RetrogeneDB ID: retro_ecab_572

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:8846585..8847196(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: REXO2
• Ensembl ID: ENSECAG00000005988
• Aliases: None
• Description: RNA exonuclease 2 [Source:HGNC Symbol;Acc:17851]

Sequence

>retro_ecab_572
ATGGTGACGGGAGAGAGCATGGCTCAGCAGATGGTCTGAGTGGACCCAGTGATGATAGGATTGGACATTGTGGAGGACCA
GATAATTGAGATGGCCTGTCTGATAACTGACTCTGATCTCAACATTTTAGCTGAAGGTCCTACACTGATTATAAAACAGC
CAGACAAATTACTGGACATCATGTCAGATTAGCGCAAGAAGCATCATGTAAGTCTGGTCTAACCAAAGCAGTGAGGGAGA
GTACAATGACATTGTAGCAGGCAGACTATGAATTTCTCTCCTTTGTACAATAGCAGGCACTTCTGGTGCTCTGTCCACTT
GCAGGAAATTCAATTCATGCAGATAAGAAGTTTCTTGAAAAATACATGCTCCAGTTTGTAAAACATCTTCGTTAGAGAAT
AAGTGATGTGAGCACTGTTAAAGAACCGTGCAGATGCTGGTATCCAGAAGAATATGAATTTGCACCAAAGAAGGCCGCTT
CTCACAGGGCTCTTGATGACATTAGTGAAAGCACCAAAGAACTTTGGTTTTACTGAAATAACATCTTCACGAAAATAACA
GATGAAAAGAGGAAAATTACAGAAAATTGGGAAAATAAGAAGACTGTGAGT

Alignment

ORF - retro_ecab_572 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.64 %
• Parental protein coverage: 86.5 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAGESMAQRMVWVDLEMTGLDIEKDQIIEMACLITDSDLNILAEGPNLIIKQPDELLDSMSDWCKEHHG
          M..GESMAQ.MV.VD..M.GLDI..DQIIEMACLITDSDLNILAEGP.LIIKQPD.LLD.MSD..K.HH.
Retrocopy MVTGESMAQQMV*VDPVMIGLDIVEDQIIEMACLITDSDLNILAEGPTLIIKQPDKLLDIMSD*RKKHHV

Parental  -KSGLTKAVKESTMTLQQAEYEFLSFVRQQTPPGLCPLAGNSVHADKKFLDKYMPQFMKHLHYRIIDVST
          .KSGLTKAV.ESTMTL.QA.YEFLSFV..Q....LCPLAGNS.HADKKFL.KYM.QF.KHL..RI.DVST
Retrocopy <KSGLTKAVRESTMTL*QADYEFLSFVQ*QALLVLCPLAGNSIHADKKFLEKYMLQFVKHLR*RISDVST

Parental  VKELCRRWYPEEYEFAPKKAASHRALDDISESIKELQFYRNNIFKKKTDEKKRKIIENGENEKTVS
          VKE.CR.WYPEEYEFAPKKAASHRALDDISES.KEL.FY.NNIF.K.TDE.KRKI.EN.EN.KTVS
Retrocopy VKEPCRCWYPEEYEFAPKKAASHRALDDISESTKELWFY*NNIFTKITDE-KRKITENWENKKTVS

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	19.77 RPM
SRP021940_cerebellum	0.00 RPM	13.40 RPM
SRP021940_embryo	0.00 RPM	7.36 RPM
SRP021940_placental_villous	0.00 RPM	76.79 RPM
SRP021940_synovial_membrane	0.00 RPM	39.94 RPM
SRP021940_testis	0.00 RPM	30.44 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_572 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_572 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_572 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013497	1 retrocopy	retro_chof_40,
Callithrix jacchus	ENSCJAG00000012434	1 retrocopy	retro_cjac_1493,
Dipodomys ordii	ENSDORG00000011255	1 retrocopy	retro_dord_374,
Equus caballus	ENSECAG00000005988	1 retrocopy	retro_ecab_572 ,
Myotis lucifugus	ENSMLUG00000009030	1 retrocopy	retro_mluc_1861,
Monodelphis domestica	ENSMODG00000013913	1 retrocopy	retro_mdom_1575,
Tarsius syrichta	ENSTSYG00000002237	1 retrocopy	retro_tsyr_1177,