RetrogeneDB ID: retro_ppat_18

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS544945.1:1707595..1708294(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S56_237V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S283_25V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_18
ATGAGCAGCTCGGTAGTCGCCACCTCTGCTTCGGGTGCGGCTGGGGGTCACAAATCCAGGAGCGCTGGGAAAGGGAGAAG
GAGAAGAGCAGCAGCCGAGCAGCGAAGAATTGAGCAACAGAGGTGGGGAGGGTATGCACAGGACGATGAGGAGGATTTCA
GTGTGGTAGCTGCTCCTAGCCCTCCCACCTCACGACGCCGTTCGAGGCGGCGGGATTCAGTCGAAGATCGTCGGGAGGAT
TCCTTCGACTTGACAAGGAGTGATCATCTCGCAGCGTTCGATGACATTGGTGCGGACTTGGAACTCGCTCTGGCGTTGTC
TGTTTCATTTGCGGAGACGAACCCAGGATTCGTTCATCGGACTGACAGGTCCTTCGCACCGCTCATCGTTGACATGACGT
ACGAGAGCTTGGTGCAGCTGGAGGACGTGCGTTGCGTTGCATCCGCTGCAACGGTGGCCGCCTTGCCTGTGTGCTTGCCG
GAGAAAGTACCCGAAGCAGTCTCCGAGGCGTGTGTGATTTGCCAAGAGGAATTCGAGGACGCCGACTCGCAAGTGCAGCT
CCCATGCTCCCATGTCTTTCATCAGCCTTGCGGAGCTCACTGGCTACTCATTCACTCCAAGCTCTGCCCTATTTGCAAAC
ACGATGTTACAGAAAGTGCTGCAGCTGAGACAACATCACCATCATCTCAGTCTCGTTAA

Alignment

ORF - retro_ppat_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 85.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKAGKGRRRRQAAEQRRIEQQRWGQYVEDEDEDFSVVV-PSPSNLRRRARRSLRRNSARDDLEEYLNGLA
          R.AGKGRRRR.AAEQRRIEQQRWG.Y..D..EDFSVV..PSP...RRR.R...RR.S..D..E.....L.
Retrocopy RSAGKGRRRRAAAEQRRIEQQRWGGYAQDDEEDFSVVAAPSPPTSRRRSR---RRDSVEDRREDSFD-LT

Parental  NDDHITGVDG-DQDLDLALALSFSLAEQTSTTHVAQFGRSNPSSIADMSYENLVQLESVRCVASATLVAA
          ..DH....D....DL.LALALS.S.AE.T....V....RS....I.DM.YE.LVQLE.VRCVASA..VAA
Retrocopy RSDHLAAFDDIGADLELALALSVSFAE-TNPGFVHRTDRSFAPLIVDMTYESLVQLEDVRCVASAATVAA

Parental  LPVCCFKKEQAAASDEASEVCVICQGEYEHGDLQVNLPCHHGFHQACGAEWLLSYSKLCPVCKYDVTEVA
          LPVC...K...A.....SE.CVICQ.E.E..D.QV.LPC.H.FHQ.CGA.WLL..SKLCP.CK.DVTE.A
Retrocopy LPVCLPEKVPEAV----SEACVICQEEFEDADSQVQLPCSHVFHQPCGAHWLLIHSKLCPICKHDVTESA

Parental  TTEASS
          ..E..S
Retrocopy AAETTS

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_18 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	PP1S283_25V6	1 retrocopy	retro_ppat_18 ,