RetrogeneDB ID: retro_ecab_853

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:25975861..25976740(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1CC
• Ensembl ID: ENSECAG00000017228
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, gamma isozyme [Source:HGNC Symbol;Acc:9283]

Sequence

>retro_ecab_853
TCCAAGCCTGGCAAGAATGTCCAGCTACAGGAGAATGAAATCAGAGGACTCTGCTTAAAGTCTCGAGAGATCTTTCTCAG
CCAGCCTATCCTACTAGAACTTGAAGCGCCACTCAAAATATGTGGTGATATCCAGGGGCAATACTATGATTTGCTTCAAC
TTCTCAAGTACGGTGGTTTCCCACCCAGAAAGCAACTACTTGTTTCTTGGGGACTATGTGGACAGCGGGAAGCAGTCGTC
AGAGACTAGTGCCTCTTAATGGCTTCCAAAATCAAACATCCTGAGAATTTTTTTCTTCTCAGAGAAAACCACGAATGTGC
CAGCATCAATAGAATTTATGGATCTTATGATAAATGTAAAAGAAGATATAACATTAAACTGTGGAAAACTTTCACAGGCT
GCTTTAATTATTTACCAATAGCAGTCATCGTGGATGAGAAAATATTCTGCTGTCATGGAGGTTTATCACCAGATCTTCCA
ACTGTGGAGGAGATTCGGTGAATTATGTGACCAACTGATGTACTGGATCAAGGTCTTCTTTGCAATCTTTTGTGGTCTGA
CCCCAATAAAGATGTCTTAGGCTGGGGTGAAAATGACAGAGCAGTGTCCTTCACATTTGATGCAGAAGTAGTTGCAAAAT
TTCTCCTTAAGCATGATTTGGATCTTATATGTAGAGCCCATCAGGTGGCTGAAGATGGATATGAATTTTTTGCAAAGAGG
CAGTTGGTCACTCTGTTTTCTGCACCCAGTTATTATGGCAAGTTTGATAACGCAGGTGCCATGATGAATGTGGACAAAAC
ACTAATGTGCTCTTTTCAGGTATTAAAGCCTGCAGAGAAAAAGAAGCTGAATGCCACGAGACCCGTAACACCTCCAAGG

Alignment

ORF - retro_ecab_853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.12 %
• Parental protein coverage: 96.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFP-PESNYLFL
          SKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDI.GQYYDLL.L..YGGFP.PESNYLFL
Retrocopy SKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIQGQYYDLLQLLKYGGFP>PESNYLFL

Parental  GDYVDRGKQSLETI-CLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCL
          GDYVD.GKQS.ET..CLL.A.KIK.PENFFLLR.NHECASINRIYG.YD.CKRRYNIKLWKTFT.CFN.L
Retrocopy GDYVDSGKQSSETS<CLLMASKIKHPENFFLLRENHECASINRIYGSYDKCKRRYNIKLWKTFTGCFNYL

Parental  PIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVLGWGENDRGVSFTFGA
          PIA.IVDEKIFCCHGGLSPDL...E.IR.IM.PTDV.DQGLLC.LLWSDP.KDVLGWGENDR.VSFTF.A
Retrocopy PIAVIVDEKIFCCHGGLSPDLPTVEEIR*IM*PTDVLDQGLLCNLLWSDPNKDVLGWGENDRAVSFTFDA

Parental  EVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPA
          EVVAKFL.KHDLDLICRAHQV.EDGYEFFAKRQLVTLFSAP.Y.G.FDNAGAMM.VD.TLMCSFQ.LKPA
Retrocopy EVVAKFLLKHDLDLICRAHQVAEDGYEFFAKRQLVTLFSAPSYYGKFDNAGAMMNVDKTLMCSFQVLKPA

Parental  EKKKPNATRPVTPPR
          EKKK.NATRPVTPPR
Retrocopy EKKKLNATRPVTPPR

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	0.24 RPM	28.10 RPM
SRP021940_cerebellum	0.16 RPM	96.07 RPM
SRP021940_embryo	0.95 RPM	53.93 RPM
SRP021940_placental_villous	0.00 RPM	59.13 RPM
SRP021940_synovial_membrane	0.41 RPM	36.87 RPM
SRP021940_testis	1.15 RPM	153.53 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_853 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_853 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_853 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013861	1 retrocopy	retro_amel_1721,
Bos taurus	ENSBTAG00000011198	2 retrocopies	retro_btau_6, retro_btau_960,
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Callithrix jacchus	ENSCJAG00000009147	7 retrocopies	retro_cjac_1062, retro_cjac_1165, retro_cjac_1408, retro_cjac_2304, retro_cjac_2535, retro_cjac_3288, retro_cjac_822,
Equus caballus	ENSECAG00000017228	1 retrocopy	retro_ecab_853 ,
Echinops telfairi	ENSETEG00000015721	1 retrocopy	retro_etel_2065,
Myotis lucifugus	ENSMLUG00000010661	2 retrocopies	retro_mluc_15, retro_mluc_2217,
Mus musculus	ENSMUSG00000004455	5 retrocopies	retro_mmus_2274, retro_mmus_2968, retro_mmus_3418, retro_mmus_851, retro_mmus_925,
Sorex araneus	ENSSARG00000000571	1 retrocopy	retro_sara_700,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,