RetrogeneDB ID: retro_ppat_24

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS544914.1:1841269..1841542(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S19_83V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_24
ATGAGAAAAGAAATTGAGAAGAAATTAGTATTAATTTGTGAGCATAGCTTTAAAGAAATTGTTACTCTACAATTGAGTCT
AAGTAAAGTTATTTTGAGTGATTTTCATTGAAAACTTGATCTACAATTAATTGTGACTACTAAAATATTGGATGCAATGA
GTGGCATAGATATCTTCCTATTTAGAAAGCTCTTACTATGGTTTTATCCTTATTTCATAAAGCTTGTCTGCAATGACCAA
ATGAAAGTGAAGAAGGTATTAGGAGAATTCTTT

Alignment

ORF - retro_ppat_24 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.65 %
• Parental protein coverage: 57.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LREEGERQLVSFCGHVLKEVAALQPGLSEAVLSDFHRALDLRSAVTAEVLKAMRDMDTLLFKKHLPEFYP
          .R.E.E..LV..C.H..KE...LQ..LS...LSDFH..LDL...VT...L.AM...D..LF.K.L..FYP
Retrocopy MRKEIEKKLVLICEHSFKEIVTLQLSLSKVILSDFH*KLDLQLIVTTKILDAMSGIDIFLFRKLLLWFYP

Parental  YFTKLICSDQMDVRKALGKLF
          YF.KL.C.DQM.V.K.LG..F
Retrocopy YFIKLVCNDQMKVKKVLGEFF

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_24 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	PP1S19_83V6	1 retrocopy	retro_ppat_24 ,