RetrogeneDB ID: retro_ppat_17

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS544915.1:1115734..1116658(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S26_126V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S4_43V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_17
ATGGTAGCCACTTCGTATTATGAAGGCTTCCAAGGCTGGAGACTAGTCTTGTGTGTGACATGCATTGTGTCCAATCTGCA
GATACTACTGGTGCTTGGCCAATATGAAGGCTCTAACAGCGGGTCGACAAAATTCATGACAAATTACGCCAGCTCATCAG
ACGGACAGCATTTTCGCATCCTCAGCAACGGACAACAGGTGCAGCTTCTCCTAGACGAGCACTCCGCTTCTGGATTTGTC
TCCAAACACAAGTATATGTTTGGGAGGATTGGGATGCGGATAAAGCTTGTTCCAGGCAATTCAGCCGGGACGGTTACTGC
GTACTACTTGTCTTCCGACACTGCGCGTCATGACGAAATGGACTTCGAGTTCCTTGGTAATGTATCAGGCCAGCCCTACA
TCCTGCAGACGAACATCTACGCAGGGGGGAAGGGACAGCGGGAGCAGAGAATTTATCTTTGGTTCGACCCTTCAGCTGAC
TTCCATGAATACTCTGTTTTGTGGAATAGAAAGCAGATTGTGTTCTATGTTGACGACACTCCCATTCGGATGTTCAAGAA
CAACAAGGCTGCTCTTGGGCAGGATTATCCAGATTCTCAGGCAGTGGGGATTTACAGCAGCATTTGGAATGGGGAGAACT
GGGCAACCAATGACGGCTGGGTGAAACTCAATTGGACTTACGCTCCTTTCATCGTCACATATGAGAAGTTCAATGTAGAT
GCCTGCCTTGCGCTGCAACACAGCAGCGATCCTTGCATTGCAGCAACGAACGGTTGGTGGGAGGAGTCGGAGTACGAGAC
CCTGAATTTCAAGGATGTCGAGCGACTCAACTGGGTGAAGGAAAATTATGTCGTGTACAATTACTGCACTGATCGAGGGA
GAAACCCTATTCGACCAATTGAATGCGATATCAATATTTTGTGA

Alignment

ORF - retro_ppat_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.87 %
• Parental protein coverage: 93.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VMCVIWTMA-MNMITVLGQGTGSLTGAVTFLENYESQSDSQHFRILNDGHQVQLVLDEYAASGFGSKYQY
          V.CV...........VLGQ..GS..G...F..NY.S.SD.QHFRIL..G.QVQL.LDE..ASGF.SK..Y
Retrocopy VLCVTCIVSNLQILLVLGQYEGSNSGSTKFMTNYASSSDGQHFRILSNGQQVQLLLDEHSASGFVSKHKY

Parental  LFGKIGMRMKLVPGNSAGTVTAYYMSSQTPGLHDEMDFEFLGNVTGQPYILQTNIYANGEGKREQRIYLW
          .FG.IGMR.KLVPGNSAGTVTAYY.SS.T...HDEMDFEFLGNV.GQPYILQTNIYA.G.G.REQRIYLW
Retrocopy MFGRIGMRIKLVPGNSAGTVTAYYLSSDT-ARHDEMDFEFLGNVSGQPYILQTNIYAGGKGQREQRIYLW

Parental  FDPTSDFHSYSVLWNTQQIVFYVDNTPIRVFKNNKD-IGVPYPDSKPVGIYSTIWNGENWATNDGWVKLN
          FDP..DFH.YSVLWN..QIVFYVD.TPIR.FKNNK...G..YPDS..VGIYS.IWNGENWATNDGWVKLN
Retrocopy FDPSADFHEYSVLWNRKQIVFYVDDTPIRMFKNNKAALGQDYPDSQAVGIYSSIWNGENWATNDGWVKLN

Parental  WTYAPFVATYESFNVDACRVDNGDTASCMAQTSSWWMSSEYQTLGAYQVNQLEWVRNNYLLYDYCADRKR
          WTYAPF..TYE.FNVDAC.........C.A.T..WW..SEY.TL....V..L.WV..NY..Y.YC.DR.R
Retrocopy WTYAPFIVTYEKFNVDACLALQHSSDPCIAATNGWWEESEYETLNFKDVERLNWVKENYVVYNYCTDRGR

Parental  SPAPPPECARNPL
          .P..P.EC..N.L
Retrocopy NPIRPIECDINIL

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_17 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Physcomitrella patens	PP1S4_43V6	1 retrocopy	retro_ppat_17 ,
Sorghum bicolor	Sb06g027670	1 retrocopy	retro_sbic_4,