RetrogeneDB ID: retro_ppat_6

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS545256.1:102797..104504(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S369_24V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S318_5V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_6
ATGGCCAAGCCATACGAAAAGAGTGTGGCCATGACAGCACCTCAACAGATGCGGGGAGTCGTCATAATTTCACTCCCAGA
CTCTGAGAGTGGGGGTAAAACAATGTGCGCCGCAATGTGGCAAGAAGGACACGAGCAACACCACCAGCAACAGCAAGTTC
AAGGTCACCAACAGCAGGAACAACAAACTTTACAAACCCCACCATTGCCGACACCTCCAGCCGCACATCCAGCACGAACC
CTTTACAAAAGGGGTAGATTATTCAAACGCGTGGTGCTGTTCTTCTTACTTTCCTTGGCTGCTCTTTACCTAGCATACAA
AATTCCAACCCTGTACTACTCAGAGATGCAACTGGAGGAAGAAAGCGAGGAGAAGGACGTTCATGTTTATACTTTGCACC
CTAAGTACTCCCCGGCCCTTATCAAGATGCGTCTAGTTGGAAGGAATCTACTGGAGCGCGATATGGAGAGGCTTAGCAAG
GCTTCTGTTCCTGAAACTGCTCAACGAACTGCTGCCTATCCAATTGGAGGAAACATTTACCCTGATGGACTGTACTACAT
GGCAATGCGCATCGGCAATCCGGCGAAGCTTTACTATCTGGATATGGACACAGGTAGCGACCTCACATGGCTGCAATGCG
ATGCTCCCTGCAGGAGCTGTGCCGTGGGACCGCACGGGCTATATGATCCCAAGAGAGCTAGGGTAGTCGATTGCCGGCGT
CCAACGTGCGCTCAAGTGCAACGAGGAGGTCAATTTACATGCTCTGGAGACGTCCGGCAATGCGATTACGAGGTGGATTA
TGTAGATGGAAGCTCCACAATGGGAATCTTGGTGGAAGACACAATCACCCTTGTTCTCACCAACGGTACTCGATTCCAAA
CCAGGGCTGTCATTGGTTGTGGGTATGATCAACAAGGGACGTTAGCAAAAGCACCCGCAGTGACGGATGGCGTAATTGGT
TTGAGCAGCTCCAAAATCTCCCTACCCTCGCAGCTAGCCGCGAAAGGCATTGCAAATAATGTCATAGGCCACTGTCTAGC
TGGTGGCAGCAACGGCGGTGGCTATCTCTTCTTCGGAGATACATTAGTACCCGCTCTGGGCATGACATGGACCCCGATGA
TCGGAAGGCCTTTGGTGGAAGGCTACCAAGCACGGCTCCGCAGCATCAAATATGGAGGGGAAGTTCTCGAGCTTGAGGGC
ACGACAGATGATGTGGGTGGGGCGATGTTTGACAGTGGAACTTCTTTCACATACCTCGTCCCAAATGCCTACACTGCTGT
TCTTTCTGCTGTGGTAAGACAGGCACAGAGGAGCGGCCTTGAGAGGATAAAAACCGACACCACCTTGCCCTTTTGCTGGC
GTGGTCCCTCTCCGTTTGAATCTGTTGCAGATGTTAGTGCATACTTCAAAACGGTGACCCTGGACTTCGGTGGAAGCACC
TGGTGGTCATCAGGCAAGCTGCTTGAGCTCTCCCCAGAGGGCTATCTCATTGTCTCCACGCAAGGTAATGTTTGTCTTGG
TGTTCTGGATGCAAGTGTTGCAAGCCTGGAGGTTACAAACATCCTTGGAGACATTTCCATGCGGGGATATCTTGTTGTGT
ATGACAACATGCGAGAACAGATCGGGTGGGTGAGACGGAACTGCTACAACCGACCCAGAACTGCCACCTCTCAGATTCTA
TCAACTGTGGCGCACCTGTTTGATTAA

Alignment

ORF - retro_ppat_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.11 %
• Parental protein coverage: 95.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HQDPSQMHLPALLPPQPAIAGSSGRSFLRRRRRMTKVMGFLIMLIFAILLGLRAPNLLTTEHQ--QENED
          HQ...Q..L.....P.P..A....R....R.R....V..F......A..L....P.L...E.Q...E.E.
Retrocopy HQQQEQQTLQTPPLPTPP-AAHPARTLYKRGRLFKRVVLFFLLSLAALYLAYKIPTLYYSEMQLEEESEE

Parental  KRVHVYTLYPKFTTVPIKMTQIRRTLLERDLSRLGKSSVGNHSVR---FHVGGNIYPDGLYYMALLLGSP
          K.VHVYTL.PK.....IKM....R.LLERD..RL.K.SV.....R......GGNIYPDGLYYMA...G.P
Retrocopy KDVHVYTLHPKYSPALIKMRLVGRNLLERDMERLSKASVPETAQRTAAYPIGGNIYPDGLYYMAMRIGNP

Parental  PKLYFLDMDTGSDLTWAQCDAPCRNCAIGPHGLYNPKKAKVVDCHLPVCAQIQQGGSYECNSDVKQCDYE
          .KLY.LDMDTGSDLTW.QCDAPCR.CA.GPHGLY.PK.A.VVDC..P.CAQ.Q.GG...C..DV.QCDYE
Retrocopy AKLYYLDMDTGSDLTWLQCDAPCRSCAVGPHGLYDPKRARVVDCRRPTCAQVQRGGQFTCSGDVRQCDYE

Parental  VEYADGSSTMGVLVEDTLTVRLTNGTLIQTKAIIGCGYDQQGTLAKSPASTDGVIGLSSSKVALPAQLAE
          V.Y.DGSSTMG.LVEDT.T..LTNGT..QT.A.IGCGYDQQGTLAK.PA.TDGVIGLSSSK..LP.QLA.
Retrocopy VDYVDGSSTMGILVEDTITLVLTNGTRFQTRAVIGCGYDQQGTLAKAPAVTDGVIGLSSSKISLPSQLAA

Parental  KGIIKNVLGHCLADGSNGGGYLFFGDELVPSWGMTWTPMMGKPEMLGYQARLQSIRYGGDSLVLNNDEDL
          KGI..NV.GHCLA.GSNGGGYLFFGD.LVP..GMTWTPM.G.P...GYQARL.SI.YGG..L.L...E..
Retrocopy KGIANNVIGHCLAGGSNGGGYLFFGDTLVPALGMTWTPMIGRPLVEGYQARLRSIKYGGEVLEL---EGT

Parental  TRSTSSVMFDSGTSFTYLVPQAYASVLSAVEKQAKQSGLLRVKSDTTLPYCWRGPSPFQSITDVHQYFKT
          T......MFDSGTSFTYLVP.AY..VLSAV..QA..SGL.R.K.DTTLP.CWRGPSPF.S..DV..YFKT
Retrocopy TDDVGGAMFDSGTSFTYLVPNAYTAVLSAVVRQAQRSGLERIKTDTTLPFCWRGPSPFESVADVSAYFKT

Parental  LTLDFGGRNWFATDSTLDLSPQGYLIVSTQGNVCLGILDASGASLEVTNIIGDVSMRGYLVVYDNVRDRI
          .TLDFGG..W......L.LSP.GYLIVSTQGNVCLG.LDAS.ASLEVTNI.GD.SMRGYLVVYDN.R..I
Retrocopy VTLDFGGSTWWSSGKLLELSPEGYLIVSTQGNVCLGVLDASVASLEVTNILGDISMRGYLVVYDNMREQI

Parental  GWIRRNCHSRPTKTSSQFVSQVTSL
          GW.RRNC..RP....SQ..S.V..L
Retrocopy GWVRRNCYNRPRTATSQILSTVAHL

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_6 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	PP1S318_5V6	1 retrocopy	retro_ppat_6 ,