RetrogeneDB ID: retro_ecab_53

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:34783906..34784272(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000003000
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000011843
• Aliases: None
• Description: None

Sequence

>retro_ecab_53
GGCGCCCCTGTGGATCTGGAGTTGAAGAAGGTTTTCACAGAGCTTCAAGCCAAAGCTATCGACACTCAACAGAAAGTGAA
GCTTGCAGACATAGAGATTGAACAGCTAAACAGAACGAAAAAGCATGCACATCTTACAGATACAGAGATTATGACTTTGG
TAGATGAGACTAACATATATCAAGGTGTAGGAATAATGTTTATTCTTCAATCCAAGGAGGTAATTCACAATCAGCTGTCA
GAGAAACAGAAAATAGCAGAAGAAAAAAGTAAAGAATCGGAACAGAAAAAGTCCTACCAGCAGTGGAGCATGAAGGAAGC
TGAGGACAACATCCGGGAGATGCTGCCGGCACGAAGGGCCCAGTAG

Alignment

ORF - retro_ecab_53 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.33 %
• Parental protein coverage: 98.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APVDLELKKAFTELQAKVIDTQQKVKLADIQIEQLNRTKKHAHLTDTEIMTLVDETNMYEGVGRMFILQS
          APVDLELKK.FTELQAK.IDTQQKVKLADI.IEQLNRTKKHAHLTDTEIMTLVDETN.Y.GVG.MFILQS
Retrocopy APVDLELKKVFTELQAKAIDTQQKVKLADIEIEQLNRTKKHAHLTDTEIMTLVDETNIYQGVGIMFILQS

Parental  KEVIHNQLLEKQKIAEEKIKELEQKKSYLERSVKEAEDNIREMLMARRAQ
          KEVIHNQL.EKQKIAEEK.KE.EQKKSY...S.KEAEDNIREML.ARRAQ
Retrocopy KEVIHNQLSEKQKIAEEKSKESEQKKSYQQWSMKEAEDNIREMLPARRAQ

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	4.43 RPM
SRP021940_cerebellum	0.00 RPM	5.66 RPM
SRP021940_embryo	0.03 RPM	12.25 RPM
SRP021940_placental_villous	0.00 RPM	7.65 RPM
SRP021940_synovial_membrane	0.03 RPM	4.91 RPM
SRP021940_testis	0.00 RPM	31.84 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_53 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_53 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_53 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005742	8 retrocopies	retro_cfam_1742, retro_cfam_1893, retro_cfam_1943, retro_cfam_251, retro_cfam_276, retro_cfam_417, retro_cfam_788, retro_cfam_997,
Equus caballus	ENSECAG00000011843	1 retrocopy	retro_ecab_53 ,
Erinaceus europaeus	ENSEEUG00000005357	1 retrocopy	retro_eeur_537,
Echinops telfairi	ENSETEG00000019281	1 retrocopy	retro_etel_1629,
Felis catus	ENSFCAG00000001272	1 retrocopy	retro_fcat_1323,
Homo sapiens	ENSG00000113068	1 retrocopy	retro_hsap_2606,
Macropus eugenii	ENSMEUG00000002726	3 retrocopies	retro_meug_380, retro_meug_686, retro_meug_801,
Microcebus murinus	ENSMICG00000000349	1 retrocopy	retro_mmur_1121,
Oryctolagus cuniculus	ENSOCUG00000009432	4 retrocopies	retro_ocun_1049, retro_ocun_1885, retro_ocun_804, retro_ocun_999,
Otolemur garnettii	ENSOGAG00000003376	6 retrocopies	retro_ogar_1025, retro_ogar_1216, retro_ogar_1412, retro_ogar_2217, retro_ogar_3129, retro_ogar_89,
Pan troglodytes	ENSPTRG00000017310	1 retrocopy	retro_ptro_1757,
Rattus norvegicus	ENSRNOG00000018653	1 retrocopy	retro_rnor_985,