RetrogeneDB ID: retro_ecab_234

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:25355750..25356356(-)
• Located in intron of: ENSECAG00000011892

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A36
• Ensembl ID: ENSECAG00000010094
• Aliases: None
• Description: solute carrier family 25 (pyrimidine nucleotide carrier ), member 36 [Source:HGNC Symbol;Acc:25554]

Sequence

>retro_ecab_234
GCCATTCGCACACATCCACTGGAAGGTGTAATAACACATCTGTGGTCTTCTGTTGTGATGCTTTCTATCTCTGAAGTTTA
GCTGAACATCATAGCTAGAGCTAGTGTCAACTGGACCAGCCTCTCCTGGATCTTTCCACTGCCTGAAGGTGACCTTGGGA
AAAGCAGTCTTCTTCCTTGTTTAAGAGGATTAGGCTCCAGTTTATTGGGGATTGCCTCTTCCAGAACATTCTTTGCCGCT
TATTCAAACTGCAAGGAAAAGTTGAATGGTGTATTTGATCCTGATTCTGCCCCATGCATGGTTTTGGCTGCAGTGGCTTA
TTTTACTACAATCACAGCAACCAATCCCATTTGGCTACTAAAGAGTTGGTTACAGCCTGATGCAAGGAACCATGGGAAAA
AGCAAATGGGTGCTTTTGAATGTGCTCATGAAGTGTATTAGACAGATGACCCAAGAGGACTTTATAGGGGCATGTCTGCT
TCATATGGTAGCATATCAGGGACTGTTATTCATTTGGTTATTTGTGAAAATATTAAGCAGAAACTACTGGAATAAAAGAT
TACTTCGATGATGGAAGATGATAAGGAGTCTGTGAAAGAAGCATCA

Alignment

ORF - retro_ecab_234 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.22 %
• Parental protein coverage: 68.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AILTCPLEVVKTRLQSSSVTLYISEVQLSTMAGASVNRV-VSPGPLHCLKVIL-EKEGPRSLF-RGLGPN
          AI.T.PLE.V.T.L.SS.V.L.ISEV.L...A.ASVN....SPG..HCLKV.L.EK....SLF.RGLG..
Retrocopy AIRTHPLEGVITHLWSSVVMLSISEV*LNIIARASVNWT>ASPGSFHCLKVTL>EKQSS-SLF>RGLGSS

Parental  LVGVAPSRAIYFAAYSNCKEKLNGVFDPDSTQVHMISAAMAGFTAITATNPIWLIKTRLQLDARNRGEKR
          L.G.A.SR...FAAYSNCKEKLNGVFDPDS....M..AA.A.FT.ITATNPIWL.K..LQ.DARN.G.K.
Retrocopy LLGIASSRT-FFAAYSNCKEKLNGVFDPDSAPC-MVLAAVAYFTTITATNPIWLLKSWLQPDARNHGKKQ

Parental  MGAFECVRKVYQTDGLRGFYRGMSASYAGISETVIHFVIYESIKQKLLDYKAPSTVENDEESVKEAS
          MGAFEC...VY.TD..RG.YRGMSASY..IS.TVIH.VI.E.IKQKLL..K..S..E.D.ESVKEAS
Retrocopy MGAFECAHEVY*TDDPRGLYRGMSASYGSISGTVIHLVICENIKQKLLE*KITSMMEDDKESVKEAS

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	19.95 RPM
SRP021940_cerebellum	0.05 RPM	17.14 RPM
SRP021940_embryo	0.08 RPM	17.03 RPM
SRP021940_placental_villous	0.00 RPM	21.79 RPM
SRP021940_synovial_membrane	0.00 RPM	11.56 RPM
SRP021940_testis	0.00 RPM	12.15 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_234 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_234 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_234 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000010094	1 retrocopy	retro_ecab_234 ,
Felis catus	ENSFCAG00000027489	1 retrocopy	retro_fcat_1680,
Macaca mulatta	ENSMMUG00000022153	1 retrocopy	retro_mmul_2243,
Mus musculus	ENSMUSG00000032449	1 retrocopy	retro_mmus_2007,
Oryctolagus cuniculus	ENSOCUG00000002085	1 retrocopy	retro_ocun_361,
Pteropus vampyrus	ENSPVAG00000007958	1 retrocopy	retro_pvam_719,
Sus scrofa	ENSSSCG00000011669	1 retrocopy	retro_sscr_871,
Tupaia belangeri	ENSTBEG00000001759	1 retrocopy	retro_tbel_3349,
Tursiops truncatus	ENSTTRG00000003288	2 retrocopies	retro_ttru_1146, retro_ttru_947,
Vicugna pacos	ENSVPAG00000008292	1 retrocopy	retro_vpac_603,