RetrogeneDB ID: retro_ecab_847

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:95544763..95545313(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSECAG00000020187
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 2 [Source:HGNC Symbol;Acc:3293]

Sequence

>retro_ecab_847
AGCAAGTTCGAAGCATTGGAAGATGACGACGGTGGAGTCCCTGATCAGAATGAAGAAAAGAGTACATAGAAGGATGATGA
GAAGGAAAAAAACAGCATAAGGCAGGAGTCAGGCCTGCAGCCAGAGCAAGGCTGTTGTCCCCGGGCCGCAGAGCATCCCC
ACAGTATGATACCCTTCCTGGTGCTCCAGGAGAAACCCAGCCGTCCCTCGAGCCCGCAGAGCTACGAGCAGAATGTCAAG
CAGATTGGCCCCTTTGCCTCCATGGAGCAGGTATGCAGATTTTACAGGCATGTGGTACCTCTCTGGACCCTGACAGGCCA
CAGTGACTTCCATCTCTTCAAAGAAGGAATTGAGCCCACATGGGAGGATGATGCACATAAAAATGGTGGTGGTAGATGAT
TTGGCTGTGGAAGGGCGTGGCATCCTGTTGCTGGGAGAATCTCATTCCGGCCGCGTTGGGGGACAGTTCGGGGTCAGGGA
GGAGATCTGAGGGCCTGTGGTCTCCGTGAGGTTTCAGGAGGACAATATTTCAATATGGAGTAGCCTGGCA

Alignment

ORF - retro_ecab_847 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.62 %
• Parental protein coverage: 75.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  NKFDALKDDDSGDHDQNEENSTQKDGEKE-KAERDKSQGSSKRKAVVPGP-AEHPL-QYN-YTFWYSRRT
          .KF.AL.DDD.G..DQNEE.ST.KD.EKE.K.....SQ..S..KAVVPGP.AEHP..QY..Y..W.SRR.
Retrocopy SKFEALEDDDGGVPDQNEEKST*KDDEKE>KTA*GRSQACSQSKAVVPGP<AEHPH<QYD<YPSWCSRRN

Parental  PG-RPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKW-I
          P..RP.S.QSYEQN.KQIG.FAS.EQ..RFY.H.V....LTGHSDFHLFKEGI.P.WEDDA.KNGG....
Retrocopy PA<RPSSPQSYEQNVKQIGPFASMEQVCRFYRHVVPLWTLTGHSDFHLFKEGIEPTWEDDAHKNGGGR<M

Parental  IRLRKGLASRCWENLILAMLGE-QFMVGEEICGAVVSVRFQEDIISIWNKTA
          I.L.KG.AS.CWENLI.A.LG..QF.V.EEI.G.VVSVRFQED.ISIW...A
Retrocopy IWLWKGVASCCWENLIPAALGD<QFGVREEI*GPVVSVRFQEDNISIWSSLA

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	7.61 RPM
SRP021940_cerebellum	0.05 RPM	11.48 RPM
SRP021940_embryo	0.05 RPM	17.08 RPM
SRP021940_placental_villous	0.19 RPM	17.99 RPM
SRP021940_synovial_membrane	0.14 RPM	10.84 RPM
SRP021940_testis	0.00 RPM	9.02 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_847 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_847 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_847 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1232

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Callithrix jacchus	ENSCJAG00000013786	2 retrocopies	retro_cjac_1061, retro_cjac_2717,
Equus caballus	ENSECAG00000020187	2 retrocopies	retro_ecab_300, retro_ecab_847 ,
Homo sapiens	ENSG00000135930	1 retrocopy	retro_hsap_2689,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Pan troglodytes	ENSPTRG00000013043	1 retrocopy	retro_ptro_1816,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101,
Tupaia belangeri	ENSTBEG00000004455	11 retrocopies	retro_tbel_1299, retro_tbel_2197, retro_tbel_2623, retro_tbel_2680, retro_tbel_3932, retro_tbel_4471, retro_tbel_4622, retro_tbel_536, retro_tbel_616, retro_tbel_650, retro_tbel_714,