RetrogeneDB ID: retro_ppat_29

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS544936.1:307404..307926(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S54_157V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_29
CAAAATTTTATACAAGAGATTAAGGTTCAAAAGTTAGTTCTGAATATCTCTATTGGTAAGAGCGGAGATTGTCTTATTCA
AGGCTTCAAATTGTTGGAACAACTTAGTGGCCAAAGTCTTCTCTTCTCTAAAGCAAGGTACATTATCTACTCTTTTGGAA
TCAAGTGTAATAAGAAGATTGCATGCTACATAATTGTTTGTGGCAAAAAAACTATGCAATTGTTAGAGAATAGTTTAAAG
GTGAAGAAATACAAATTTCTATGTTGCAACTTCAATGAATTAGATTGCTTTGATTTTGGAATCTAAGAGCATATTGATCT
TGGTATCAAGTACAATCCTTCTATTAATATCTACAAAATAGACTTTTATATTGTTCTTGAGCACCCAAGTTATAAAGTCA
AAAGAAAATATAAAGCTAAATCTTGCATTGGTATTCAATACCACATTATCAAGAAAGATATCATGAAGTGGTTCTAGGTT
AAATACAAGAGAGTGATTTTAAACAAGTCTCAAACCATAGCA

Alignment

ORF - retro_ppat_29 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.37 %
• Parental protein coverage: 96.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QNSMREIKVQKLVLNISVGESGDRLTRASKVLEQLSGQSPVFSKARYTVRSFGIRRNEKIACYVTVRGEK
          QN...EIKVQKLVLNIS.G.SGD.L....K.LEQLSGQS..FSKARY...SFGI..N.KIACY..V.G..
Retrocopy QNFIQEIKVQKLVLNISIGKSGDCLIQGFKLLEQLSGQSLLFSKARYIIYSFGIKCNKKIACYIIVCGXX

Parental  AMQLLESGLKVKEYELLRRNFSESGCFGFGIQEHIDLGIKYDPSTGIYGMDFYVVLERPGYRVGRRRRAK
          .MQLLE..LKVK.Y..L..NF.E..CF.FGI.EHIDLGIKY.PS..IY..DFY.VLE.P.Y.V.R...AK
Retrocopy XMQLLENSLKVKKYKFLCCNFNELDCFDFGI*EHIDLGIKYNPSINIYKIDFYIVLEHPSYKVKRKYKAK

Parental  SRVGIQHRVTKEDAMKWFQVKYEGVILNKSQAIA
          S..GIQ....K.D.MKWF.VKY..VILNKSQ.IA
Retrocopy SCIGIQYHIIKKDIMKWF*VKYKRVILNKSQTIA

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_29 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Populus trichocarpa	POPTR_0006s19540	1 retrocopy	retro_ptri_35,
Physcomitrella patens	PP1S54_157V6	2 retrocopies	retro_ppat_28, retro_ppat_29 ,