RetrogeneDB ID: retro_ecab_856

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:30642752..30643066(-)
• Located in intron of: ENSECAG00000014292

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000012904
• Aliases: None
• Description: None

Sequence

>retro_ecab_856
GTAGAAAGCATTGGAAATAAAGCAGAGCATCGGGAAGAGAAAATTAGCAAGCTTGAAGATAGAAATCTAGAAATGTTTCA
GGTGGAAGAGGAGAGAGAACTTAGATTTTTTAAAAATGGAGAAATTCTATGAGAAATATCTTAGTTAGTAAAAGCAACAT
AAGGATAATGGGTATCCCAGAAGGAAAAAAGAGGGAGAAAGGAGCAGAGAACCTATTTAAAGAAATAATAGCTGAGAATT
TCTCAAACCTGGGGAAGAAACTGGATATACAAGTACATGAAGATAATAGAACACCTAATTATCTCAATGCAAAG

Alignment

ORF - retro_ecab_856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.56 %
• Parental protein coverage: 59.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VESINNRMDQAEETC-ELEDRTFEIIQ-SEENKEKRMK-KIKDSLLEKYLTIRKSNIRIIGIPEGEEKQK
          VESI.N.....EE....LEDR..E..Q..EE......K.K...S.........KSNIRI.GIPEG....K
Retrocopy VESIGNKAEHREEKISKLEDRNLEMFQVEEERELRFFK<KWRNSM--RNILVSKSNIRIMGIPEGKKREK

Parental  DTESLFKEIIAENFPNLGKKLDLQVHEANRTPNYIKAK
          ..E.LFKEIIAENF.NLGKKLD.QVHE.NRTPNY..AK
Retrocopy GAENLFKEIIAENFSNLGKKLDIQVHEDNRTPNYLNAK

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.03 RPM	0.00 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.06 RPM	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_856 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_856 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_856 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000012904	11 retrocopies	retro_ecab_1003, retro_ecab_1068, retro_ecab_1117, retro_ecab_155, retro_ecab_407, retro_ecab_695, retro_ecab_702, retro_ecab_768, retro_ecab_856 , retro_ecab_877, retro_ecab_906,