RetrogeneDB ID: retro_ppat_32

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS544998.1:1006767..1007324(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S25_8V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_32
TCTCGCCATGCGCTCTCACTCTAAATAAGTTTGAATAAGATTCAGATCTTCAAGGTAGGTAAAGTGGTTACGATGCAGTG
AAGAGAATCCAGTCAATTCGAGCACAAGTTGTGGATAATTAACTGGAATCAAAGGAGACTTCTGCTACTGCTACTTCGCA
AAAGACTACCCACTACTACTTGATTGCGAATGCAAAGTTTGTGTGGGATGACGAAGAGCATTTCCAAGAGCAAATGCAAG
AGAAGTCACGTATGTACGAAGAGCATAACAAGGAACAAGATTTCTAGATAGTGATTGAACCTAAGTTCCTCAACAGCAAC
CAGAGGTTGCTAATCAAGTGGGTAGGCTGGCTGTTGCACTCATGTCAATTGACAAAGTTGGATCACGATTCAAGAAGCTA
AGGTTGAACAAAGGGCTGAAGGGGAAACTTGCTCTGAATTCTCTAGATGCTGCATTGATAGGCAAGCTGACCACTGCCAC
ATTGAACGACCAACAAGGTGGATTGCCCTTATCCCAATTATGAGGGTGACTGGTGGACTCCGTTCCTGTACAAGAAG

Alignment

ORF - retro_ppat_32 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.2 %
• Parental protein coverage: 81.66 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SPRALTLNESVNKIQIFS-GRQSGYDGVRRIQPIRAQAVDNELESNGTSATATSQKTTFFYLVANAKFML
          S..AL.L..S.NKIQIF..GR.SGYD.V.RIQ.IRAQ.VDN.LES..TSATATSQKTT..YL.ANAKF..
Retrocopy SRHALSL*ISLNKIQIFK<GR*SGYDAVKRIQSIRAQVVDN*LESKETSATATSQKTTHYYLIANAKFVW

Parental  DDEEHFQEQMQEKLRMYGERNKEQDFWIVLEPEFLD-KQPEVAKRVGRPAVALVSTDKVWITFMKLRLDR
          DDEEHFQEQMQEK.RMY.E.NKEQDF.IV.EP.FL...QPEVA..VGR.AVAL.S.DKV...F.KLRL..
Retrocopy DDEEHFQEQMQEKSRMYEEHNKEQDF*IVIEPKFLN<QQPEVANQVGRLAVALMSIDKVGSRFKKLRLNK

Parental  VLKGELIVNSADEALTGKLTTVT-FERPAKWIA-PYPKYEGDWWTPFLYKK
          .LKG.L..NS.D.AL.GKLTT.T..ERP..WIA.PYP.YEGDWWTPFLYKK
Retrocopy GLKGKLALNSLDAALIGKLTTAT<IERPTRWIA<PYPNYEGDWWTPFLYKK

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_32 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	PP1S25_8V6	1 retrocopy	retro_ppat_32 ,