RetrogeneDB ID: retro_ppat_9

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS546691.1:19..1144(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S8328_1V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S400_36V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_9
ATGCTGCAACGCATCTACGGCACTGCTTTTCCGAACAAAGCCCAGCTGGATGAACATCTGCACATGCTCGAAGAAGCGAA
AAAACGGGATCACCGTAAACTCGGCAAAGAGCTTGAACTGTTCATGTTCTCCGAAGAAGCTCCCGGCATGCCCTTCTATC
TGCCCAAAGGCATGACTGTCCGCACTGAACTGGAGCAGTTCTCCCGTGAGCTGCAATTGCAAGAGGGATATCAGGAAGTC
CGGACTCCTCTCATGATGAACAACCGGTTGTGGGAGCAATCCGGCCACTGGGAGCATTACAAGGACAACATGTATTTTTC
GGAAGTAGACGATGCGACTTTTGCACTCAAACCGATGAACTGCCCCGGGCACATGCTGATCTTCAAAAATACACTCCATT
CCTATCGCGAATTACCGATTCGCATGATGGAATTCGGTCAGGTTCACCGTCATGAATTCTCAGGTGCCCTGAACGGCATG
ATGCGTGTGCGGACATTCTGCCAGGATGATGCCCATCTCTACGTCATGCCAGAGCAGATCGAGGACGAGATCAATCAGGC
GATCTCACTGATCGGACGTATGTACGATATCTTTGGTTTCGAATATAAGATTGAATTGTCCACTCGTCCGGAAGATTCCA
TGGGATCTGAGGAACTGTGGGATCAGGCGGAACGCGCATTGCAAAATGTTCTGGATCGTCGGGGCGTGCAGTATCGCATT
AACGAAGGGGACGGTGCCTTTTATGGACCAAAAATTGACTTTCATATCCTTGATGCGCTGAAGCGTAGCTGGCAGTGCGG
AACAATCCAGCTTGATTTTCAAATGCCGGAGAAGTTCGACCTCACTTACATTGGCGAAGATAGCCTGAAACACCGTCCTG
TCGTGATCCATCGTGCCATCTATGGTTCCATCGATCGTTTCATCGGCATCCTGACTGAGCACTATGCAGGTGCGTTCCCA
CTCTGGCTCGCACCTGTGCAAGTGAAGCTGCTGCCTGTATCAGATCATTACGCAGACTACGCACTCCAAGTACAGAGCCA
GCTCCGAGCTGCGGGCATTCGAGTAGAAACAGATTTGCGCAGCGAGAAGCTCGGGTACAAAATCCGTGAAGCCCAGATGG
AAAAA

Alignment

ORF - retro_ppat_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.01 %
• Parental protein coverage: 54.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQRVYGISYPDNKLLKEYLHNVEEAKKRDHRKLGQQQELFFFHELSPGSCFFLPHGARIYNKLQAFIRDE
          LQR.YG...P....L.E.LH..EEAKKRDHRKLG...ELF.F.E..PG..F.LP.G......L..F.R..
Retrocopy LQRIYGTAFPNKAQLDEHLHMLEEAKKRDHRKLGKELELFMFSEEAPGMPFYLPKGMTVRTELEQFSREL

Parental  YRKRGYEEVVSPNMFNMQLWETSGHAANYKDNMFTFEVEKQEFGLKPMNCPGHCLIFDHRVRSYRELPLR
          ....GY.EV..P.M.N..LWE.SGH...YKDNM...EV....F.LKPMNCPGH.LIF.....SYRELP.R
Retrocopy QLQEGYQEVRTPLMMNNRLWEQSGHWEHYKDNMYFSEVDDATFALKPMNCPGHMLIFKNTLHSYRELPIR

Parental  LADFGVLHRNELSGALSGLTRVRRFQQDDAHIFCMESQLLTEVKGALDFLEFAYGVFGFTFELELSTRPE
          ...FG..HR.E.SGAL.G..RVR.F.QDDAH...M..Q...E...A.......Y..FGF....ELSTRPE
Retrocopy MMEFGQVHRHEFSGALNGMMRVRTFCQDDAHLYVMPEQIEDEINQAISLIGRMYDIFGFEYKIELSTRPE

Parental  KYLGEIETWNRAEKALEAALNAFGKPWQINEADGAFYGPKIDITVFDALKRKFQCATIQLDFQLPIRFNL
          ...G..E.W..AE.AL...L...G....INE.DGAFYGPKID....DALKR..QC.TIQLDFQ.P..F.L
Retrocopy DSMGSEELWDQAERALQNVLDRRGVQYRINEGDGAFYGPKIDFHILDALKRSWQCGTIQLDFQMPEKFDL

Parental  SYSTEDEAKREKPVIIHRAILGSVERMFAILLEHYAGKWPFWLSPRQCIVCPVSEKFTHYAVEVRDAINA
          .Y..ED..K...PV.IHRAI.GS..R...IL.EHYAG..P.WL.P.Q....PVS.....YA..V.....A
Retrocopy TYIGEDSLK-HRPVVIHRAIYGSIDRFIGILTEHYAGAFPLWLAPVQVKLLPVSDHYADYALQVQSQLRA

Parental  AGYFCEADVTDRKLQKKIREAQL
          AG...E.D....KL..KIREAQ.
Retrocopy AGIRVETDLRSEKLGYKIREAQM

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_9 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	PP1S400_36V6	1 retrocopy	retro_ppat_9 ,