RetrogeneDB ID: retro_ecab_911

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:61772425..61773132(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP4C
• Ensembl ID: ENSECAG00000022179
• Aliases: None
• Description: protein phosphatase 4, catalytic subunit [Source:HGNC Symbol;Acc:9319]

Sequence

>retro_ecab_911
ATGGCAAAGATCAACTACATGGACAAGCAGATGGAGCAGCTGCTGTGTTGTGAGATCATCAAGGAGAGGGAAGTCAAGCC
CTGTGCGTTAAGGCCAGAGAGATCTTGGTAGAAGACAGCAGCATGCAGAGGCGTGGACTCTCCAGCCACAGTATGTGGCA
ACATCCATGGACAAGTCTATGACCTCTAGGAGCTGTTAGAGTAGGTGGCAACTTCCCTGAGACCAACTACCTCTTCACAG
GAGACATTGTGGATCGTGGTTACTATGGCATCATTGAACGTTCCTCTTTCTGTTGGACGTTGAGGTTTGTTATCCTTACC
GCATCACCCTGATCCCAGGCAACCATGAGAGCCACCAGACCACCCAGGTCTACAGCTCTTATGATGACTGCCCGCGTAAA
TATGGCTTGGTGACTATGTAGCAGTACTGCCCTGAGATCTTTGACTACCACAGCTTTGTTGGCCGTCATCTATGATAAGA
TCTTCTGCATGCACAGAGGCCTCTCCCCATCCATGTAGACCCTGGACCAGACCCAGAGGGTTGACCGAAAGTCAGGGGTG
CCTCATGACTGGCCCATGAGTGACCTGCTCAAGTCTGACCATGAAGATACAACAGGCTGGGATGCGAGCCCCCGTAGGGC
TGGCTACCTGTTTGGCAGTGAGTTGGTGGCCCAGTTCCATGCAGCCAATGGCATTGACATGACCTGC

Alignment

ORF - retro_ecab_911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.05 %
• Parental protein coverage: 76.55 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAEISDLDRQIEQLRRCELIKESEVK-ALCAKAREILVEESNVQR-VDSPVTVCGDIHGQFYDLKELF-R
          MA.I...D.Q.EQL..CE.IKE.EVK.ALC.KAREILVE.S..QR.VDSP.TVCG.IHGQ.YDL.EL..R
Retrocopy MAKINYMDKQMEQLLCCEIIKEREVK<ALCVKAREILVEDSSMQR>VDSPATVCGNIHGQVYDL*ELL<R

Parental  VGGDVPETNYLFMGDFVDRGFYS-VE-TFLLLLALKVRYPDRITLIRGNHESRQITQVYGFYDECLRKYG
          VGG..PETNYLF.GD.VDRG.Y...E.TFL.LL...V.YP.RITLI.GNHES.Q.TQVY..YD.C.RKYG
Retrocopy VGGNFPETNYLFTGDIVDRGYYGIIE<TFLFLLDVEVCYPYRITLIPGNHESHQTTQVYSSYDDCPRKYG

Parental  SVTVWRYCTEIFDYLS-LSAIIDGKIFCVHGGLSPSIQTLDQIRTIDRKQEVPHDGPMCDLLWSDPEDTT
          .VT...YC.EIFDY.S.L.A.I..KIFC.H.GLSPS..TLDQ....DRK..VPHD.PM.DLL.SD.EDTT
Retrocopy LVTM*QYCPEIFDYHS>LLAVIYDKIFCMHRGLSPSM*TLDQTQRVDRKSGVPHDWPMSDLLKSDHEDTT

Parental  GWGVSPRGAGYLFGSDVVAQFNAANDIDMIC
          GW..SPR.AGYLFGS..VAQF.AAN.IDM.C
Retrocopy GWDASPRRAGYLFGSELVAQFHAANGIDMTC

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	19.60 RPM
SRP021940_cerebellum	0.00 RPM	46.17 RPM
SRP021940_embryo	0.00 RPM	98.69 RPM
SRP021940_placental_villous	0.05 RPM	80.49 RPM
SRP021940_synovial_membrane	0.00 RPM	72.39 RPM
SRP021940_testis	0.00 RPM	199.82 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_911 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_911 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_911 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015223	1 retrocopy	retro_amel_286,
Canis familiaris	ENSCAFG00000017089	1 retrocopy	retro_cfam_16,
Ciona savignyi	ENSCSAVG00000004266	1 retrocopy	retro_csav_27,
Equus caballus	ENSECAG00000022179	1 retrocopy	retro_ecab_911 ,
Felis catus	ENSFCAG00000014171	1 retrocopy	retro_fcat_1043,
Macropus eugenii	ENSMEUG00000000397	5 retrocopies	retro_meug_1014, retro_meug_1188, retro_meug_1336, retro_meug_560, retro_meug_859,
Ornithorhynchus anatinus	ENSOANG00000008136	1 retrocopy	retro_oana_25,
Pan troglodytes	ENSPTRG00000007984	1 retrocopy	retro_ptro_28,
Tursiops truncatus	ENSTTRG00000005532	1 retrocopy	retro_ttru_1015,