RetrogeneDB ID: retro_ppat_10

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS544890.1:1964379..1965144(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S1_315V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S70_177V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_10
ATGGGGTCAGTATTCATGCTATCTCTCTGGGGTCTGAGGTTGGTGGAGCCTCCTGACGTGGATGCCGAGTTCTGGAAAGG
ACTTGCTCCTGTAGCAATTTTGCATACAATTGGTTTTGTGGCGGCAACTGTGAGCTTGTCCAAGATTGCCGTATCGTCCC
ACCACATCATCAAGAGCTTAGAACCAGCCTGCAGTGTGATAATTTCGAAGCTGTTCATGGGGGAGGATTTCCCCTTGTCC
GTGTATTTTTCTATAGTGCCTATCATTGGGGGCTGCGGGTTAGCCGCTGCCTCAGAGGTGGATTTCAGCATGATAGGGTT
CTTGGGGGCCATGCTTTCCAACATTGCATTCGTGTTTCGCAACATTGCTTCGAAGAGGGGAATGAAGGCAGGCAAGAGTG
TGGGGGGCATGAATTACTATGCGTGCTTGAGCATGATGTCTTTCGTGCTCCTCTTGCCCTTTGCCTTCGTTGTTGAAGGT
CCTAAAGTTTGGGCGGCCGGATGGACCACGGCAATTCAGTCCGTTGGTAGACAGTTTCCTCTCTGGGTGGTGTTGCAATG
TTTGCTCTACCACTTGCACAACCAAGTGTCGTATATGTCCTTGGATCAAATCTCTCCCCTCTCCTTCAGCATCGGCAACA
CCATGAAGCGGGTGACAGTGATTGCTACCTCAATCCTCATTTTTCGCAACCCAGTCAGTCCCATCAATGCTATCGGTGCT
GCAATTGCGATTCTCGGAACGTTTTTTTACTCTCAGGCCAAGTGA

Alignment

ORF - retro_ppat_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.54 %
• Parental protein coverage: 60.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSAIMLISWALRIVPAPDVDAEFWKGLFPVALAHTIGHVAATVSMSKVAVSFTHIIKSAEPAFSVVIQRL
          GS..ML..W.LR.V..PDVDAEFWKGL.PVA..HTIG.VAATVS.SK.AVS..HIIKS.EPA.SV.I..L
Retrocopy GSVFMLSLWGLRLVEPPDVDAEFWKGLAPVAILHTIGFVAATVSLSKIAVSSHHIIKSLEPACSVIISKL

Parental  FLGENFPLPVYLSLLPIVGGCGLAAATELNFNMTGFVGAMVSNIAFVFRNIFSKKGMTTGKSVGGMNYYA
          F.GE.FPL.VY.S..PI.GGCGLAAA.E..F.M.GF.GAM.SNIAFVFRNI.SK.GM..GKSVGGMNYYA
Retrocopy FMGEDFPLSVYFSIVPIIGGCGLAAASEVDFSMIGFLGAMLSNIAFVFRNIASKRGMKAGKSVGGMNYYA

Parental  CLSMMSLVLLTPFAVAVEGPKAWMAGWDVANATVGPQIFWWVVAQSVFYHLYNQVSYMSLNEISPLTFSI
          CLSMMS.VLL.PFA..VEGPK.W.AGW..A...VG.Q...WVV.Q...YHL.NQVSYMSL..ISPL.FSI
Retrocopy CLSMMSFVLLLPFAFVVEGPKVWAAGWTTAIQSVGRQFPLWVVLQCLLYHLHNQVSYMSLDQISPLSFSI

Parental  GNTMKRVTVIVSSIIIFHTQVRPVNAVGAAIAILGTFLYSQAK
          GNTMKRVTVI..SI.IF...V.P.NA.GAAIAILGTF.YSQAK
Retrocopy GNTMKRVTVIATSILIFRNPVSPINAIGAAIAILGTFFYSQAK

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_10 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 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00062p00036220	1 retrocopy	retro_atri_14,
Brassica oleracea	Bo9g118840	1 retrocopy	retro_bole_30,
Musa acuminata	GSMUA_Achr7G03380_001	1 retrocopy	retro_macu_2,
Medicago truncatula	MTR_2g022700	1 retrocopy	retro_mtru_13,
Solanum tuberosum	PGSC0003DMG400025495	1 retrocopy	retro_stub_39,
Populus trichocarpa	POPTR_0001s44610	1 retrocopy	retro_ptri_19,
Physcomitrella patens	PP1S70_177V6	1 retrocopy	retro_ppat_10 ,
Prunus persica	PRUPE_ppa006608mg	1 retrocopy	retro_pper_3,
Arabidopsis lyrata	scaffold_802017.1	1 retrocopy	retro_alyr_24,
Solanum lycopersicum	Solyc07g064270.2	1 retrocopy	retro_slyc_32,
Theobroma cacao	TCM_030978	1 retrocopy	retro_tcac_18,
Vitis vinifera	VIT_10s0116g00760	1 retrocopy	retro_vvin_26,