RetrogeneDB ID: retro_ecab_305

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 14:1085820..1086820(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R2A
• Ensembl ID: ENSECAG00000019205
• Aliases: None
• Description: protein phosphatase 2, regulatory subunit B, alpha [Source:HGNC Symbol;Acc:9304]

Sequence

>retro_ecab_305
ACCAATGATAAAACAATCAAAGTATGGAAAATCAGTGAAAGGGACAAAAGACCAGAAGTGCGTAAGTTGAAAGAGGAAGG
CAGAAGATAGAGACCCTACCACAGTCACTGTACTATGAACGCCAGTCTTGAGGCCCATGGATCTAATGGCTGAGGCCAGT
GCATGAATAATACTTGCCAATGCTCACACATATCACATCAACTCAACTTCTATTAATAGTGATTACGAAATCTATTTATC
TGCAGGTGATTTGCGGATTAATTTTTGGCATCTGGAAATTACAGGCAGGAGTTCTAATGTTGTGGACATGGAGCCTGCCA
ATATGGAAGAGCTAAGAGAGGTGACTGCAGCAGCAGAATTCCACGCAAACAGCCGTAACACATCAGTACACAGCAGCAGT
GAAGGAACTATTCGGTTATGTGACATGAGGGCATCTGCCCTCTGTGACAGGCACTCTAAACTGTTTGAAGAACCTGAAGA
TCCCAGTAACAGGTCTTTTTTTCCTGAAATCATCTCCTCTATTTCTGATGTAAAATTCAGCCATTGTGGTCAATATGTGA
TGACTAGAGACTATTTCTCAGTCAAAACTTGGGACTTAAATATGGAAAACAGGCCTTTGGGAACATACAAGGTGCATGAA
TACGTCAGAAGTAAACTTTGTTCACTGTATGAAAATGACTGCATATTTGACAAATCCGAATGTTGTTGGAATGGATCTGA
CAGTGTTGTCATGACTGGATCTTGCAATAATTTTGTCAGAATGTTTGACAGGAACACAAAGCGAGACATAACCCTAGAAG
CATCACGGAAAAACAACAAACCCCGCATGGTTCTGAAGCCACACAAAGTCTGTGCAAGTGGCAACGGAAAGAAGGATGAA
ATAAGTGTCGACAGCCTAGACTTCAGCAAGAAAATACTTCATACGGCCTGGCAGCCCAAGGAAAATATCACTGCTGTAGC
TACTACAAACGATCTGGATATATTTCAAGACAAGGTGAAT

Alignment

ORF - retro_ecab_305 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.28 %
• Parental protein coverage: 79.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TNDKTIKLWKISERDKRPEGYNLKEEDGRY-RDPTTVTTLRVPVFRPMDLMVEASPRRIFANAHTYHINS
          TNDKTIK.WKISERDKRPE...LKEE.GR..RDPTTVT.L..PV.RPMDLM.EAS...I.ANAHTYHINS
Retrocopy TNDKTIKVWKISERDKRPEVRKLKEE-GRR>RDPTTVTVL*TPVLRPMDLMAEASA*IILANAHTYHINS

Parental  ISINSDYETYLSADDLRINLWHLEITDRSFNIVDIKPANMEELTEVITAAEFHPNSCNTFVYSSSKGTIR
          .SINSDYE.YLSA.DLRIN.WHLEIT.RS.N.VD..PANMEEL.EV..AAEFH.NS.NT.V.SSS.GTIR
Retrocopy TSINSDYEIYLSAGDLRINFWHLEITGRSSNVVDMEPANMEELREVTAAAEFHANSRNTSVHSSSEGTIR

Parental  LCDMRASALCDRHSKLFEEPEDPSNRSFFSEIISSISDVKFSHSGRYMMTRDYLSVKIWDLNMENRPVET
          LCDMRASALCDRHSKLFEEPEDPSNRSFF.EIISSISDVKFSH.G.Y.MTRDY.SVK.WDLNMENRP..T
Retrocopy LCDMRASALCDRHSKLFEEPEDPSNRSFFPEIISSISDVKFSHCGQYVMTRDYFSVKTWDLNMENRPLGT

Parental  YQVHEYLRSKLCSLYENDCIFDKFECCWNGSDSVVMTGSYNNFFRMFDRNTKRDITLEASRENNKPRTVL
          Y.VHEY.RSKLCSLYENDCIFDK.ECCWNGSDSVVMTGS.NNF.RMFDRNTKRDITLEASR.NNKPR.VL
Retrocopy YKVHEYVRSKLCSLYENDCIFDKSECCWNGSDSVVMTGSCNNFVRMFDRNTKRDITLEASRKNNKPRMVL

Parental  KPRKVCASGKRKKDEISVDSLDFNKKILHTAWHPKENIIAVATTNNLYIFQDKVN
          KP.KVCASG..KKDEISVDSLDF.KKILHTAW.PKENI.AVATTN.L.IFQDKVN
Retrocopy KPHKVCASGNGKKDEISVDSLDFSKKILHTAWQPKENITAVATTNDLDIFQDKVN

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	15.58 RPM
SRP021940_cerebellum	0.00 RPM	24.20 RPM
SRP021940_embryo	0.03 RPM	26.75 RPM
SRP021940_placental_villous	0.00 RPM	24.92 RPM
SRP021940_synovial_membrane	0.00 RPM	16.28 RPM
SRP021940_testis	0.06 RPM	22.06 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_305 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_305 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_305 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	ENSECAG00000019205	1 retrocopy	retro_ecab_305 ,
Monodelphis domestica	ENSMODG00000016691	1 retrocopy	retro_mdom_529,
Mus musculus	ENSMUSG00000022052	1 retrocopy	retro_mmus_874,