RetrogeneDB ID: retro_ppat_1

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS544922.1:1028651..1030523(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S33_172V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S381_15V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_1
ATGGGAGTTCTAGGTCTTCTCTTCTGCCCTCGCCCGCCGCATCGCTCTTCCCTCGCCGCCTTCGTCCGCTATTTGCCCGC
CCTCTCGCAGCCCGCGCCCGCAACCGCATCCGCGACCGCCATCGCTTGCCCTTCCTTTCCACCCTCTCTCCGCCCTGTGC
TTGATAATGGCCTGATCTGCGGTCCTGCAGTGGTTGCGAACGTCCTCTCGGGCCGACGTACATTGTTGGGAGGCAGGAAA
GGGAGCGCTACCTTGGACCTTACGAGGACTAGAGGCGCATCCACGTTGGCGAAGGCCATGGTGTCTGAAGTCGGGTTGAC
GAAGACCGCGACGCCCGTGGTTCCTGAGATTGCTGTGAAGAGCTCCGGGCTAGAGGTGGCGAACTGGGGTGGCGATCTCT
TGGTATTGGGCGTGTTTGAGGGTTGCGCCACTAAGAGCGAGGATGGGAAATTCTCGAATTCCGAATTGGAGGCTTTGGAC
GCGCTTGTTGGTGGGCTGTTGAGCGTGGTTGCCTCTGAGGAGGAGTTCACCGGAAAGAGCGGGCAGTCGACGTTCCATCG
CGTTATTGGATGCGGGTTCAAGCGCGTGGGTTTAGTTGGGCTCGGGAAGTCGGATAAGGTTGAGACGAATAGCAAAGTGT
GGCGGAGTTTGGGCGAGAGCATTGCGACCGCCGCCGCTGCTGCCCATTCTGGTTCAGCTGCAGTCGTAGTTGTGGATGCC
GGGAGTCTGTCCGATGCGGTGAAGAAGACCGCTGCGTCGATGATCGCCACTGGCGTGATGTTGGGATCTTTCGAGGACAT
GAGATTTAAGTCCGACTTCAAGAAGCCGCAGTTGAAGGACTTGGAGCTGTTCGGCTTAGGGTCGGATGCCGACCTCGAAG
CGCAGCTAGCCCAAACCATTCAGCAATGTACAGGCGTCATCCTCGCAAAGCAACTGGTGAATGCTCCGCCTAATGTTCTT
CTTCCTAGCGTCATGGCGTGCGAGGCCGAGGCCATCGCTGCCGCACATGGCGATGTCATGACATGTAAAATCCTCGAGAA
GGAGGAGTGCGAAAAACTTGGGATGGGTGCTTACCTTGGTGTATCCGCTGCATCCACCAATCCTCCGAAATTCATCCACT
TGTGTTATTCGCCTTTGGGAGCCGTGACCACGAAATTGGCGATTGTGGGTAAGGGTTTGACATTCGACAGTGGAGGCTAC
AACTTGAAGACTGGCCCTGGCTGTATGATCGAGCTTATGAAATTCGATATGGGAGGTGCGGCAGCTGTGCTTGGAGCAGC
GAAAGCCATAGCCGCCATAAAGCCTGAGGGTGTCGAAGTCAACTTCGTCGTCGCAGCCTGTGAGAACATGATCAGTGGGG
GAGGCATGAGACCCGGCGACATTTTGACAGCCTCCAATGGAAAGACTATTGAAGTGAACAACACTGACGCCGAAGGCCGA
CTTACCTTGGCAGACGCCCTCGTGTACGCGAACAACCTCAAGGTGGACAAAATCGTGGATCTCGCAACCCTAACCGGGGC
CTGCATCATTGCTCTTGGTAACGACATCGGAGGGATGTTTACCCCCAACGATGAGCTTGCGCAGGAGCTCACAGAGGCCT
CCAAGAAAGGAGGTGAGAAGTTTTGGAGGATGCCCATGGAGGACAGCTACTTCGAAATGTTGAAATCGAACATTGCAGAC
ATGGTCAACACCGGCGGTCGTGCGGGCGGGTCCATCATAGCTTCCTTGTTTTTGAAACAGTTTGTGGATGAGAATATTCC
ATGGGCGCACTTGGACATTGCAGGACCTGTCTGGAAGGACAAGACCGGAGGGACGGGTTTTGCAGTGGCCACTCTTGTGG
AGTGGGTCGTGAAGCACAAGAAGCTGTCATAG

Alignment

ORF - retro_ppat_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.32 %
• Parental protein coverage: 58.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPSKLTQVAVMSLGTGSDRDEALRRAVCITAGVIVAKQLVAAPANVLTPGALADAAVSIAMAHSEVLTCT
          K...L.......LG...D....L........GVI.AKQLV.AP.NVL.P...A..A..IA.AH..V.TC.
Retrocopy KKPQLKDLELFGLGSDADLEAQLAQTIQQCTGVILAKQLVNAPPNVLLPSVMACEAEAIAAAHGDVMTCK

Parental  ILEKVDCEALGMGAFLGVANGSDQPPKFIHLKYCPPDGVVYKRVAIVGKGICFDSGGYNIKTGANCAVEL
          ILEK..CE.LGMGA.LGV...S..PPKFIHL.Y.P..G.V....AIVGKG..FDSGGYN.KTG..C..EL
Retrocopy ILEKEECEKLGMGAYLGVSAASTNPPKFIHLCYSPL-GAVTTKLAIVGKGLTFDSGGYNLKTGPGCMIEL

Parental  MKFDMGGAGAALGAASAIGALKPKGVEVHFISAACENMISGKGMRPGDIVTAMNGITIEVNNTDAEGRLT
          MKFDMGGA.A.LGAA.AI.A.KP.GVEV.F..AACENMISG.GMRPGDI.TA.NG.TIEVNNTDAEGRLT
Retrocopy MKFDMGGAAAVLGAAKAIAAIKPEGVEVNFVVAACENMISGGGMRPGDILTASNGKTIEVNNTDAEGRLT

Parental  LADSLVYACRLRVDAIVDLATLTGACVVALGHEVGGFFTPSATMAQQLETAAQIAGEKIWRMPLVEQYKQ
          LAD.LVYA..L.VD.IVDLATLTGAC..ALG...GG.FTP....AQ.L..A....GEK.WRMP....Y..
Retrocopy LADALVYANNLKVDKIVDLATLTGACIIALGNDIGGMFTPNDELAQELTEASKKGGEKFWRMPMEDSYFE

Parental  TLESPIADLVNTSGRDGGSIKAALFLKEFVDPGMEWAHLDIAGPVWNRKTGTATGYPVRTLVKWI
          .L.S.IAD.VNT.GR.GGSI.A.LFLK.FVD....WAHLDIAGPVW..KTG..TG..V.TLV.W.
Retrocopy MLKSNIADMVNTGGRAGGSIIASLFLKQFVDENIPWAHLDIAGPVWKDKTG-GTGFAVATLVEWV

Legend:

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

Expression

RNA-Seq

Physcomitrella patens was not studied using RNA-Seq expression data.

ChIP-Seq

Physcomitrella patens was not studied using ChIP-Seq data.

EST

Physcomitrella patens was not studied using EST data.

TSS

Physcomitrella patens was not studied using FANTOM5 data.

Lab

retro_ppat_1 was not experimentally validated.

Homology

Retrocopy orthology:

Physcomitrella patens 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Physcomitrella patens	PP1S381_15V6	1 retrocopy	retro_ppat_1 ,