RetrogeneDB ID: retro_ppat_33

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS545020.1:334642..335401(+)
• 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_33
GTAATCAAAGATATGAGGTTCAATTCTTTTTGCAATGATATCAAGCTTGAAAACCTACTCATATTCAATCCAATTAAAGA
TGTAAGATTGTCCAATTCTTTTGGCAATAATATCAAGCTTAAACACTTCTTTGTATTCAATGTATTCAAAGATAAGAGGT
TGCTTAAATCTATTGGCAATAATGTCAAGCTAGAGCACTTCCTAATATCCAATATAATTAAAGATATGAGTTTACTTAAT
TCTTTTGGCAATAATGCCAACTTTAAATACCATCTCAATCTCAATGTAGTTAAAGATGTGAGATTGCCTAATTCTTTTGG
CAATGATGTGAAGCTTAAACACTTCTTTAAAAACCATCTCAATCTCAATGAAGTCAAAGTTGTGAGGTTGTCCAATTCTT
TAGGCAATGATGTCTAGCCATTATATTTATGCAGATTCAATATAGTCAAAGATATAAAACTGTTTAATTTTTATAGCAAT
GATATCAAGCTTTTACACCTTCTAATGTCCAATTCAATAAAAGATGTGATATTGCCTAATTCTTTTGATAATGATATTAA
GCTTGAACATCCTTGCATATTTAATATAATCAAAGATGTGAGGTTGCTTAATTCATTTGGCATTAAATTCAAGCTTAAAT
ACTCTCTAAAATCTAATTTAGTGAAAGATGTGAATTTGTCTAACTCTTTTGGAAATAATATCAAGTTTGAACATCCTCTT
ATATCTAATTTAGTCAAAGATATGAAGTTGCCCAATTCT

Alignment

ORF - retro_ppat_33 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.51 %
• Parental protein coverage: 53.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVKDVRLPNSFGNNVKLEQSLISNSIKDVRLSNSFGNDIKLEQYLLYKVDIDVRLLNSFGNDVKLEQSLI
          V.KD.R..NSF.N..KLE..LI.N.IKDVRLSNSFGN.IKL.......V..D.RLL.S.GN.VKLE..LI
Retrocopy VIKDMRF-NSFCNDIKLENLLIFNPIKDVRLSNSFGNNIKLKHFFVFNVFKDKRLLKSIGNNVKLEHFLI

Parental  SNSIKDVRLPNSFGNDVKLEKYLIFKVVKDVRLPNSFGNNVKLEQF----LISNSIKDVRLSHSFGNDIK
          SN.IKD..L.NSFGN.......L...VVKDVRLPNSFGN.VKL..F....L..N..K.VRLS.S.GND..
Retrocopy SNIIKDMSLLNSFGNNANFKYHLNLNVVKDVRLPNSFGNDVKLKHFFKNHLNLNEVKVVRLSNSLGNDV*

Parental  LEQYLLYKVDKDVRLPNSFGNDVKLEQYLIFKVVKDVRLPNLFGNDVKLEQYLIFKVVKDVRLPNSFGND
          ..........KD..L.N...ND.KL...L.....KDV.LPN.F.ND.KLE...IF...KDVRL.NSFG..
Retrocopy PLYLCRFNIVKDIKLFNFYSNDIKLLHLLMSNSIKDVILPNSFDNDIKLEHPCIFNIIKDVRLLNSFGIK

Parental  VKLEQYLIFKVVKDVRLPNSFGNDIKREHRLIFQVVKDVRLPNS
          .KL...L....VKDV.L.NSFGN.IK.EH.LI...VKD..LPNS
Retrocopy FKLKYSLKSNLVKDVNLSNSFGNNIKFEHPLISNLVKDMKLPNS

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_33 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,