RetrogeneDB ID: retro_ecab_898

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:30215060..30215483(-)
• Located in intron of: ENSECAG00000018636

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM242
• Ensembl ID: ENSECAG00000016335
• Aliases: None
• Description: transmembrane protein 242 [Source:HGNC Symbol;Acc:17206]

Sequence

>retro_ecab_898
ATGGAGGCGGCGGGTGCTGGGAGTGGGGAGCCGGCCCCGCGCCTAGAGGCTCCGGGGTCCGCCGAGGACCGGCTTTTCCT
GGTGAAAGGTGGAATTTTCCTTGGTACTGTTGCTGCAGCTGGAATGCTGGCTGGATTTGTAACAACGTTGTCATTGGCTA
AAAAGAAAAGCCCTGAATGGTTCAATAAGGGAAGCGTGGCCACGGCCGCCTTACCGGAGAGTGGCTCTTCCCTTGCCTTG
CGAGCCCTGGGCTGGGGCTCCCTTTACGCGTGGTGTGGGGTTGGCGTGATCAGCTTCGCAGTCTGGAAAGCCTTAGGAGT
TCACAGTATGAAAGACTTTCGAAATAAAATGCAATCAATATTTCCAGCAATTCCCAAGAACGCCGAATCGGCTGTTGAGT
GGGAGGAAGCATTGAAATCCAAA

Alignment

ORF - retro_ecab_898 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEAAGAGSGEPAPRLEAPGSAEDRLFLVKGGIFLGTVAAAGMLAGFVTTLSLAKKKSPEWFNKGSVATAA
          MEAAGAGSGEPAPRLEAPGSAEDRLFLVKGGIFLGTVAAAGMLAGFVTTLSLAKKKSPEWFNKGSVATAA
Retrocopy MEAAGAGSGEPAPRLEAPGSAEDRLFLVKGGIFLGTVAAAGMLAGFVTTLSLAKKKSPEWFNKGSVATAA

Parental  LPESGSSLALRALGWGSLYAWCGVGVISFAVWKALGVHSMKDFRNKMQSIFPAIPKNAESAVEWEEALKS
          LPESGSSLALRALGWGSLYAWCGVGVISFAVWKALGVHSMKDFRNKMQSIFPAIPKNAESAVEWEEALKS
Retrocopy LPESGSSLALRALGWGSLYAWCGVGVISFAVWKALGVHSMKDFRNKMQSIFPAIPKNAESAVEWEEALKS

Parental  K
          K
Retrocopy K

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	0.10 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.06 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_898 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_898 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_898 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009699	1 retrocopy	retro_amel_1551,
Cavia porcellus	ENSCPOG00000022213	1 retrocopy	retro_cpor_160,
Equus caballus	ENSECAG00000016335	1 retrocopy	retro_ecab_898 ,
Homo sapiens	ENSG00000215712	1 retrocopy	retro_hsap_1016,
Macaca mulatta	ENSMMUG00000011814	1 retrocopy	retro_mmul_812,
Nomascus leucogenys	ENSNLEG00000010676	1 retrocopy	retro_nleu_222,
Otolemur garnettii	ENSOGAG00000007646	1 retrocopy	retro_ogar_946,
Pongo abelii	ENSPPYG00000017271	1 retrocopy	retro_pabe_853,
Pan troglodytes	ENSPTRG00000018735	1 retrocopy	retro_ptro_747,