RetrogeneDB ID: retro_amel_1721

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194088.1:131157..131719(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1CC
• Ensembl ID: ENSAMEG00000013861
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, gamma isozyme [Source:HGNC Symbol;Acc:9283]

Sequence

>retro_amel_1721
TATGATGAATGAAAAATAAGATATAACATTAAACTATGGAAAACTTTCACAGGCTGCTTTAACTATTTACTGATGGCAGC
CATCTTGGATGAGAAGATATTCTGCTGTCATGGAGGTTTATCACCAGATCTTCAATCTATGGAGCAGATTCAGGGAATTA
TGAGACCAATTAACATACCAGATCAAGGTCTTCTTTGTGATCTCTTGTGGTCTGACCTTGATAAAGATGTCTTAGGCTGG
GGTGAAAATGACAGAGGCGTGTCCTTCACACTTAGCGTAGAAGTGGTTGCAAAATTTCTCCATAAGCAGGATTTGGATCT
TATATGTAGAGCCCATGAGGTGGTTGAAGATGGATATGAATCTTTTTGCGAAGAGGCAGTTGGTCACTCTGTTTTCCGCA
CCCAGCTATTGTGGAGAGTTTGACAATGCAGGTGCCATGATGAGTATGGATGAACCGCTAATACGTTCTTTTCGGATTTG
AAAGCCAGCAGAGAAAAAGAAGCTGAATGCCATGAGACCTGTAACACCTCCAAGAAGTATGATTGCAAAGAAAGCAAAGA
AA

Alignment

ORF - retro_amel_1721 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.51 %
• Parental protein coverage: 58.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLW
          YDE.K.RYNIKLWKTFT.CFN.L..AAI.DEKIFCCHGGLSPDLQSMEQI..IMRP...PDQGLLCDLLW
Retrocopy YDE*KIRYNIKLWKTFTGCFNYLLMAAILDEKIFCCHGGLSPDLQSMEQIQGIMRPINIPDQGLLCDLLW

Parental  SDLDKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYE-FFAKRQLVTLFSAPNYCGE
          SDLDKDVLGWGENDRGVSFT...EVVAKFLHK.DLDLICRAH.VVEDGYE..FAKRQLVTLFSAP.YCGE
Retrocopy SDLDKDVLGWGENDRGVSFTLSVEVVAKFLHKQDLDLICRAHEVVEDGYE>LFAKRQLVTLFSAPSYCGE

Parental  FDNAGAMMSVDETLMCSFQILKPAEKKKPNATRPVTPPRGMITKQAKK
          FDNAGAMMS.DE.L..SF.I.KPAEKKK.NA.RPVTPPR.MI.K.AKK
Retrocopy FDNAGAMMSMDEPLIRSFRI*KPAEKKKLNAMRPVTPPRSMIAKKAKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_1721 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1721 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,