RetrogeneDB ID: retro_ppat_3

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS545186.1:44729..45284(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S297_8V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S115_90V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_3
ATGCTCAATACCCGTCAAGCCATGACGGACGAAGGTGAAGTAATTGCTGAAGGCAAGGCTAAGGCACCGCTCGAGCCTCC
CATATACGACTTCGTTGTGAAGGACTTGAGCGGCGAAGACTTTCAGTTGAGCGTGTACAAGGGGAAGGTTCTGCTCATTG
TCAATGTCGCGTCCCTGTGCGGGTTGACGACCCAACACTACACAGAGCTCACAGAACTCCACACCAAGTACAGAGAAAAA
GGTTTGGAGATTCTGGCATTTCCTTGCAACCAATTCGGACGGTTGGAGCAAGGGGACAACGAACAGATCAAGGAATTTGT
TACTACGAAATTTCAGGCTGAGTTCCCCGTCTTTGACAAGGTCCATGTGAATGGTCCTCAGGAGTTACCGCTGTTCAAGT
ACCTGAAATCGCAGAAGGGATGCGGCGTGTTGGGCGACAGCATCAAGTGGAATTTCACCAAATTCCTCGTCGACAAGAGC
GGTAATGTGTTTCAACGCTACGCTCCCACCATTCCTCCTTCCAAGATAGAAAATGACATTCAATCATGTTTGTAA

Alignment

ORF - retro_ppat_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.06 %
• Parental protein coverage: 63.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IYDFVVKDIDGNDVELSKYKGKVLLIVNVASACGLTTTNYTELAGIYSKYKNQDFEILAFPCNQFGGQEP
          IYDFVVKD..G.D..LS.YKGKVLLIVNVAS.CGLTT..YTEL.....KY.....EILAFPCNQFG..E.
Retrocopy IYDFVVKDLSGEDFQLSVYKGKVLLIVNVASLCGLTTQHYTELTELHTKYREKGLEILAFPCNQFGRLEQ

Parental  GSNAQIKQFACTRFKAEFPIFDKVDVNGPQEAPVYKFLKSQKRGSILGDTIKWNFAKFLVDKNGNVVDRY
          G.N.QIK.F..T.F.AEFP.FDKV.VNGPQE.P..K.LKSQK....LGD.IKWNF.KFLVDK.GNV..RY
Retrocopy GDNEQIKEFVTTKFQAEFPVFDKVHVNGPQELPLFKYLKSQKGCGVLGDSIKWNFTKFLVDKSGNVFQRY

Parental  APTTPPSKIENDIQKYL
          APT.PPSKIENDIQ..L
Retrocopy APTIPPSKIENDIQSCL

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_3 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Physcomitrella patens	PP1S115_90V6	2 retrocopies	retro_ppat_12, retro_ppat_3 ,
Triticum aestivum	Traes_6DL_F16253948	1 retrocopy	retro_taes_2,