RetrogeneDB ID: retro_ptri_44

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: scaffold_1299:5464..6208(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0012s12400
• Aliases: None
• Description: None

Sequence

>retro_ptri_44
AGCCACTGCCGTCTCCGAAATCGTGAACGAAACCGATTTCACAGGTGACGCGTGGATTGGTCACCACTAACAGCCCCTGG
TGACTCAGAAATAGTCAACGAAAACTGGTTCGCTGCTGACTTAGAAATCATCACCTAAAAACCTTCGAAAGGTGACGCGT
GGATTCGGAAGTGCTCGCAGCCCCTGTTGACTCAGAAAAAGTCAACGAAAACTAATTCAGTGGCGACTGGGAAATCGTCG
ACGAAACAAGTTCCAAAGGTGACAAGTGGATTCTTCAGCGCGCCCAGCCCCTTTTGACTTAGAAACTGTTAATGAAAACT
GAGCCCCTGCCATCTCCGAAATCGTGAGCTAAACCAATTCCAAAGGTGACGCGTGGATTCGGAAGTGCTCGCAGCCCCTG
TTGGCTCAGAAAAAGTCAACGAAAACTGAGTCGGTGGCGACTGGGAAATTGTCAACGAAACAAGTTCCAAAGGTGACTAG
TTGATTCTTCAGCGCGCCGAGCCCCTATTGACTTAGAAACTGTTAATGAAAACATAGCCACTACCGTCTCCGAAATCGTG
AACGAAACCGATTCCACAGGTGACGCGTGGATTGATCACCACTAACAGCCCCTGGTGACTCAGAAATAGTCAACGAAAAC
TGGTTCGCTGCCGACTTAGAAATCATCACCTAAAAACCTTCGAAAGGTGACGCGTGGATTTGGAAGTGCTCGCAGCCCCT
GTTGACTCAGAAAAAGTCAACGAA

Alignment

ORF - retro_ptri_44 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.4 %
• Parental protein coverage: 58.77 %
• Number of stop codons detected: 11
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRCSLINHHRNSFQRRRVDSEALAAPVDLEKVNENGVAASSEIITETPFKGHAWIRESSQPLLTYKMSTK
          S.C.L.N..RN.F.R.RVD...L.AP.D.E.VNEN..AA..EIIT..P.KG.AWIR..SQPLLT.K.STK
Retrocopy SHCRLRNRERNRFHR*RVDWSPLTAPGDSEIVNENWFAADLEIIT*KPSKGDAWIRKCSQPLLTQKKSTK

Parental  TESVMIGKSSPKHLSKVTCGFVSARSPCLLRNIQRKQCRCRLGNHQRNNFQRRRVDSEELIAPVDSEKVN
          T.SV..GKSS.K...KVT.GF.SA.SP..LRN...K...C.L.N...N.FQR.RVDSE.L.APV.SEKVN
Retrocopy TNSVATGKSSTKQVPKVTSGFFSAPSPF*LRNC**KLSPCHLRNRELNQFQR*RVDSEVLAAPVGSEKVN

Parental  ENGVGATWEIISETPSKGDTLIWKRSLAL-VDSEKVKENGVGAHWEIVTETPSKGDAWIQKSTQPLLTKK
          EN.VG..WEI..ET.SKGD.LI..R...L..D.E.V.EN......EIV.ET.S.GDAWI....QPL.T.K
Retrocopy EN*VGGDWEIVNETSSKGD*LILQRAEPL<IDLETVNENIATTVSEIVNETDSTGDAWIDHH*QPLVTQK

Parental  KSTKMESVATRKSSPKHLPKVTRGFGSA-AALVDYKKVNE
          .STK..S..T.KSSPK.L.KVTRGFGSA.AA.VD..KVNE
Retrocopy *STKTGSLPT*KSSPKNLRKVTRGFGSA>AAPVDSEKVNE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Populus trichocarpa was not studied using RNA-Seq expression data.

ChIP-Seq

Populus trichocarpa was not studied using ChIP-Seq data.

EST

Populus trichocarpa was not studied using EST data.

TSS

Populus trichocarpa was not studied using FANTOM5 data.

Lab

retro_ptri_44 was not experimentally validated.

Homology

Retrocopy orthology:

Populus trichocarpa 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
Populus trichocarpa	POPTR_0012s12400	1 retrocopy	retro_ptri_44 ,