RetrogeneDB ID: retro_ecab_631

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 24:45036376..45036681(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSTD1
• Ensembl ID: ENSECAG00000000506
• Aliases: None
• Description: thiosulfate sulfurtransferase (rhodanese)-like domain containing 1 [Source:HGNC Symbol;Acc:35410]

Sequence

>retro_ecab_631
CCTGGGCTCTGTCTGCTCCCAGCTTCCAACTGGGCTAGCTCAGTATATGTGAGGTCTGGGACGCGGAGGCAGCTGGGACC
TTGCCCTGGGTGCTCAACATCCCGGTGTCTAAGTTAGAAAGCACCCTGCAGATGGAGGCAGCTGCTTCCCAGGCTTCGTA
CTCCACTGAGAAGCCAAAGCTGGAAGATGAGAATCTCGTTTTGTCAGACAGGGGCTTGCAGGCCACTCAGTGGGCCCAGG
GACCTGGATTCACAGGTGCTCGCAGCCACGCAGGGGCCTACAGAGAATGGTTCCAGTAGGAAGGT

Alignment

ORF - retro_ecab_631 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.68 %
• Parental protein coverage: 92.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PELRSLLALGRARLIDVRSR-EEAAAGTIPGALNIPVSELESALQMEPAAFQALYSTQKPKLEDENLIFF
          P.L..L.A...A....VRS.....AAGT.P..LNIPVS.LES.LQME.AA.QA.YST.KPKLEDENL...
Retrocopy PGLCLLPASNWASSVYVRSG<DAEAAGTLPWVLNIPVSKLESTLQMEAAASQASYSTEKPKLEDENLV--

Parental  CQMGKRGLQATQLAQGLGYTGARNYTGAYREWLQQEG
          .....RGLQATQ.AQG.G.TGAR...GAYREW.Q.EG
Retrocopy --LSDRGLQATQWAQGPGFTGARSHAGAYREWFQ*EG

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	0.57 RPM
SRP021940_embryo	0.00 RPM	1.41 RPM
SRP021940_placental_villous	0.00 RPM	3.90 RPM
SRP021940_synovial_membrane	0.00 RPM	1.76 RPM
SRP021940_testis	0.00 RPM	3.13 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_631 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_631 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_631 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000000506	1 retrocopy	retro_ecab_631 ,
Equus caballus	ENSECAG00000024361	1 retrocopy	retro_ecab_791,
Sarcophilus harrisii	ENSSHAG00000016118	1 retrocopy	retro_shar_517,