RetrogeneDB ID: retro_ppat_12

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS544987.1:6683..7196(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S98_2V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S115_90V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_12
ATGGCGGGGTCAAAAGAAGCCGGCCAAACGATTTACGACTTCGTTGTGAAGGACATCGACGGCAGCGATGTCGAGTTGAG
CAAGTACAGGGGCAAGGTGCTGTTGATTGTTAACGTTGCGTCGAAGTGCGGGTTGACGACTACCAATTACAAAGAGCTCG
CGGACGTGTACACTAAATACAAGAGTCAGGATTTTGAGATTTTGGCATTCCCTTGCAATCAGTTCGGAGGACAGGAGCCT
GGGACGAATGAGCAGATCAAGGAATTTGCGTGCACGAGGTTTAAAGCCGAGTACCCTATTTTCGACAAGATCAATGTGAA
TGGTCCTCAGGAGGCACCACTCTACAAGTATTTGAAGTTGCAGAAAGGAGGCGGATGGTTGTTGGGGGATAGCATTAAGT
GGAATTTCGCCAAGTTTCTCGTGGACAAGAATGGGAACGTCGTGGACCGCTTTGCACCCACTACTCCTCCTTCAAAGATA
GAGAAGTCTATCGAAACTTATTTGAGCAGGTAG

Alignment

ORF - retro_ppat_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.64 %
• Parental protein coverage: 67.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAQVQSGSSIYDFVVKDIDGNDVELSKYKGKVLLIVNVASACGLTTTNYTELAGIYSKYKNQDFEILAFP
          A.....G..IYDFVVKDIDG.DVELSKY.GKVLLIVNVAS.CGLTTTNY.ELA..Y.KYK.QDFEILAFP
Retrocopy AGSKEAGQTIYDFVVKDIDGSDVELSKYRGKVLLIVNVASKCGLTTTNYKELADVYTKYKSQDFEILAFP

Parental  CNQFGGQEPGSNAQIKQFACTRFKAEFPIFDKVDVNGPQEAPVYKFLKSQKRGS-ILGDTIKWNFAKFLV
          CNQFGGQEPG.N.QIK.FACTRFKAE.PIFDK..VNGPQEAP.YK.LK.QK.G...LGD.IKWNFAKFLV
Retrocopy CNQFGGQEPGTNEQIKEFACTRFKAEYPIFDKINVNGPQEAPLYKYLKLQKGGGWLLGDSIKWNFAKFLV

Parental  DKNGNVVDRYAPTTPPSKIENDIQKYL
          DKNGNVVDR.APTTPPSKIE..I..YL
Retrocopy DKNGNVVDRFAPTTPPSKIEKSIETYL

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_12 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Physcomitrella patens	PP1S115_90V6	2 retrocopies	retro_ppat_12 , retro_ppat_3,
Triticum aestivum	Traes_6DL_F16253948	1 retrocopy	retro_taes_2,