RetrogeneDB ID: retro_ppat_26

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS544927.1:1893938..1894705(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S32_278V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_26
GGTTTTAGGATTAACAATACTTTATATGGATCCAAGTAAAAAATGCTTGATAAAATGAGTGTAGAATATACCAACAACCT
CACAAAGACATTGAAAGATAATAACCTCAAGTATACATGGGGAATGTGACTGTGAAGTTGGAAATTTTATATAGATTTTT
GTTTGAACATTGAGAAGAATGTGCTAATTGCCTTTCAAACTTGTAAGCAATTTTAAAAATAGAAGTTGTGGCTTATAAAT
GAAATCATCCACAATTCAAGTATAAATTAAAAGTTAGTTCATAAGGCTACATACAAACTATCAATTAATAAGAAAAAATC
AGAATCTTTGTTGTAGACCAAGGTAATATTATTCTACTAAAATTTGATGCTTTTTTTTAAGAGATGCAGATTCTTGAGAA
CAAGAAAGCACTAATTGTAGATACAACATACTTGTAGTTGTCTAACATTTGGAATAGAATAGAGAAGCACAAAAAAATCA
TGTACATATCTATAATGCATAGAAAATATATCCTTAAGTTGATAGTTTCTACTACTTCTTTTATTAGAAAATAAACCATA
GAAAAGAATATAAAAAAGACAACTTATATTTACAAATACATTTTGGGTAGAATGCTAAATGTCTCCAATAGAAAGAAAGA
GGAATTTCTTCAAATAGTTCAAGTATGCCAATTTAAAGGGCTTTAACTCAAATATAGATTTGAAAAAATTAGAATTGCTA
ATCAAAAAAGAATATTGAAGAAGAAGACGAAAGGGATTAGAAAGCTA

Alignment

ORF - retro_ppat_26 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.38 %
• Parental protein coverage: 53.32 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GEKYNKTGYGYKKEMLDKMSVEYTSNLVKTLKENNFEYTWG-NVTVKLANSY-GFCWGVERAVQIAYEAR
          G...N.T.YG.K..MLDKMSVEYT.NL.KTLK.NN..YTWG.NVTVKL...Y..FC...E..V.IA....
Retrocopy GFRINNTLYGSK*KMLDKMSVEYTNNLTKTLKDNNLKYTWG<NVTVKLEILY>DFCLNIEKNVLIAFQTC

Parental  KQFPEQKLWLTNEIIHNPTVNQKMTDMGISELSVTENGKD-FSVVDQGDVVILPAFGASVQEMQILDDKK
          KQF...KLWL.NEIIHN...N.K........LS..........VVDQG....L..F.....EMQIL..KK
Retrocopy KQF*K*KLWLINEIIHNSSIN*KLVHKATYKLSINKKKSE<IFVVDQGNIILLK-FDXXXXEMQILENKK

Parental  VQIVDTTCPWVSKVWNTVEKHKKGTYTSVIHGKYAHEETVATASFAGKYIIAKNIKEATYICDYILGGKL
          ..IVDTT....S..WN..EKH....Y.S..H.KY.....V.T.SF..K..I.KNIK..TYI..YILG..L
Retrocopy ALIVDTTYL*LSNIWNRIEKHXXXMYISIMHRKYILKLIVSTTSFIRK*TIEKNIKKTTYIYKYILGRML

Parental  DGSSGTKEDFLEK-FKYAISKGFDPDTDL-EKVGIANQTTMLKGETEEIGKL
          ..S...KE.FL...FKYA..KGF....DL.EK..IANQ...LK..T..I.KL
Retrocopy NVSNRKKEEFLQI>FKYANLKGFNSNIDL<EKIRIANQKRILKKKTKGIRKL

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_26 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	PP1S32_278V6	1 retrocopy	retro_ppat_26 ,