RetrogeneDB ID: retro_ppat_38

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS545147.1:324151..324458(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S257_105V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_38
TGCAATCAATCTTTCAAAATGGCAATGCCAATGAGCTTAGAAAGTCTAGAGTAGAAGAGGCCATTGAGACAGTCTACTAT
ATTTGGATCACTCTTCCCTCCAAAATGTGAAGAACCTCGAGAAAGTGTGCGCCAACTTAATCAAGGATGCTGAGGACAGG
AGGCTCAAGGTGTAGGGACCAGCGCATATGTCTATCAAAGTACTCACAACCACCGTCTGCAGAACTCAAATGCCAATCTC
ACCAAGATCAGTACAAAAAAGAAAACTAAGAATTCAACAAATTCATCACATAATTGCTCTCCACACA

Alignment

ORF - retro_ppat_38 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.48 %
• Parental protein coverage: 51.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CDQSLRMAMPM-KPGKVGVEEAVETVHRIRITLSSK-NVKNLEKVCADLIKGAKDKRLKVKGPVRMPTKV
          C.QS..MAMPM....K..VEEA.ETV..I.ITL.SK.NVKNLEKVCA.LIK.A.D.RLKV.GP..M..KV
Retrocopy CNQSFKMAMPM<ELRKSRVEEAIETVYYIWITLPSK<NVKNLEKVCANLIKDAEDRRLKV*GPAHMSIKV

Parental  LHITTRKSPCGEGTNTWDRFELRVHK--RVIDLHS
          L..T.................LR.......I.LH.
Retrocopy LTTTVCRTQMPISPRSVQKRKLRIQQIHHIIALHT

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_38 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica rapa	Bra028263	1 retrocopy	retro_brap_31,
Solanum tuberosum	PGSC0003DMG400000965	3 retrocopies	retro_stub_104, retro_stub_108, retro_stub_65,
Solanum tuberosum	PGSC0003DMG400003291	1 retrocopy	retro_stub_105,
Physcomitrella patens	PP1S257_105V6	1 retrocopy	retro_ppat_38 ,