RetrogeneDB ID: retro_ecab_290

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 13:42390704..42391237(-)
• Located in intron of: ENSECAG00000000792

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACER3
• Ensembl ID: ENSECAG00000026842
• Aliases: None
• Description: alkaline ceramidase 3 [Source:HGNC Symbol;Acc:16066]

Sequence

>retro_ecab_290
CTACTGGATGAACTCCCAATGATGTACAGCTGTTGTGTATTTGTGTACTGCATGTTTGAACGTTTCAAGATGAAGAACTC
AGTAAACTATCATCTGCGTTTTACCTTAATTCTCTTCAGTTTAAAGTCACCACAGTTTGCCTTAAGGTAAAGGAGCCTGT
ATTTCAGCAGGTCATGCATGGAATGTTGGTCTTCACATTAGCACTTCCATCTGTTTATATTGTTACATAGGTTTATCCAT
GGCTAAGAGGACTCGGTTTTACATCCTTGGGTCTATTTTTATTGGGATCTTTATTATAGAACACAGATAACATCTTTTGC
GAATCACTAAGGAACTTTCGAAAGAAGGTGCCACCTATCATAGGTGTTACCACACAATTTCAGGCATGGTGGCATATTTT
AACTGGCCTTGGTTCTTATCTTCACATCCTTTTCAATTTATATACAAGAACACTTTACCTGAGATACAGGCCAAAAGTGA
AGTTTCTCTTGGGAATCTGGCCAGTGATCCTGTTTGAGCCTCTCAGGAAGCAC

Alignment

ORF - retro_ecab_290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.68 %
• Parental protein coverage: 76.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLDELPMIYSCCIFVYCMFECFKMKNSVNYHLLFTLVLFSLI-VTTVYLKVKEPIFQQVMYGMLVFTLVL
          LLDELPM.YSCC.FVYCMFE.FKMKNSVNYHL.FTL.LFSL..VTTV.LKVKEP.FQQVM.GMLVFTL.L
Retrocopy LLDELPMMYSCCVFVYCMFERFKMKNSVNYHLRFTLILFSLK<VTTVCLKVKEPVFQQVMHGMLVFTLAL

Parental  RSVYIVTWVYPWLRGLGYTSLGLFLLGFLLWNIDNIFCESLRNFRKKVPPIIGVTTQFHAWWHILTGLGS
          .SVYIVT.VYPWLRGLG.TSLGLFLLG.LL.N.DNIFCESLRNFRKKVPPIIGVTTQF.AWWHILTGLGS
Retrocopy PSVYIVT*VYPWLRGLGFTSLGLFLLGSLL*NTDNIFCESLRNFRKKVPPIIGVTTQFQAWWHILTGLGS

Parental  YLHILFR-EIETFSLNLFPK-QFLFGIWPVILFEPLRKH
          YLHILF.....T..L...PK..FL.GIWPVILFEPLRKH
Retrocopy YLHILFNLYTRTLYLRYRPKVKFLLGIWPVILFEPLRKH

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	0.41 RPM	2.83 RPM
SRP021940_cerebellum	0.52 RPM	3.22 RPM
SRP021940_embryo	0.28 RPM	2.61 RPM
SRP021940_placental_villous	0.87 RPM	4.86 RPM
SRP021940_synovial_membrane	0.69 RPM	5.33 RPM
SRP021940_testis	1.47 RPM	10.10 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_290 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_290 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000026842	1 retrocopy	retro_ecab_290 ,
Sus scrofa	ENSSSCG00000014873	1 retrocopy	retro_sscr_601,