RetrogeneDB ID: retro_ppat_2

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS545066.1:130434..132261(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S177_28V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S51_338V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_2
ATGGAACAATCCTTTCACCCCACAATGGCTGCGAAGCACAGAGTCATGCTGCTCGCGAGCGCCATGATTCTTCTGGCGGC
GTTGTTTTCCCCCGTCGAAGCCTCCCACAAGGATTGGCACCAGCTCGGCGTCGAGAGCATCAAGAGCTCCTCTTCTGCGA
CCCACGTCTATCAGCCTTACCGCACGGCGTACCACTTCCAGCCGCGCAAGAATTGGATGAACGACCCCAACGGGCCGCTC
TACTACAAGGGATGGTATCACTTCTTCTACCAGTACAACCGCGACGCAGCCGTGTGGGGAAACATCACATGGGGGCACGC
CGTGTCGAGGGACATGGTGCACTGGCGGACACTTCACACCGCGCTCAAGGGCGACAAGTGGTATGACATGAAGGGTGTGT
GGTCCGGATCCGCCACTTTCCTGGACAATGGAGTCCCCGTGCTGCTCTACACGGGCTGGGCGATCAATGGCACAGACCAG
TCGTCCATTCGTGGTCAGACGCAAGCAATGGCGGTGCCGGAAGATCCGTCGGATCCCCTGCTGCGTGAGTGGGACAAGTC
GCCACACAACCCGATTGCCTTGGCACCACCCGGATTCAACGACAGCATGTTCCGTGACCCGACCGAGGCGTGGAAGGGAT
ACGATGGGGTGTGGCGTATGTTGGTGGGGGCAGTCAAAGGGACCGATCAGTCAATCGGAACTGCGCTTCTGTACAAGAGT
ACGGATTTCAACAAGTGGAATTTCACTGGGGAGATCCAGTCGGTGGCCGGCACGGGAATGTGGGAGTGTCCCGACATTTA
CCCTGTCCATGTTAAGGAGAAGACGGGGTTGAGGCTGTCCGCGAGGGGGCCACATGTGAAGCATGTCCTTAAGGTGAGCT
TGGATAGGAACAAGCACGATTATTACTCCGTGGGTACTTACGACGAGAAGACGGACTTATACACCCCGGATGATACCAAG
TTGGACACGGGATTGGGACTACGGTACGACTACGGGAAGTTTTACGCGTCGAAGACTTTCTTCGATCAGAATAAGAACCG
GCGGGTATTGTGGGGTTGGGCAAATGAGTCTAGCAGTGTGCAGGATGATATAGAGAAGGGGTGGTCTTCGGTGCAGTGCT
TGCCGAGGCATATCTGGTTGGATGAAGAATCGAGTGCGAATTTGGTGCAGTGGCCGATTGAGGAAGTCGATAAGCTTCGG
CGGAATGAAATGACGGAGAAGAATGTGGAGGTTGGGGTGGGTAAGGTTGTGCCCGTCAAGGCGGCGAAGGGCGCGCAGCT
TGACATTGTGGTAGATTTCGCCCTGCCTGAGAAGAGCGAGGGATTGGAACAAAACCCAAACCTGCTGGCGGAGATGGGAC
ATTTGACATGCAGCGATTTGGTAACCAAGGGGTCGAATGCAGCTGGACCACATAGCTTCGGCCCGTTTGGTGTTCACGTG
CTTGCGACCGGTGATCTCCAGGAGCGGACGTCCATCTTCTTCCATTTGATACACGATGGCAAGCACCAGAACTGGAAGAC
GCTCTTCTGCGGCGACCAGAGCCAATCCTCCTTGCAGCAGGACGTCGACAAGACGGTGTATGGGTCCTACGTGCGCGTGG
ATGACAGCGACAAGGTGCTGTCCGTGCGCATTCTCGTCGACCACTCCATCGTGGAGAGCTTCGCCCAAGGCGGCCGCACG
GTAATGACATCCAGAGTATACCCGGAGCTGGCGGTGAAAGACGCCGCTCACGTGTTTTTGTTCAACAACGGTACTGAGCC
CGTGACAGTGAAATCGGTATCCACCTGGGAGATGAAGAGTGTCAACATCAAGTTTTACAAACCTTGA

Alignment

ORF - retro_ppat_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.48 %
• Parental protein coverage: 77.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TGNSFENKQVQARADPEDPSDPLLRKWVKAPYNPIAPIPPGYNSSQFRDPTEAWRLSDGMWRMLVGANAG
          T..S....Q.QA.A.PEDPSDPLLR.W.K.P.NPIA..PPG.N.S.FRDPTEAW...DG.WRMLVGA..G
Retrocopy TDQSSIRGQTQAMAVPEDPSDPLLREWDKSPHNPIALAPPGFNDSMFRDPTEAWKGYDGVWRMLVGAVKG

Parental  EGGLIGTALLYKSTDFQTWNFSNRLHENPTTGMWECPDLFPVRIKGRKGLNASAVGKGVLHVLKVSLDLN
          ....IGTALLYKSTDF..WNF.........TGMWECPD..PV..K...GL..SA.G..V.HVLKVSLD.N
Retrocopy TDQSIGTALLYKSTDFNKWNFTGEIQSVAGTGMWECPDIYPVHVKEKTGLRLSARGPHVKHVLKVSLDRN

Parental  KHDYYSVGNYLTETDTYKPLIAEIDTGIGLRYDYGKYYASKTFFDPIRQRRIVYGWTNESTSTMDDVAKG
          KHDYYSVG.Y...TD.Y.P.....DTG.GLRYDYGK.YASKTFFD....RR...GW.NES.S..DD..KG
Retrocopy KHDYYSVGTYDEKTDLYTPDDTKLDTGLGLRYDYGKFYASKTFFDQNKNRRVLWGWANESSSVQDDIEKG

Parental  WAGLQSIPRIVYLDQRANTSLIQWPIEEVQTLRRKKITVKDVNLEGGEVARLMDVSGVQLDIEVAFKIPD
          W...Q..PR...LD......L.QWPIEEV..LRR...T.K.V....G.V.......G.QLDI.V.F..P.
Retrocopy WSSVQCLPRHIWLDEESSANLVQWPIEEVDKLRRNEMTEKNVEVGVGKVVPVKAAKGAQLDIVVDFALPE

Parental  VKQG-STPTELIAESGPSICSQ---KGASMRG--MYGPFGLLVLASNDLTEQTAVYFYFVFT-KKDGWKT
          ...G......L.AE.G...CS....KG....G....GPFG..VLA..DL.E.T...F......K...WKT
Retrocopy KSEGLEQNPNLLAEMGHLTCSDLVTKGSNAAGPHSFGPFGVHVLATGDLQERTSIFFHLIHDGKHQNWKT

Parental  LVCSDQSRSTVSMNLTPDKTTYGSYVRVYDDEKLLKLRLLVDHSVVETFAQGGRTVITTRVYPKFAQSKN
          L.C.DQS.S........DKT.YGSYVRV.D..K.L..R.LVDHS.VE.FAQGGRTV.T.RVYP..A....
Retrocopy LFCGDQSQSSLQQDV--DKTVYGSYVRVDDSDKVLSVRILVDHSIVESFAQGGRTVMTSRVYPELAVKDA

Parental  ARVFLFNNGSETVNVDSATVWNMATV
          A.VFLFNNG.E.V.V.S...W.M..V
Retrocopy AHVFLFNNGTEPVTVKSVSTWEMKSV

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_2 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	PP1S51_338V6	1 retrocopy	retro_ppat_2 ,