RetrogeneDB ID: retro_ppat_34

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS545023.1:866553..867588(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S508_25V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_34
CCTAATTTATTTAGCAACAATGTTAAGCTTGAATAATCAATTATATCAAAGATAATCAATAATGTAAGATTTACCAATTA
ATTTGGTAATTATATCAAACTTGAGCATCTCAATAAAGCTAAGGTAATCAAAGATGTGAGTTTGCCATATGAACTTAAGA
AGAATATCAAACTAGAGCAATTTGACATAGCTAAAGTAATCAAAGATATGAGATTTTCAAATGAATTTGGCAATGATGTC
TAGCTTGAGCACTCCCTTATATTTAAAATAATCAAAGATATAAAATAGCCAAATGAACTTAGCAATGATGTCAAGCTTGA
GCATTTTCTAATATTTTAAGTACTCAAAGATATAAGACTACCTAATTTATTTGGTAATAATATCAAATTTAGGTACTCAC
TATATTGAAGATAAGTAACAATGAAAGATTACATAATTTATTTGGCAAAAATTTCAAGATTGAGCATTTTCTTATATTTA
AGGTAGTTAAAGATGTAAGATTGCCTAAATCATATGGCAATGATATCAAGCTTGAGCACCTCCATATCTTTAAAGTAGTC
AAAGATGAGTGATTGGCTAATCTATTTGATAATGATGTCAAATTTAAACAACCATTTATGAAAAATGAAATTAAAGATGT
AAGATTGCCTAATTCTTTTGGTAATGATGTCAAGCTTGAATACCTCCATATATCTAAAGTAGTTAAAGATGTAAGATTAT
CAAATGAATTTGGCAATGATATTAATCTTAAACAACTATTTATATAAATTTTAGTCAAAGATGTAAGTTTTTCTACTTTA
TTTAGTAATGATGTCAAGTTTGAACACTAACTTATATCTAGGTTAGTCAAAGAAGTGAAATTGCCTAATTTATTTGACAA
AAAATGTCAAGTTTGAGCATTTTCTCATATTTGAGGTAATCAAAGATTTGAAGTTGTCCAATTTATTTGACAATGATGTC
AAGCTTGAGTACCTCCACATATTCAAGATAGTCAAAGATTTGAGGTTGTCTAATTCATTTGGTAATAATGTTAAA

Alignment

ORF - retro_ppat_34 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.91 %
• Parental protein coverage: 74.03 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PNSFGNDVKLEQYLIFKVVKDVRLPNSFGNNVKLEQSLISNSIKDVRLSNSFGNDIKLEQYLLYKVDIDV
          PN.F.N.VKLE...I.K....VR..N.FGN..KLE.......IKDV.L.......IKLEQ....KV..D.
Retrocopy PNLFSNNVKLE*SIISKIINNVRFTN*FGNYIKLEHLNKAKVIKDVSLPYELKKNIKLEQFDIAKVIKDM

Parental  RLLNSFGNDVKLEQSLISNSIKDVRLPNSFGNDVKLEKYLIFKVVKDVRLPNSFGNNVKLEQFL-ISNSI
          R..N.FGNDV.LE.SLI...IKD...PN...NDVKLE..LIF.V.KD.RLPN.FGNN.K....L.I....
Retrocopy RFSNEFGNDV*LEHSLIFKIIKDIK*PNELSNDVKLEHFLIF*VLKDIRLPNLFGNNIKFRYSL<ILKIS

Parental  KDVRLSHSFGNDIKLEQYLLYKVDKDVRLPNSFGNDVKLEQYLIFKVVKDVRLPNLFGNDVKLEQYLIFK
          ...RL...FG...K.E..L..KV.KDVRLP.S.GND.KLE...IFKVVKD..L.NLF.NDVK..Q.....
Retrocopy NNERLHNLFGKNFKIEHFLIFKVVKDVRLPKSYGNDIKLEHLHIFKVVKDE*LANLFDNDVKFKQPFMKN

Parental  VVKDVRLPNSFGNDVKLEQYLIFKVVKDVRLPNSFGNDIKREHRLIFQVVKDVRLPNSFGNDVKLEQYLI
          ..KDVRLPNSFGNDVKLE...I.KVVKDVRL.N.FGNDI......I...VKDV.....F.NDVK.E..LI
Retrocopy EIKDVRLPNSFGNDVKLEYLHISKVVKDVRLSNEFGNDINLKQLFI*ILVKDVSFSTLFSNDVKFEH*LI

Parental  FKVVKDVRLPNSFG-NDVKLEQYLIFKVVKDVMLPYSFGNDVKLEHLAIYKIVKDVRLPNSFGNDVK
          ...VK.V.LPN.F....VK.E..LIF.V.KD..L...F.NDVKLE.L.I.KIVKD.RL.NSFGN.VK
Retrocopy SRLVKEVKLPNLFD>KNVKFEHFLIFEVIKDLKLSNLFDNDVKLEYLHIFKIVKDLRLSNSFGNNVK

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_34 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Physcomitrella patens	PP1S508_25V6	3 retrocopies	retro_ppat_33, retro_ppat_34 , retro_ppat_36,