RetrogeneDB ID: retro_ppat_15

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS545102.1:392437..393076(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S213_64V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S108_86V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_15
ATGACGTTGCTATCGGTTGCGCTAGTTGCATTCCTGGCTATCTTCCATTCTTCCCCCCCGCCTGTCGAGGCCGCCACTGA
GGCCAAGGAGGTGACACATGGAAGTGTGATAAAGCTCATGCACCTACGCACCAAGTACCGGTTGCACTCGCACGACGTCC
CCTATGCTACTGGCAGTGGACAACAATCCGTGACTGCCTTCCCAGGCGTTGAGGACTCTAACAGTTACTGGAGGGTGCAG
ATAGTAGACGAAGATCACGAGCATGAGCAAGGCGATGTTATTTCGAATGGTGCCCTAGTGCGTCTCCAGCATGCGCGGAC
GCGCAAATGGCTCCACAGTCATGAACATCGATCTCCCATTACTGGAAACCTTGAGGTTAGTGCCTTCGGAGGAGATGAGC
AATCTGACTCTGGTGACTATTGGAAACTGGAAATCGAGGGTAAGGGGAGCGTCTGGACACTAGGTCAGCAAGTTAGGTTT
CTGCACGTTGCTACCAATGGCTACCTTCACAGCCATAACAAGAAGTTCAGCCAATTAGATCAACAAGAGGTGTGCGGAGT
GACAAGGAAGAATTCGGATAATCTCTGGACAGCTGCGGAAGGAATTTATTTTCTTACGAAAGGTGGTAGTATAGAATGA

Alignment

ORF - retro_ppat_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.84 %
• Parental protein coverage: 68.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALISLALVVLLALLHPSFSPSVEGASNGKEVTYGSMIKLQHDRTKFRLHSHEVPYGSGSGQQSVTAFPG
          M.L.S.ALV..LA..H.S..P.VE.A...KEVT.GS.IKL.H.RTK.RLHSH.VPY..GSGQQSVTAFPG
Retrocopy MTLLSVALVAFLAIFHSS-PPPVEAATEAKEVTHGSVIKLMHLRTKYRLHSHDVPYATGSGQQSVTAFPG

Parental  VEDGNSYWAVKPSSDDESIEQGDVIPNGSIVRLQHMRTRKWLHSHLHPSPISGNLEVSAFGGDDQSDTGD
          VED.NSYW.V.....D...EQGDVI.NG..VRLQH.RTRKWLHSH.H.SPI.GNLEVSAFGGD.QSD.GD
Retrocopy VEDSNSYWRVQIVDEDHEHEQGDVISNGALVRLQHARTRKWLHSHEHRSPITGNLEVSAFGGDEQSDSGD

Parental  YWRLEIEGKGKVWMQDQKVRLRHVDTNGYLHSHDKKYSRIVSGQQEVCGMGKKNADNLWTAAEGIYFLTR
          YW.LEIEGKG.VW...Q.VR..HV.TNGYLHSH.KK.S.....QQEVCG...KN.DNLWTAAEGIYFLT.
Retrocopy YWKLEIEGKGSVWTLGQQVRFLHVATNGYLHSHNKKFSQL--DQQEVCGVTRKNSDNLWTAAEGIYFLTK

Parental  ATTVE
          ....E
Retrocopy GGSIE

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_15 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Physcomitrella patens	PP1S108_86V6	1 retrocopy	retro_ppat_15 ,