RetrogeneDB ID: retro_ppat_5

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS544926.1:1739861..1741217(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S37_264V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S2_113V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_5
ATGTCGATTAGCAATGGGGAGTTGAAGCATGGCGTTTCGTGCAAACGTGGTCTGAGGGAGCGAGCGGACACGGACTTGGA
TATGGGACATACCGGCCCCGCTATCAAGAAATTTCCAGATCCAGTGCAAACGTTAGCAAATGTGCATCAGGGGCTCGGGC
AGCATGGTGGCGTGAATGTGGCGATCGAGGCGTCCTCGACGTTTGCTATCGTGGAGCCCCAGACGCTGAACAAACTGTTC
TCGGGAGAGCTCGGGACCGACCATGGACTATACCTGTACAGCCGCCACTTCAATCCGACAGTGCTAAGCTTGGGCCGCAA
AATGGCGGCTCTCGAAGACACAGAGGCCGCTTACTGCACTGCGAGCGGCATGTCCGCTATAGCCGCAGTCATGCTTCAGC
TCTGCAGCAGCGGTGACCACATCGTAGCATCAAACCGGTTGTATGGTGGTACTCATGCGTTGCTGGCGCACTTCCTCCCC
CGTACTTGCAACATAAAGACGACATTCGTAGATGTGGACGACTTGGACGCGGTGCATGCTGCCGTGCAACCAAATTCGAA
GGTGCTGTACTTTGAATCGCTGTCGAATCCGCGGCTATATGTGGCGAACATTCCAGCTCTTGCGCACCTAGCGCACAGCC
GGGGCTTGACGGCGGTAGTCGACAACACTTTTGCGCCTCTGCTTCTCTCTCCAGCGAGATTGGGCGCCGACGTCGTTGTG
CACAGCTTGTCGAAGTACATCAGTGGCGCGGGCGATATCATCGCCGGTGCGGTATGCGGACCGGCGGAGCTCATCAGCGC
AATGATGGACCTCCACCATGGCGCGCTCATGCTACTGGGTCCGACGATGGACCCCCACGTCGCATTCCAGGTCGGCCTTC
GCATCCCGCACCTCTCAATTCGGATGAAGGAGTTTGGGATTCGGGCCTTGCTTTACGCCAAGCGCCTGAAGAAGTTGGGA
TTGAAGGCGATTTACCCCGGGCTACAGGACCACCCCCACCACGCGCTCATGACGAAGCTCTTGAACGACGGCTATGGCTA
CGGTGGGATGATGTGCTTGGATTTAGACACGAAGGAGAGAGCGCAGGATTTTATGCGCTACTTGCAGAACGTAGCCCATT
TCGGCTGGATGGCTGTGAGTTTAGGGTACCACGACACGCTCATGTCGTGTTCGGGATCGAGTACAAGCTCGGGCTTGACG
AGCGAGGAGAAAGCTGTGTCTGGAATTTCCCCGGGGCTTGTGCGCATGTCGATTGGGTTCACGGGGTCGACCGAGCAGCG
ATGGAAGCAGCTCTTGGACGCTTTGATTGCTCTTAAGCTGGTGCCACCTCAAGCTGTAGACTCGAGTGTTCGATGA

Alignment

ORF - retro_ppat_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.14 %
• Parental protein coverage: 97.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GIVVNGVVGQKRTREDSD-DEDMKLDCEVLRKWMDPVQGLANMRREFGEHGGVNMSIEASTTFTVMEPET
          G....GV......RE..D.D.DM........K..DPVQ.LAN.....G.HGGVN..IEAS.TF...EP.T
Retrocopy GELKHGVSCKRGLRERADTDLDMGHTGPAIKKFPDPVQTLANVHQGLGQHGGVNVAIEASSTFAIVEPQT

Parental  MSKLFEGKLGPDRDFYIYSRHYNPTVLNLSRQMAAMEGTQAAYCTASGMSAISSVLTQLCNSGDHIVASN
          ..KLF.G.LG.D...Y.YSRH.NPTVL.L.R.MAA.E.T.AAYCTASGMSAI..V..QLC.SGDHIVASN
Retrocopy LNKLFSGELGTDHGLYLYSRHFNPTVLSLGRKMAALEDTEAAYCTASGMSAIAAVMLQLCSSGDHIVASN

Parental  RLYGGTHALLAHFFPRKNNITTTFVDVADVSAVKEAIRPSTKVLYFESVSNPQLVVANIPVLAGVAHEKG
          RLYGGTHALLAHF.PR..NI.TTFVDV.D..AV..A..P..KVLYFES.SNP.L.VANIP.LA..AH..G
Retrocopy RLYGGTHALLAHFLPRTCNIKTTFVDVDDLDAVHAAVQPNSKVLYFESLSNPRLYVANIPALAHLAHSRG

Parental  VKVVVDNTFAPIIMSPIRYGADVVVHSLTKFISGSSDIIAGAVCGPADLISSMMGLTQGALMLQGPTMNP
          ...VVDNTFAP...SP.R.GADVVVHSL.K.ISG..DIIAGAVCGPA.LIS.MM.L..GALML.GPTM.P
Retrocopy LTAVVDNTFAPLLLSPARLGADVVVHSLSKYISGAGDIIAGAVCGPAELISAMMDLHHGALMLLGPTMDP

Parental  QIAFQLAMRLPHLELRMKEHCDRALIYSRRLKKLGMKVIYPGLEEHPQHNLMKKLLNEGYGFGGMLCLDL
          ..AFQ...R.PHL..RMKE...RAL.Y..RLKKLG.K.IYPGL..HP.H.LM.KLLN.GYG.GGM.CLDL
Retrocopy HVAFQVGLRIPHLSIRMKEFGIRALLYAKRLKKLGLKAIYPGLQDHPHHALMTKLLNDGYGYGGMMCLDL

Parental  ESTEIANDLLRHLQNVSLFGLMAVSLGYHDTLMSCSGSSTSSELSKEEQNSAGISAGLVRMSIGFTGSVE
          ...E.A.D..R.LQNV..FG.MAVSLGYHDTLMSCSGSSTSS.L..EE....GIS.GLVRMSIGFTGS.E
Retrocopy DTKERAQDFMRYLQNVAHFGWMAVSLGYHDTLMSCSGSSTSSGLTSEEKAVSGISPGLVRMSIGFTGSTE

Parental  KRWSQLLDALTSLKLVPDSA
          .RW.QLLDAL..LKLVP..A
Retrocopy QRWKQLLDALIALKLVPPQA

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_5 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	PP1S2_113V6	1 retrocopy	retro_ppat_5 ,