RetrogeneDB ID: retro_ecab_69

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:10802865..10803486(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000002027
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000021789
• Aliases: None
• Description: None

Sequence

>retro_ecab_69
ATGGACTCCGCAGGTCCAGATACCAACCTGACTTCTCCTAACAAAGGTCTGCTGTCCGACTCCATGACAGATGTCCCTGT
CGACACGGCGGTGGCTGCCCAGACTCCTGCTGTGGAGGGTCTGTCGGAGGCTGAGGAGGAGGAGCTCAGGGCTGAGCTCG
CAAAGGTGGAAGAAGAAATTGTCACTCTGCGCCGGGTTCTGGCAGCGAAGGAGAGACATTGCGGAGAGCTCAAAAGGAAG
CTGGGCCTCTCTGCCTTGGAGGGCCTGAAGCAGAACCTGTCCAGGAGCTGGCATGATGTGCAGGTCTTTAACGCCTATAT
GAAAACTTCTGAGAAACCTGGAGAGTGGAATGAGAAAGTGACCCAGTCTGACCTCTACAAGAAGACTCAGGAGACTCTCT
CTCAGGCGGGACAGAAGACTTCAGCTGCCCTGTCTACCATGGGCTCTGCCATCAGCAGGAAGCTAGGAGGCATGAGGAAC
TCTGCAACCTTCAAGTCGTTTGAAGACCGAGTTGGGACCATAAAGTCTAAGGTTGTGGGTGGCAGAGAGAATGGCAGTGA
CAACCTTCCCTCCCCGACTGGGAGTGGAGACAAGCCCCTGCCAGATCACACGCCTTTCTAA

Alignment

ORF - retro_ecab_69 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.22 %
• Parental protein coverage: 72.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDSAGQDINLNSPNKGLLSDSMTDVPVDTAVAAQTPAVEGLSEAEEEELRAELAKVEEEIVTLRQVLAAK
          MDSAG.D.NL.SPNKGLLSDSMTDVPVDTAVAAQTPAVEGLSEAEEEELRAELAKVEEEIVTLR.VLAAK
Retrocopy MDSAGPDTNLTSPNKGLLSDSMTDVPVDTAVAAQTPAVEGLSEAEEEELRAELAKVEEEIVTLRRVLAAK

Parental  ERHCGELKRKLGLSALEGLKQNLSRSWHDVQVSNAYMKTSEKLGEWNEKVTQSDLYKKTQETLSQAGQKT
          ERHCGELKRKLGLSALEGLKQNLSRSWHDVQV.NAYMKTSEK.GEWNEKVTQSDLYKKTQETLSQAGQKT
Retrocopy ERHCGELKRKLGLSALEGLKQNLSRSWHDVQVFNAYMKTSEKPGEWNEKVTQSDLYKKTQETLSQAGQKT

Parental  SAALSTMGSAISRKLGDMRARPFSHSF
          SAALSTMGSAISRKLG.MR......SF
Retrocopy SAALSTMGSAISRKLGGMRNSATFKSF

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	0.35 RPM	25.38 RPM
SRP021940_cerebellum	0.16 RPM	19.73 RPM
SRP021940_embryo	0.13 RPM	34.83 RPM
SRP021940_placental_villous	0.53 RPM	25.60 RPM
SRP021940_synovial_membrane	0.58 RPM	34.89 RPM
SRP021940_testis	0.26 RPM	31.97 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_69 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_69 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_69 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003663	1 retrocopy	retro_acar_36,
Dasypus novemcinctus	ENSDNOG00000014930	1 retrocopy	retro_dnov_1582,
Equus caballus	ENSECAG00000021789	1 retrocopy	retro_ecab_69 ,
Otolemur garnettii	ENSOGAG00000013689	1 retrocopy	retro_ogar_3142,