RetrogeneDB ID: retro_ppat_13

Retrocopy location

• Organism: Moss (Physcomitrella patens)
• Coordinates: DS545033.1:863249..864260(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PP1S144_110V6
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PP1S17_293V6
• Aliases: None
• Description: None

Sequence

>retro_ppat_13
ATGGCTAAGATGACGAAGTTGTCGGCTTTGAGGGTGTTGCTGTTTGTGTGGCTCGCGGCTGAGCTTTCATTAGCCAACGC
GCACGTTGGCCATTCTCATTCGGGAGATTCTGAGGGACCGGGTTTGAGGGATAAAAGTTTGATACTTACTAAGGTTTACG
CATTGCTTATTGTATTCTTTGCCACGTTCCTGGGAGGTATTTCGCCCTACTTCTTCCGGTGGAATGAAGCGTTTTTAGTT
CTTGGAACCCAGTTCGCTGGTGGGGTATTTCTAGCGACAGCCATGATTCACTTCCTCGGCGATTCGCATGACGTCTTCAG
GAGATTGAGACCGACTTCATTCTACGCGTATTCAGAGATGCTCGCCGTTGTCGGGTATCTGCTGACTATGCTCGCAGATG
TGGCGATTCAGAGTGTCCACGATCGCAAGGTATCCACGGTTCAGGGTGCCCACGATTACCTGTCTGAGAAGAGAGCGGCT
GCGGATGTGGAGAGCCCAACTGAATCTTCGGAAACCAAAGCGGCGATTCAGTCGAGTTACAACCTCAGCGACGCTGTGCT
CCTGATCTTTGCGTTGTGCTTTCACTCTATCTTTGAAGGGATCGCTATCGGGGTGGCGGCGACGAAGGACGACACATGGA
CGTCACTGTGGACAGTATCGCTTCACAAGGTCTTCGCTGCCATAGCGATGGGCATCGCGCTCCTGCGCATGCTGCCAAAT
CGGCCCCTCCTACAGTGCGTCCTGTACGCATTCGCATTCGCTATCTCCACCCCTATTGGTGTTGCCATCGGGATCATCAT
CAACTCCACGGTCGAGGGCCGCATCGCAGATTGGATCTACGCCGTCTCCATGGGCATTGCCACCGGAGTGTTCGTCTATG
TTGCAATCAATCACTTGCTAGCCAAAGGGCATAAGCCTAACAAAAAAGTTGCTCTTGACCGACCTCTTTGGCGCTGGGCG
GCCGTTGTGCTTGGGGCTACCTTGATCGGTATCGTCATGATTTGGGATTAA

Alignment

ORF - retro_ppat_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.18 %
• Parental protein coverage: 91.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTLLLIFAVWIELAAAHGGAADEATPEDGPPPNLRAKGLILVKVYCLIIVFFVTLLGGISPYFVPWNASF
          V.L....A....LA.AH.G........D...P.LR.K.LIL.KVY.L.IVFF.T.LGGISPYF..WN..F
Retrocopy VLLFVWLAAELSLANAHVGHSHSG---DSEGPGLRDKSLILTKVYALLIVFFATFLGGISPYFFRWNEAF

Parental  LVLGTQYAAGVFLTTALLHFLSDAHNIFQALT-TKQYAFAEMLAIAGYLITLFGDLIIQRLILRGARSSA
          LVLGTQ.A.GVFL.TA..HFL.D.H..F..L..T..YA..EMLA..GYL.T...D..IQ....R......
Retrocopy LVLGTQFAGGVFLATAMIHFLGDSHDVFRRLRPTSFYAYSEMLAVVGYLLTMLADVAIQSVHDRKVSTVQ

Parental  QLGSLDGEKDGAAKLDEKGRA-EVNATLLHRASFGDTLLLILALCFHSVFEGIAIGVSVTKQDAWKAFWT
          .......EK..AA.........E..A.........D..LLI.ALCFHS.FEGIAIGV..TK.D.W...WT
Retrocopy GAHDYLSEKRAAADVESPTESSETKAAIQSSYNLSDAVLLIFALCFHSIFEGIAIGVAATKDDTWTSLWT

Parental  ITLHKVFAAIAMGIALLRMLPNRPLLSCFCYSFAFAISTPIGIAIGIIIDATTEGAVADWIYAIAMGLAT
          ..LHKVFAAIAMGIALLRMLPNRPLL.C..Y.FAFAISTPIG.AIGIII..T.EG..ADWIYA..MG.AT
Retrocopy VSLHKVFAAIAMGIALLRMLPNRPLLQCVLYAFAFAISTPIGVAIGIIINSTVEGRIADWIYAVSMGIAT

Parental  GVFIYVAINHLLGKEYMPS-KTSVEQPFKKFIALTLGAATMAIVMIWD
          GVF.YVAINHLL.K...P..K.....P.....A..LGA....IVMIWD
Retrocopy GVFVYVAINHLLAKGHKPNKKVALDRPLWRWAAVVLGATLIGIVMIWD

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_13 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Physcomitrella patens	PP1S17_293V6	1 retrocopy	retro_ppat_13 ,
Sorghum bicolor	Sb01g032670	1 retrocopy	retro_sbic_18,