RetrogeneDB ID: retro_ppat_20

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: scaffold_15:261763..262768(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S15_43V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S145_102V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_20
ATGGCTAAGAAGACACATAACTCCGTTGCTCTTGCGATTGCTCGAGAGGACCGGAGGAACAAATTCATCACTGCGGCCGC
GGGAGCGGGAGCAGGGATGCTGGCAGCGACTTTTGTGTGCCCATTGGATGTGGTCAAAACTCGGTTGCAAGTGAATCGGA
TGGGCTACGAGAACATCAACGGCATGATGGTTTTAGGGCATTTGGGTACAATATTCAAGAAGGAGGGGGTGAAAGGGCTA
TATTGTGGTTTCTCCTCCACCATGGTTGCTCTACTTGTCAACTGGGCTGTATATTTCACCGTGTATGAGCAGCTGAAAGG
TATGCTTCAGGCACGGGAAGCGCGGAAGAATGGAGGAGTTGTCGGCAAGGGAGGCGCGTATGCACATCCGCCGAAGCTTT
CAGTAGGTGCGAATATGTTGGCTTCGGCAGGTGCAGGGGCAACCACTATTTTAGTTACAAATCCACTATGGGTTGTGAAA
ACCAGGATTCAAACACAAAGTTTGAGACCTGATCTGATTCCTTATAAAGGTGTGGCATCAGCCCTTCATCGAATTTTTCG
TGAGGAGGGTGCTCGAGGTCTTTACAGCGGAGTGGTGCCGGCTCTAGCGGGTATAAGCCATGTTGCCATTCAGTTCCCTT
TGTTTGAGTTTCTGAAGAATCAGCTGGCTCTGAGAGAAGGCACTACAGTAGACAAACTACCTGTAGGTCAGGTGGCAATG
GCTACATCTGCAGCCAAGGTCATTGCATCTACTATCACATACCCACATGAGGTTGTTCGGTCGAGACTACAAGAACAAGG
CGTTGCGAGGCTTGAAAAACTGCGGTATACCGGAGTCGTCGATTGCATTAAGAAAATAACGGCTCATGAAGGAATACGAG
GATTTTACCTTGGATATGCAACCAACTTGATGCGAACCACTCCTGCTGCAGTGATAACATTCACAAGCTTTGAAATGATT
CTTAGGCAGCTGAAAATTATCTTCCCTCCTCGTAGAGAGGATTAG

Alignment

ORF - retro_ppat_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.38 %
• Parental protein coverage: 65. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AHTSDHKMTPAAHVAAAAGAGTATILVTNPLWVVKTRLQTQRLRTDIVPYKGTFSALNRILAEEGFRGLY
          A.....K....A...A.AGAG..TILVTNPLWVVKTR.QTQ.LR.D..PYKG..SAL.RI..EEG.RGLY
Retrocopy AYAHPPKLSVGANMLASAGAGATTILVTNPLWVVKTRIQTQSLRPDLIPYKGVASALHRIFREEGARGLY

Parental  SGIVPALAGISHVAIQFPVYEYLKEYFAQKDGTTVEALSTRNVAIASSLSKVTASTLTYPHEVVRSRLQE
          SG.VPALAGISHVAIQFP..E.LK...A...GTTV..L....VA.A.S..KV.AST.TYPHEVVRSRLQE
Retrocopy SGVVPALAGISHVAIQFPLFEFLKNQLALREGTTVDKLPVGQVAMATSAAKVIASTITYPHEVVRSRLQE

Parental  QGYSKGVHIRYTGVVDCIRKISIEEGVKGFYRGCATNLMRTTPAAVITFTSFELILRHLHTLFPVKHQ
          QG.......RYTGVVDCI.KI...EG..GFY.G.ATNLMRTTPAAVITFTSFE.ILR.L...FP....
Retrocopy QGVARLEKLRYTGVVDCIKKITAHEGIRGFYLGYATNLMRTTPAAVITFTSFEMILRQLKIIFPPRRE

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_20 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Physcomitrella patens	PP1S145_102V6	1 retrocopy	retro_ppat_20 ,