RetrogeneDB ID: retro_ecab_300

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 14:72288773..72289505(+)
• 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_300
ATGAACAACAAGTTCGACGCATTGAAAGATGATGACAGTGGGGACCATGATCAGAATGAAGAAAACAGCACACAGAAAGA
TGGTGAGAAGGAAAAAACAGAATGAGACAAGAGTCAGGGCAGCAGCAAGAGGAAGGCTGTTGTCCCAGGACCAGCAGAGC
ATCCCCTGCAGTACAACTGCACTTTCTGGTACTCCAGGAGAACCCCCGGCCGGCCTACCAGCTCACAGAGCTACGAACAG
AACATCAAACAGATCGGCACCTTTGCCTCTGTGGAGCAGTTCTGGAGGTTTTACAGCCACATGGTACGTCCCGGGGACCT
GACGGGCCACAGTGACTTCCATCTCTTCAAAGAAGGAATTAAACCCATGTGGGAGGATGATGCAAATAAAAATCGTGGCA
AGTGGATTATTCGGCTGCGAAAGGGCTTGGCAACCCGTTGCTGGGAGAATCTCATCCTGGCCATGTTGGGGGAGCAGTTC
ATGGTTGGGGAGGAGATCTGTGGGGCTGTGGTCTCTGTCCAGTTCCAGGAGGACATTATTTCAATATGGAATAAGACTGC
CAGTGACCAAGCAACCATAGCCCTAATCCGGGATACACTTTGGCGAGTGCTTAATCTACCTCCCAACACCATTATGGAAT
ACAAAACCCACACCGACAGCAACAAAATGCCAGGCAGCCTGGGCCCCCAAAGGCTCCTTTTTCAAAACCTCTGGAAGCCG
CGGTTGAATGTG

Alignment

ORF - retro_ecab_300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.49 %
• Parental protein coverage: 99.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNNKFDALKDDDSGDHDQNEENSTQKDGEKEKAERDKSQGSSKRKAVVPGPAEHPLQYNYTFWYSRRTPG
          MNNKFDALKDDDSGDHDQNEENSTQKDGEKEK.E.DKSQGSSKRKAVVPGPAEHPLQYN.TFWYSRRTPG
Retrocopy MNNKFDALKDDDSGDHDQNEENSTQKDGEKEKTE*DKSQGSSKRKAVVPGPAEHPLQYNCTFWYSRRTPG

Parental  RPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLR
          RPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKN.GKWIIRLR
Retrocopy RPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNRGKWIIRLR

Parental  KGLASRCWENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVLNLPPNT
          KGLA.RCWENLILAMLGEQFMVGEEICGAVVSV.FQEDIISIWNKTASDQAT.A.IRDTL.RVLNLPPNT
Retrocopy KGLATRCWENLILAMLGEQFMVGEEICGAVVSVQFQEDIISIWNKTASDQATIALIRDTLWRVLNLPPNT

Parental  IMEYKTHTDSIKMPGRLGPQRLLFQNLWKPRLNV
          IMEYKTHTDS.KMPG.LGPQRLLFQNLWKPRLNV
Retrocopy IMEYKTHTDSNKMPGSLGPQRLLFQNLWKPRLNV

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	0.31 RPM	11.48 RPM
SRP021940_embryo	0.20 RPM	17.08 RPM
SRP021940_placental_villous	0.48 RPM	17.99 RPM
SRP021940_synovial_membrane	0.05 RPM	10.84 RPM
SRP021940_testis	0.13 RPM	9.02 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_300 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_300 has 0 orthologous retrocopies within eutheria group .

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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,