RetrogeneDB ID: retro_ppat_36

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS545073.1:712541..713573(+)
• 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_36
AATTTATTTGGCAATGATTTCAAGCTTAAACACTTCCATATATGTATGGTAGTCAAAGATTTGAAGTTACCTAATTCATT
TTACAATAATGTTAAGCTTAAATACCTTGATATATCTAAGATAGTCATATATGTGAGATTATCCAATTCATTTGATAATA
CTAATAAGCTCAAGTACCTTAATGTATCAAAAGTAGTAAAAAATATGAGGTTGTTCAAATCATTTAGAAATGTTAAGCTT
GAGCACTTCTACATATATATAATAGTCAAAGTTGTAAGGATGACTAATTTATTTAATAGTGATGTAAAATTTGAGCACCT
CCATAATTTTAAAGCAATTAGAGATGTAAATATGCCTAATTTATTTAAAAATAATGTGAAGCTTGATCACTCCCTTATAT
ATAATGTAGGTAAAGATGTAAATTGGTCCAATTTATTTAGCAATAATATCATGCTTGAAAACTCTCTTATATTTAAGGTA
GTCAAGGAGGTAAAGTTGCCTAATTCATTTGGCAATGATGTCAAGTTTGAATACTTACTTATGTCTAAGGTAGTCAAAGA
TATAAGGTTATCAAATTTATTTAGTAATGATAACCTTAAGCACCTATCTATACCAAAAGTAATCAAAGATATGAGGGTAT
CTAATTCATTTGGCAATGATGCCAAGCTTGAGCACCAAATTTTATTTAATATATTCAAAGATGTGAGATTATCCAATTCA
TTTGGCAATGATGTCAAGCTTGAATACTTATTTGTATCCAAGGTAGTCAAAAATGTGAGATTATCCAATTCATTTGGCAA
TGATCTTAAACTTGAGCTTTTTTTCATATTTAAGATAGTCAAAGTTTTAACATTGTTCAATTCATGTGGCAATAAAGTCA
ACCTTGAATACCTACTTATATCCAAAGTAGTTAAAGATGTGAAGTTGCTCAATTCATTAGGCAATAAAATCAAGTTTGAA
TACTCATTTATATCTAAGATAGTCAAAGATGTAAGTTTGTCCAATTTATTTGGTAATAATGTCAACCTTGAA

Alignment

ORF - retro_ppat_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.36 %
• Parental protein coverage: 74.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NSFGNDVKLEQYLIFKVVKDVRLPNSFGNNVKLEQSLISNSIKDVRLSNSFGNDIKLEQYLLYKVDIDVR
          N.FGND.KL....I..VVKD..LPNSF.NNVKL....IS.....VRLSNSF.N..KL......KV....R
Retrocopy NLFGNDFKLKHFHICMVVKDLKLPNSFYNNVKLKYLDISKIVIYVRLSNSFDNTNKLKYLNVSKVVKNMR

Parental  LLNSFGNDVKLEQSLISNSIKDVRLPNSFGNDVKLEKYLIFKVVKDVRLPNSFGNNVKLEQFLISNSIKD
          L..SF.N.VKLE...I....K.VR..N.F..DVK.E....FK...DV..PN.F.NNVKL...LI.N..KD
Retrocopy LFKSFRN-VKLEHFYIYIIVKVVRMTNLFNSDVKFEHLHNFKAIRDVNMPNLFKNNVKLDHSLIYNVGKD

Parental  VRLSHSFGNDIKLEQYLLYKVDKDVRLPNSFGNDVKLEQYLIFKVVKDVRLPNLFGNDVKLEQYLIFKVV
          V..S..F.N.I.LE..L..KV.K.V.LPNSFGNDVK.E..L..KVVKD.RL.NLF.ND..L....I.KV.
Retrocopy VNWSNLFSNNIMLENSLIFKVVKEVKLPNSFGNDVKFEYLLMSKVVKDIRLSNLFSND-NLKHLSIPKVI

Parental  KDVRLPNSFGNDVKLEQYLIFKVVKDVRLPNSFGNDIKREHRLIFQVVKDVRLPNSFGNDVKLEQYLIFK
          KD.R..NSFGND.KLE....F...KDVRL.NSFGND.K.E......VVK.VRL.NSFGND.KLE...IFK
Retrocopy KDMRVSNSFGNDAKLEHQILFNIFKDVRLSNSFGNDVKLEYLFVSKVVKNVRLSNSFGNDLKLEXXXIFK

Parental  VVKDVRLPNSFGNDVKLEQYLIFKVVKDVMLPYSFGNDVKLEHLAIYKIVKDVRLPNSFGNDVKLE
          .VK...L.NS.GN.V.LE..LI.KVVKDV.L..S.GN..K.E...I.KIVKDV.L.N.FGN.V.LE
Retrocopy IVKVLTLFNSCGNKVNLEYLLISKVVKDVKLLNSLGNKIKFEYSFISKIVKDVSLSNLFGNNVNLE

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_36 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 ,