RetrogeneDB ID: retro_ppat_7

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS545200.1:98451..98991(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S311_14V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S17_153V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_7
ATGGTTTGCATACGGCAAGCAACCGTAGACGACCTGCTGGCAATGCAGAGTTGCAATTTGATGTGTTTGCCGGAGAATTA
CCAAATGAAGTATTACTTCTATCATATTTTGTCGTGGCCGCAGCTGCTCTATGTTGCAGAGGATTACAACAAGAAGATAG
TCGGATACGTGCTGGCCAAGATGGAGGAGGACGCGGAGGAATGCCACGGGCATATCACTTCGCTGGCTGTGTTGCGGACA
CACCGTAAGTTAGGGCTGGCTACGAAGCTCATGACTGCGGCGCAGCAGTGCATGCAGGAGGTGTTTGGGGCGGAGTATGT
GTCGTTGCATGTGCGCAAGAGCAACCGTGCCGCATTTCACTTGTACACGGAGACGTTGGGGTATAGGATTACGGATGTTG
AGGCCAAGTATTATGCGGATGGGGAGGATGCCTATGACATGCGGAAGACCTTGAAACCTGGCAAGGCTGATAATTCGTTC
TCAGGTGTGGACTCAAAGGTGGATTCCAAGTCTGACTTAAAGGCTGATTCAAAGTCTTAG

Alignment

ORF - retro_ppat_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.42 %
• Parental protein coverage: 80.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVCVRQATFDDLLDIQNINAVCLPENYRLNFYINHILTWPRLLHVAED-NRKIVGYVLGSLDEELSYCHG
          MVC.RQAT.DDLL..Q..N..CLPENY....Y..HIL.WP.LL.VAED.N.KIVGYVL....E....CHG
Retrocopy MVCIRQATVDDLLAMQSCNLMCLPENYQMKYYFYHILSWPQLLYVAEDYNKKIVGYVLAKMEEDAEECHG

Parental  QIASLAVLRTHRNRGYATKLMRAAEQAMRDVYGAGSVSLHVRKMNNAAFCLYSKTLGYKVKIFETAYYRD
          .I.SLAVLRTHR..G.ATKLM.AA.Q.M..V.GA..VSLHVRK.N.AAF.LY..TLGY.....E..YY.D
Retrocopy HITSLAVLRTHRKLGLATKLMTAAQQCMQEVFGAEYVSLHVRKSNRAAFHLYTETLGYRITDVEAKYYAD

Parental  GADAYEMIK
          G.DAY.M.K
Retrocopy GEDAYDMRK

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_7 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	PP1S17_153V6	1 retrocopy	retro_ppat_7 ,