RetrogeneDB ID: retro_ppat_4

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS544916.1:1699012..1700035(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S27_234V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S12_249V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_4
ATGGCTGAAAATCTGGCGTCCTCCATGGCTAACCTGCGCACGCCCAGCTCTGGGGGGATGATTGTTTCTTTCGGGGAGCT
CCTCATCGACTTCGTGTCAACAGTTGCCGGTGTATCGTTGGCTGATGCGCCAGCTTTTAAGAAAGCCCCCGGGGGAGCCC
CTGCCAATGTCGCCGTGGGAGTTAGCAGGCTTGGCGGTCGCTCAGCCTTCATTGGGAAAGTAGGCGACGATGAGTTCGGG
CGCATGCTGGCGGACGTGCTGGAGAAGAATGGTGTGAACGTCAAGGGACTGCGCTTCGACATCGTCGCGCGCACCGCACT
CGCTTTCGTTGCGCTGAAAGAATGCGGGGAACGGGAATTCATGTTCTTCCGAAACCCAAGCGCGGACATGCTTATGGTCC
CCTCAGATCTCGACGAGGGATTGATCCGAAACGCCGAGGTGTTCCACTACGGGTCGATCTCGTTGATATCCGAGCCGTCG
CGCTCGACGCATCTAGCGGCCATGAAGCTGGCGAAGCAGAGTGGAGCACTGATGTCTTATGACCCCAACTTGCGGTTGGC
GCTCTGGCCATCCCCCGAGGCTGCTCGGAGGGAGATTTTGAACATCTGGAATGAGGCCGACATTATCAAAGTTTCGGACG
AGGAGGTGAAATTCCTGACCAACGGAGGGGATGACAAGTTGGACGAGGTGGTGCTCGGGACTCTGTGGCACGACAAGCTG
AAGCTCCTGCTGGTCACTGATGGCCCCGAAGGGTGTCGGTACTACACCCCCACGTTCAAGGGCCACGTCGACTCCTTCAA
GGTGGCGGCAATCGACACTACGGGAGCGGGCGACGCTTTCGTCGCGGGATTGTTACAAACCCTTGCGCAAAACAAGAGCA
TCTTGTCCGACGAGCCGGCGTTGCGAGCTGCATTGCGGTTTGCGTGTGCGTGCGGGGCGATCACGACCACCGAGCGGGGC
GCAATCCCCGCCATGCCGGACTTGGCCGCGGTGACGAGGTTTATGGGTACCGTGGCCGCTTGA

Alignment

ORF - retro_ppat_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.91 %
• Parental protein coverage: 98.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MENADMNSAGGLIVAYGELLIDFVPTVAGVSLAEAPAFKKAPGGAPANVAVCVSRLGGNAAFIGKVGDDE
          M.N....S.GG.IV..GELLIDFV.TVAGVSLA.APAFKKAPGGAPANVAV.VSRLGG..AFIGKVGDDE
Retrocopy MANLRTPSSGGMIVSFGELLIDFVSTVAGVSLADAPAFKKAPGGAPANVAVGVSRLGGRSAFIGKVGDDE

Parental  FGHMLADVLMSNKVDVEGLRFDSNARTALAFVTLRSDGEREFMFFRNPSADMLMVPSELDEDLIRRSSTF
          FG.MLADVL..N.V.V.GLRFD..ARTALAFV.L...GEREFMFFRNPSADMLMVPS.LDE.LIR....F
Retrocopy FGRMLADVLEKNGVNVKGLRFDIVARTALAFVALKECGEREFMFFRNPSADMLMVPSDLDEGLIRNAEVF

Parental  HYGSISLISEPSRSTQCAAMKLARESGSLMSYDVNLRLALWPSPEAAHEGIMSIWDQADLIKVSDEEVKF
          HYGSISLISEPSRST..AAMKLA..SG.LMSYD.NLRLALWPSPEAA...I..IW..AD.IKVSDEEVKF
Retrocopy HYGSISLISEPSRSTHLAAMKLAKQSGALMSYDPNLRLALWPSPEAARREILNIWNEADIIKVSDEEVKF

Parental  LTKGGNDKLDEVVL-SLWRPNLKLLLVTDGPDGCRYYTRGFKGRVMSFKVDAVDTTGAGDAFVGGLLHIL
          LT.GG.DKLDEVVL..LW...LKLLLVTDGP.GCRYYT..FKG.V.SFKV.A.DTTGAGDAFV.GLL..L
Retrocopy LTNGGDDKLDEVVLGTLWHDKLKLLLVTDGPEGCRYYTPTFKGHVDSFKVAAIDTTGAGDAFVAGLLQTL

Parental  AKNKGLLDDEIALRSALQFACACGAITTTGKGAIPSMPDRKAVLKLIG
          A.NK..L.DE.ALR.AL.FACACGAITTT..GAIP.MPD..AV....G
Retrocopy AQNKSILSDEPALRAALRFACACGAITTTERGAIPAMPDLAAVTRFMG

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_4 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	PP1S12_249V6	1 retrocopy	retro_ppat_4 ,