RetrogeneDB ID: retro_ppat_8

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS545202.1:198991..199798(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S313_58V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S100_99V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_8
ATGAAAATGTCGACACTGGCGTTCTGTGCGGTACTGCTGTTGTTCCTAGAGCTACTGGGTCTCCCAGTTGCTTTCTGCGG
CACCTTGGCTCTAAGCGGGTACAATGAACAGTGGATGGCCGGACATGCCACATGGTACGGGGAACCTCTTGGTGAAGGAT
CCAGTGGTGGCGCTTGTGGCTACACAAAGCTTGCGGATACACCATATGGACCCAAAATTGCAGCGGGAAACGATCCAATT
TTCCAAGGAGGTAGCGGATGCGGCGCATGCTTCGAGGTGAAGTGCAACTATCCATCTTGCAAGTCCGAGCCAACCCGGAT
TATCATCACAGACCAATGTCCTGGAGGAACTTACTGCAGCACATCTCAGCCTGCATTCGACCTGAGTGGCGCTGCTATCA
GCGACATGGCTGTTTCGGGTAAGGACGGAGAACTGCGCAACATTGGGTTATACGACATCCTGTACAAGAGAGTGCCATGC
GAGTACCCGAATCAGAATATTGCCTTCCAGGTCGACGCAGGCTCATCTGCTTTCTGGTTGTCGCTCCTGGTGAAGTATAT
GGGAGGGCCTGGCGATATTGAAAGTGTCGAAATTCGTACAACGGGGAGCTCATCTTTCCAACCAGCAAAGCACAACTGGG
GTGCCAGCTGGATGCTCATCAACACGTCCGGCCAGCCATTCAAAGGCCCTTACGACGTCAAGATTGTGTCCAAGTTAAAC
GGTCATACTGTCATCGCCGAGAAAGCGATTCCTGAGTTTTTTGAACCAGGGAAGCTTTACGAGAGCAACGTGCAGATGGC
GTACTAG

Alignment

ORF - retro_ppat_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.25 %
• Parental protein coverage: 95.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLLWIALASVLPVAHCSGSLEASGYTASWLPGHATWYGDPYGEGSSGGACGYTELAGTPYGLSVGAGSAV
          .LL...L...LPVA.C.G.L..SGY...W..GHATWYG.P.GEGSSGGACGYT.LA.TPYG....AG...
Retrocopy LLLFLELLG-LPVAFC-GTLALSGYNEQWMAGHATWYGEPLGEGSSGGACGYTKLADTPYGPKIAAGNDP

Parental  IYQNGQGCGECYEVKCTYPSCKPTPSRIVITDFCPGGTFCSTGEPAFDLSGMAMTNMALPGRDQELRNLG
          I.Q.G.GCG.C.EVKC.YPSCK..P.RI.ITD.CPGGT.CST..PAFDLSG.A...MA..G.D.ELRN.G
Retrocopy IFQGGSGCGACFEVKCNYPSCKSEPTRIIITDQCPGGTYCSTSQPAFDLSGAAISDMAVSGKDGELRNIG

Parental  LYEIQYRRVPCYYPNQNVAFKVDPGSTPFWLSFTIEYQGGPGDIESVAIRQAGSSEFQQMQHNWGANYML
          LY.I.Y.RVPC.YPNQN.AF.VD.GS..FWLS....Y.GGPGDIESV.IR..GSS.FQ...HNWGA..ML
Retrocopy LYDILYKRVPCEYPNQNIAFQVDAGSSAFWLSLLVKYMGGPGDIESVEIRTTGSSSFQPAKHNWGASWML

Parental  ICYSGKPFKGPYDVMITAKLNGHVLIAQDAIPEYFQPGGIYESNVQLGY
          I..SG.PFKGPYDV.I..KLNGH..IA..AIPE.F.PG..YESNVQ..Y
Retrocopy INTSGQPFKGPYDVKIVSKLNGHTVIAEKAIPEFFEPGKLYESNVQMAY

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_8 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 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA033426	1 retrocopy	retro_oind_67,
Zea mays	GRMZM2G013002	1 retrocopy	retro_zmay_9,
Oryza longistaminata	KN539761.1_FG003	1 retrocopy	retro_olon_5,
Leersia perrieri	LPERR10G14060	1 retrocopy	retro_lper_25,
Oryza barthii	OBART10G18180	1 retrocopy	retro_obar_7,
Oryza glumaepatula	OGLUM10G18290	1 retrocopy	retro_oglu_25,
Oryza nivara	ONIVA10G20720	1 retrocopy	retro_oniv_16,
Oryza glaberrima	ORGLA10G0133100	1 retrocopy	retro_ogla_8,
Oryza rufipogon	ORUFI10G18850	1 retrocopy	retro_oruf_14,
Oryza rufipogon	ORUFI10G19380	1 retrocopy	retro_oruf_30,
Oryza sativa japonica	OS10G0556100	1 retrocopy	retro_osat_34,
Physcomitrella patens	PP1S100_99V6	1 retrocopy	retro_ppat_8 ,