RetrogeneDB ID: retro_ecab_188

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:131472998..131473485(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUSP5
• Ensembl ID: ENSECAG00000013514
• Aliases: None
• Description: dual specificity phosphatase 5 [Source:HGNC Symbol;Acc:3071]

Sequence

>retro_ecab_188
CTTGCAGCTCAGCGGCCCCCGGGTCTGCCTCCGTCAGGCAGGATCTGAGCCTTTTGCTCGGAGTAACCCTAGTGCTGAGC
AGATGTACAACCCATTTCACAGAAGATTGAAACCTAGGGAGCCCTCTGCCACCGGTGTGGGAAACCAGTTCTCACCATCA
CGGACAGGCCGGCTCCAGTCAGGGCGGCCCAGTCGCAATCCTTCCTTTCCTCCACCTTGGAAGTGCCTCTCAGGCATGCA
AGTGCGACTTCCTCGCCATTCTGCACATCACGGCCCTGCTGAATGTCTCGTGGCACACCCCTGAGGCCTGCACGACCCAC
CTACACTGCAAATGGATCCCGTGGAAGACAGCCAGCCACTGACATTAGCTCCCAGGTTCAAGAAGCAATAGACTTCGCTG
ACTGTCAGGGAAAAGGGAGGCAAGGTCCTGGTCCACTGTGAGGCTGGGATCTCCCTTTTGCCCACCATCTTCATGGCTTA
CCTCATG

Alignment

ORF - retro_ecab_188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.5 %
• Parental protein coverage: 60.44 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LPARRPAVYFLKGGYETFYSEYPECCVDVKPISQEKIETERALISQCGKPVLNISYRPV-YDQGGPVEIL
          L.A.RP......G....F.SE.P.C..DV.PISQ.KIET..AL...CGKPVL.I..RP....QGGPV.IL
Retrocopy LAAQRPPGLPPSGRI*AFCSE*P*C*ADVQPISQ-KIET*GALCHRCGKPVLTITDRPA<SSQGGPVAIL

Parental  PFLYLGSAYHASECEFLANLHITALLNVSRRASEACTTRLHYKWI-PVEDSH-TADISSHFQEAIDFIDC
          PFL.LGSA..A..C.FLA.LHITALLNVS....EACTT.LH.KWI.PVEDS....DISS..QEAIDF.DC
Retrocopy PFLHLGSASQACKCDFLAILHITALLNVSWHTPEACTTHLHCKWI<PVEDSQ<ATDISSQVQEAIDFADC

Parental  VREKG-GKVLVHCEAGISRSPTICMAYLM
          ...KG.GKVLVHCEAGIS..PTI.MAYLM
Retrocopy -QGKG>GKVLVHCEAGISLLPTIFMAYLM

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	0.59 RPM
SRP021940_cerebellum	0.00 RPM	27.37 RPM
SRP021940_embryo	0.00 RPM	2.40 RPM
SRP021940_placental_villous	0.00 RPM	11.21 RPM
SRP021940_synovial_membrane	0.00 RPM	1.78 RPM
SRP021940_testis	0.00 RPM	22.32 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_188 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_188 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_188 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015745	1 retrocopy	retro_amel_1630,
Dasypus novemcinctus	ENSDNOG00000001858	1 retrocopy	retro_dnov_1665,
Equus caballus	ENSECAG00000013514	2 retrocopies	retro_ecab_188 , retro_ecab_612,