCAGAGTAGGACCTGACTTCTCACATGGTGCATTATTTGGATTGAGATCTGAACTTTCCTGTGATTGAATTTCTTTTAAT
GAAGAAGATATATGGTGAAAAATAAGTATTGTGAGGAAAATCAGATCTCTTTAGTGATTCTAATGTGGTAAACTCTGCTA
TGGACATTTACAAAAACCTTTATTCTAATGATATCTTCATGCTTTGAGAGAAAAAAACACCATAGTTGTTGCACAACTGA
AACAGCTTCAAGCAGAAATGGACCAATTGTGGAAACGTTTGAACATCACAGCACTACAAGGTCAATGGCAGTCAACAAGA
GGTGGCTGGATGCTGTTTGACCACCTAGCTGACCAGCAGAGTATTAAGCAGAAACATTTAGATAGGATCTCAGGTTTGCA
AAATTCCAGTATGAATGTGCCAATTACTCAGGAGCAGCAAGGTATCTTTGCTTTTTTAGAGAGTTTGATTCAGTAATGGA
TAGAAATGCTTTGGGTTCACTCTGAGGAAAATGGGCCTCTGAAATCTTCACGCAGCCATGGAAGGCCTTGCATAATGAAA
AGAGACCACAGATCCACAGATAAAAAAATTCTGTCATTCCTCTATTCTTGTCTCATCAGCAGTGAACATGGCTCATTCAC
TGGTCTCTTTGTTCTCTTCAGTCAGCCCCAAGGCAGTTAATAACATTATTAATCTTTTCATTTACCAGCCACAGTATCTT
AAAGCAATTCAGACCATATGTGCACATATTCTCCACTATTTGACTATGGTAGTCATA

Alignment

ORF - retro_ecab_860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.02 %
• Parental protein coverage: 58.65 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AEYDLTTRIAHFLDRHLVFPLLEFLSVKEIYNEKELLQGKLDLLSDTNMVDFAMDVYKNLYSDDI-PHAL
          AE.DLT....H.LD..L.FP..EFL..K.IY.EK..L.GK.DL.SD.N.V..AMD.YKNLYS.DI..HAL
Retrocopy AE*DLTSHMVHYLD*DLNFPVIEFLLMKKIYGEK*VL*GKSDLFSDSNVVNSAMDIYKNLYSNDI<LHAL

Parental  REKRTTVVAQLKQLQAETE-PIVKMFEDPETTRQM-QSTRDGRMLFDYLADKHGFRQEYLDTL-YRYAKF
          REK.T.VVAQLKQLQAE...PIV..FE...TTR.M.QSTR.G.MLFD.LAD.....Q..LD....R.AKF
Retrocopy REKNTIVVAQLKQLQAEMD<PIVETFEHHSTTRSM>QSTRGGWMLFDHLADQQSIKQKHLDRI<LRFAKF

Parental  QYECGNYSGAAEYLYFFRVLVPATDRNALSSLWGKLASEILMQNWDAAMEDLTRLKETIDNNSVSSPLQS
          QYEC.NYSGAA.YL.FFR......DRNAL.SL.GK.ASEI..Q.W..A.....R.......NSV.....S
Retrocopy QYECANYSGAARYLCFFREFDSVMDRNALGSL*GKWASEIFTQPWK-ALHNEKRPQIHR*KNSVIPLFLS

Parental  LQQRTWLIHWSLFVFFNHP-KGRDNIIDLFLYQPQYLNAIQTMCPHILRYLTTAVI
          .QQ.TWLIHWSL......P.K...NII.LF.YQPQYL.AIQT.C.HIL.YLT..VI
Retrocopy HQQ*TWLIHWSLCSLQSAP<KAVNNIINLFIYQPQYLKAIQTICAHILHYLTMVVI

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
SRP021940_articular_cartilage	0.00 RPM	139.19 RPM
SRP021940_cerebellum	0.00 RPM	17.50 RPM
SRP021940_embryo	0.00 RPM	120.04 RPM
SRP021940_placental_villous	0.00 RPM	49.94 RPM
SRP021940_synovial_membrane	0.00 RPM	56.39 RPM
SRP021940_testis	0.00 RPM	27.62 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_860 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_860 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_860 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,