RetrogeneDB ID: retro_ppat_11

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS544895.1:3266664..3268872(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S6_407V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S45_94V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_11
ATGGCAGTTCCAACCATTCCTAGTCCAGCCTGTATCTCGCAGTCGGCTAATGGGTCCATTATCTCAACGCGACGTTCGAC
TGAAACCAACCCTCGACAGCATCCGTCGACTTCTTATCGATGCGCTGGAAGAGTAGTTAGGAGACAAGGTAGGAGCGCAA
TTAGCAGGTCTGGAAGCAGGTATTTACATGATTTAGAGGCCGGTCGTTCACTGCTGAAAAGGGTTACTCTGAGAAGAGAT
TGGGATTCTAGGTTGGATGAGAAAGACCAATATCCCAGGCTTGGTGCAAGAGCGGCTGCGACGTTTGAAGCAAAACCTGA
AAATGCTGAGAAAGATTATTCTAAAAATGGGAAAGCTGCCAATAAAGGTGTGGACAATGGGAAGGATCGATTAGCTAAAG
TTCCAATCTCGAACATCAGAAACTTTTCTATCATCGCACATATTGATCATGGGAAATCAACATTAGCCGACAAGTTGCTG
CAGACCACTGGCACCGTTCTTGCGCGAGAAATGAAGGAGCAGTTTCTCGACAACATGGACCTTGAACGAGAGAGGGGTAT
TACCATTAAGCTTCAAGCAGCTCGTATGCGCTATGTGGATGAAACCGGTGAGGCTTACTGCCTGAATTTGATTGATACTC
CGGGCCATGTGGACTTCTCGTATGAGGTGTCCAGGTCTCTGGCAGCTTGTGAAGGTGCCCTCTTGGTGGTGGATGCTTCT
CAAGGAGTAGAAGCTCAAACCTTAGCCAACGTGTATTTAGCCCTCGAATCAAACCTAGAAATTATCCCTGTGCTCAACAA
GATCGACCTTCCTGGGGCTGACCCTGAGCGCGTGCGGAGGGAGATTGAGGAGATAATAGGCTTGGATTGTAGTGAAGCCA
TTTTGTGTTCTGCAAAGGAGGGAGTTGGAATTCCCGAGATCTTGAACGCAGTGGTTAAGAAGATTCCCCCACCGAAAGAC
ACAGCCGCAGAGCCTCTTCGCGCATTGATATTCGATTCCTACTACGATTCCTATCGGGGAGTTGTCGTGTACTTCAGAGT
GATGGATGGAAGGGTGAAGAAAGGGGACTACGTTCAGTTCATGAACAGCAAGACCGAGTATCAGGTGGACGAGGTAGGAG
TTTTGTCTCCTATTCAAATGCCAGTGAATGAGTTATACGCTGGTGAGGTGGGTTACTTGTCAGCATCCATCAAATCCGTG
GCTGACGCAAGAGTTGGGGATACTATTACTACAGTTTCTCGGAAAGCTGCCCAGGCTCTACCTGGGTACCAGTTGGCTAC
TCCTATGGTGTTCTGTGGGCTGTTTCCCATCGACGCAGATCAATTTGTAGAGCTTCGAGAAGCCCTCGAAAAGTTGCAGT
TAAACGATGCAGCACTGCAATTTGAGCCAGAGACATCCAGTGCGATGGGCTTTGGTTTCCGATGTGGGTTTCTGGGTCTC
CTGCACATGGAGATCGTGCAGGAAAGACTGGAAAGAGAGTACGGCCTCGACCTCATCACCACTGCTCCCAGTGTGGTGTA
TCGTGTCCATTGCACCGATGGCACTATAACTGAATGTTCAAATCCTTCTGCTTTGCCAGATGCTGGAAAACGCAAATCCA
TCGAGGAGCCATACGTAAGAATAGAGCTTCTCACGCCGAAGGACTATATAGGTCCTTTGATGGAACTAGCACAAGAAAGG
CGTGGAGAGTTCAAGGAAATGAAATTCATTACAGAGAACCGGGCTTCGTTGGTGTACATGTTGCCCTTGGGAGAAATGGT
AGGTGACTTTTTTGATCAGCTGAAGTCACGTAGCAAAGGCTACGCAAGCATGGAGTACTCTGTCAAGGGTTATCGAGAAA
GCAAGTTGGTGAAGCTCGACATTAGGATTAATGATGAGGCTGTCGACCCCCTTGCGGTCATTGTGCACCAGGATAAGGCT
TACAGTGTTGGCCGGGCACTTACTCAACAACTGAAGAAGTTGATTCCCCGTCAGCTGTTCAAGATCCCAATCCAAGCCTG
CATCGGCTCAAAGGTGATTGCTAGTGAGAATATTGCAGCCATGCGCAAAGACGTTCTTGCAAAATGTTATGGTGGAGACA
TTAGTCGGAAGAAGAAGTTGCTGAAAAAGCAAGCTGAGGGTAAGAAGCGCATGAAGTCATTGGGCAGGGTGGATGTTCCT
CAAGACGCTTTTATGGCCATCCTAAGGTTGGAGAAAGAAGTCGTGTAA

Alignment

ORF - retro_ppat_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.28 %
• Parental protein coverage: 78.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSKKTGGANERFLLNLIDTPGHVDFSYEVSRSLAACQGVLLLVDAAQGVQAQTVANFYLAFESDLAIIPV
          R........E...LNLIDTPGHVDFSYEVSRSLAAC.G.LL.VDA.QGV.AQT.AN.YLA.ES.L.IIPV
Retrocopy RMRYVDETGEAYCLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYLALESNLEIIPV

Parental  INKIDQINADPEGVKSQLKQIFDIDPESVLLTSAKTGLGLENILPAVIERIPQPKGLVDASLRMLLLDSY
          .NKID...ADPE.V......I...D.....L.SAK.G.G...IL.AV...IP.PK......LR.L..DSY
Retrocopy LNKIDLPGADPERVRREIEEIIGLDCSEAILCSAKEGVGIPEILNAVVKKIPPPKDTAAEPLRALIFDSY

Parental  YDEYRGVICHVAVVDGVLKRGDKIESAATRQSYEIMEVGILYPELTNTGILLTGQVGYVVTGMRSTKEAR
          YD.YRGV.....V.DG..K.GD..........Y...EVG.L.P.......L..G.VGY......S...AR
Retrocopy YDSYRGVVVYFRVMDGRVKKGDYVQFMNSKTEYQVDEVGVLSPIQMPVNELYAGEVGYLSASIKSVADAR

Parental  IGDTLFH-TRSVVEPLPGFKPARHMVFAGVYPADGSDYEALSSAVERLTCNDASVSIAKETSGALGIGFR
          .GDT.....R.....LPG...A..MVF.G..P.D......L..A.E.L..NDA......ETS.A.G.GFR
Retrocopy VGDTITTVSRKAAQALPGYQLATPMVFCGLFPIDADQFVELREALEKLQLNDAALQFEPETSSAMGFGFR

Parental  CGFLGLLHMDVFHQRLEQEHGAQVITTTPTVPYIFEYSDGSKLTIQNPAALPSNPKSRLVACYEPTVMAT
          CGFLGLLHM.....RLE.E.G...ITT.P.V.Y.....DG......NP.ALP...K.......EP.V...
Retrocopy CGFLGLLHMEIVQERLEREYGLDLITTAPSVVYRVHCTDGTITECSNPSALPDAGKRKSIE--EPYVRIE

Parental  IITPSEYVGSLMTLCSERRGQQTEYSFIDGQRAMLKYRMPLREVVIDFYNELKSITSGYASFDYEEAPYQ
          ..TP..Y.G.LM.L..ERRG...E..FI...RA.L.Y..PL.E.V.DF...LKS...GYAS..Y....Y.
Retrocopy LLTPKDYIGPLMELAQERRGEFKEMKFITENRASLVYMLPLGEMVGDFFDQLKSRSKGYASMEYSVKGYR

Parental  ESDLVKLDILLNGQPVDALASICHRSKAHYVGRELCEKLKKVLDRQMFEVAIQAAIGAKVVARETLPALR
          ES.LVKLDI..N...VD.LA.I.H..KA..VGR.L...LKK...RQ.F...IQA.IG.KV.A.E...A.R
Retrocopy ESKLVKLDIRINDEAVDPLAVIVHQDKAYSVGRALTQQLKKLIPRQLFKIPIQACIGSKVIASENIAAMR

Parental  KNVLAKCYGGDVSRKRKLLEKQKEGKKRMKRVGNVDIPQEAFHSLLK
          K.VLAKCYGGD.SRK.KLL.KQ.EGKKRMK..G.VD.PQ.AF...L.
Retrocopy KDVLAKCYGGDISRKKKLLKKQAEGKKRMKSLGRVDVPQDAFMAILR

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_11 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	PP1S45_94V6	1 retrocopy	retro_ppat_11 ,