RetrogeneDB ID: retro_ecab_169

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:66681644..66682014(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLRX2
• Ensembl ID: ENSECAG00000015376
• Aliases: None
• Description: glutaredoxin 2 [Source:HGNC Symbol;Acc:16065]

Sequence

>retro_ecab_169
ATGGAGAACGGCACATCACCATCTTTGGGGAAGTCAGCAATTGCTCCTGTGAATCGGATCCAAGTAACGACTTCTGATAA
TTGTGTGGTAATTTTCTCAAAAATATCTCATTCTTACTGTACAATGGCAAAAAAAACTTTTCCATTACACAAATGTTAAT
TATAAAGTGGTAGAATTGGACATACTTGAATATGGAAGCCAGTTTCAAGATGTTCTTTACAAAATGACTGGTGAAAGAAC
TGTGCCAAGAATATTTGTCAATGTAACTTTTATTGGAGTTGCAACTGACACTGATAAGCTCCGCAAAGAAGGGAAATTGT
GTCCACTAGTTCATCAGTGTTCTTTCTTTTAAAAAAGTAAGAAGAATTTT

Alignment

ORF - retro_ecab_169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.77 %
• Parental protein coverage: 99.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGNITSSSLGNSATAPVNQIQETISDNCVVIFSKTSCSYCTMAKK-LFHDINVNYKVVELDMLEYGSQFQ
          M.N.TS.SLG.SA.APVN.IQ.T.SDNCVVIFSK.S.SYCTM....LFH..NVNYKVVELD.LEYGSQFQ
Retrocopy MENGTSPSLGKSAIAPVNRIQVTTSDNCVVIFSKISHSYCTMXXX>LFHYTNVNYKVVELDILEYGSQFQ

Parental  DALYKMTGDRTVPRIFVNGTFIGGATDTHRLHKEGKLLPLVQQCYLKKSEREDF
          D.LYKMTG.RTVPRIFVN.TFIG.ATDT..L.KEGKL.PLV.QC.........F
Retrocopy DVLYKMTGERTVPRIFVNVTFIGVATDTDKLRKEGKLCPLVHQCSFF*KSKKNF

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	3.07 RPM
SRP021940_cerebellum	0.05 RPM	16.15 RPM
SRP021940_embryo	0.00 RPM	4.25 RPM
SRP021940_placental_villous	0.00 RPM	6.50 RPM
SRP021940_synovial_membrane	0.00 RPM	3.87 RPM
SRP021940_testis	0.00 RPM	12.40 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_169 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_169 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_169 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015972	1 retrocopy	retro_btau_543,
Choloepus hoffmanni	ENSCHOG00000007274	1 retrocopy	retro_chof_2375,
Callithrix jacchus	ENSCJAG00000008562	1 retrocopy	retro_cjac_643,
Equus caballus	ENSECAG00000015376	1 retrocopy	retro_ecab_169 ,
Felis catus	ENSFCAG00000025580	1 retrocopy	retro_fcat_733,
Myotis lucifugus	ENSMLUG00000015734	1 retrocopy	retro_mluc_1008,
Tupaia belangeri	ENSTBEG00000011216	1 retrocopy	retro_tbel_1638,
Drosophila melanogaster	FBgn0036820	1 retrocopy	retro_dmel_4,