RetrogeneDB ID: retro_ecab_382

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 16:45067065..45067437(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM134
• Ensembl ID: ENSECAG00000016857
• Aliases: None
• Description: transmembrane protein 134 [Source:HGNC Symbol;Acc:26142]

Sequence

>retro_ecab_382
CCCCAGTTCAGCACTGATGACACTTTTGAGCTGTCCCTGGAGAATGTGGGCCCTGGGTTCAATGGGGTTGCCCTCTTCTG
GCCACTGCACTTCTAGCGCAGGCCTAATTTGAGATGGCCGATGAGGACAAGCAGTCCTGGCTGTGTTACGAGAACCTGGA
GAATGATGAGAGTAGATCCCAGGCCTCTCTGGAATCAGATGGGGCCGTTCAACCCAACATTCCAGCCCAACATGCATCTG
CATCTGTCAATAGTTATTTGGCACTATCAGCAAGAGTACCCAGTGCTCCTACAATGCCTGCTGCAGCTGGATTCAACACC
CTTTGATGCAGAAGAACTGCCAGTGCTGGCCTCCTTCCTGCTCCTGCTGCTG

Alignment

ORF - retro_ecab_382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.77 %
• Parental protein coverage: 65.46 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PQFSIDDAFELSLEDAGPGPESSGVTRFGPLHFERR-ARFEVAEEDKQSRLRYQNLENDEDGAQPSSEPD
          PQFS.DD.FELSLE..GPG....GV..F.PLHF.RR.A.FE.A.EDKQS.L.Y.NLENDE...Q.S.E.D
Retrocopy PQFSTDDTFELSLENVGPG--FNGVALFWPLHF*RR<A*FEMADEDKQSWLCYENLENDESRSQASLESD

Parental  GGV-STRDSVQTSIGSSQWSFSTISNSTQRSYRACCSWTQHPLIQKNRR-VVLASFLLLL
          G.V.ST..S..T.I...Q..F.TIS.STQ.SY.ACCSW.QHPL.QKN...V.....LLLL
Retrocopy GAV<STQHSSPTCICICQ*LFGTISKSTQCSYNACCSWIQHPLMQKNCQ<VLASFLLLLL

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	0.12 RPM	10.09 RPM
SRP021940_cerebellum	0.00 RPM	5.97 RPM
SRP021940_embryo	0.00 RPM	8.41 RPM
SRP021940_placental_villous	0.00 RPM	10.01 RPM
SRP021940_synovial_membrane	0.00 RPM	8.21 RPM
SRP021940_testis	0.00 RPM	26.79 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_382 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_382 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_382 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	ENSECAG00000016857	1 retrocopy	retro_ecab_382 ,
Myotis lucifugus	ENSMLUG00000005143	1 retrocopy	retro_mluc_1560,
Rattus norvegicus	ENSRNOG00000022153	1 retrocopy	retro_rnor_732,