RetrogeneDB ID: retro_ppat_35

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS545063.1:162841..163265(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S64_196V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_35
AGTGGCTGGAAGAGCCCTCCCCATCCTGACCATGAATATCGCTCAATTCTCATCAAGGAATCGGCCTAAAGTGTCAGCGA
GGTGGAAGCGCCTTGTGAGCTCTTCAGCAACTCTGTTATCGACGATGGCATTACACACAAGGAGGAGTTCAAATTGGCGT
TGTTCGGGGACAATAACAGGAAGAGTTCGTTCGCAGATCGGATATTTTACTCATTCGACCGAAACTAAATGGTGTGATCA
ATGTTGGCGTATCTGTGCGCTTTTAGAGCGTGTTCCATACAAAGGCTCGTGCTGAAGACCAAAGTAAATTTACTTTCAAG
GGTACAATCTACATCAAAGATGTTCCACAGAACGTTAAGAGGTGAAGGAAATGCTGGATGCAACCTCGTGCAAATTCACC
CTAGATTTGGCAACAGACATGATA

Alignment

ORF - retro_ppat_35 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.18 %
• Parental protein coverage: 59.83 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSWRRPP--GYEDPSVLAKETVFSVDEVEALYELFMKISHSVIDDGLIHKEEFQLALFGDSERKNLFADR
          S.W..PP....E..S.L.KE...SV.EVEA..ELF...S.SVIDDG..HKEEF.LALFGD..RK..FADR
Retrocopy SGWKSPPHPDHEYRSILIKESA*SVSEVEAPCELF---SNSVIDDGITHKEEFKLALFGDNNRKSSFADR

Parental  VFYLFDR-KQNGVIEFGEFVRSLSVFHPMARAEDKIQFAFK-LYDLHQTGYIEREEVKEMLDAILCESTL
          .FY.FDR.K.NGVI..G..VR..SVFH..ARAED...F.FK..Y.LHQ....ER.EVKEMLDA..C..TL
Retrocopy IFYSFDR<KLNGVINVGVSVRF*SVFHTKARAEDQSKFTFK<GYNLHQRCSTER*EVKEMLDATSCKFTL

Parental  DLSPEVI
          DL....I
Retrocopy DLATDMI

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_35 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	PP1S64_196V6	1 retrocopy	retro_ppat_35 ,