RetrogeneDB ID: retro_ptri_19

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 13:5607750..5609076(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0013s06910
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0001s44610
• Aliases: None
• Description: None

Sequence

>retro_ptri_19
ATGCATACTTTGAATCTTACACAATCTTCTCCTGTCACTTTCTCTAAATCCACCAACCATAGATACTCCATTAATGCTTC
TTCACTTTTAAATCCAAATCTTATCAGTAGGACTCATAATCAGACTGCCCTATTTAATAAACCCTCTACTCAGATTGGTG
CGTTAACCACCAAAGTATCAAACTTTGGCCAAATTCATGGTTACCCATTTGGCCGCTCTTCAAGATCCACTTCACAGATC
CATGATTCAGGCTTCAGAAGGGACCATTTTGACAGAATCCATGAAAACCAATCTGGGTTTTGCTCAAAGTCTGGGTCTTT
TATCACCAAAGCAGCGGCATCTGAATCTGAATCCAGCCCAGAAGGAGATGCTAGTGCAGTTTCAAAGCCAAAGTCTAAAA
CTCTCCAACTTGCACTTGTCTTTGGTCTCTGGTACTTCCAAAACGTTGTCTTTAATATTTACAACAAGAAGGCATTGAAT
GTGTTTCCATTTCCATGGTTTCTTGCTTCTTTCCAGCTTTTTGTTGGGTCCATTTGGATGTTGATTTTATGGTCATTGAA
GCTTCAACCATGTCCTAAGATCTCAAAGCCATTCATTATTGCTCTTCTTGGACCTGCGTTGTTTCACACAATAGGCCACA
TATCAGCCTGTGTTTCATTCTCTAAGGTTGCTGTTTCTTTCACTCATGTTATCAAATCATCGGAGCCTGTTTTCTCTGTT
GTTTTTTCTTCATTTCTTGGTGATACTTACCCTTTGAAAGTCTGGCTTTCTATTCTCCCTATTGTCCTTGGTTGTTCCCT
TGCTGCTGTCACTGAAGTGTCCTTTAATTTCCAAGGCTTGTGGGGTGCTTTGATTAGTAATGTTGGGTTTGTGTTAAGGA
ACATTTACTCAAAAAGGAGTTTGCAGAACTTCAAGGAAGTTGATGGACTTAACTTGTATGGTTGGATTAGCATAATCTCA
TTGTTTTATCTCTTTCCTGTTGCGGTTGTGATTGAAGGGTCTCAATGGATTCAAGGGTATCATAAGGCAATTGAGGCTGT
TGGAAAATCATCAACATTTTATATATGGGTGTTGCTGTCTGGTGTTTTTTACCATCTTTATAACCAATCATCCTACCAGG
CACTTGACGAGATTAGCCCCTTAACCTTTTCGGTAGGTAACACCATGAAGAGAGTTGTGGTGATTATTTCTACTGTCTTG
GTGTTCGGGAATCCAGTTAGGCCTCTGAATGCACTTGGATCAGCCATTGCAATATTTGGGACTTTCTTGTACTCTCAGGT
AACTGCCAAGAGAGCCAAGAAACCTGAAGTCGAAAAGCAGAACTAG

Alignment

ORF - retro_ptri_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.1 %
• Parental protein coverage: 78.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AYEADRSEPIEAPEVKSEAAKKVKIGIYFAVWWALNVVFNIYNKKVLNAFPYPWLTSTLSLACGSLMMFI
          A.E...S....A..V.....K.......F..W...NVVFNIYNKK.LN.FP.PW......L..GS..M.I
Retrocopy ASESESSPEGDASAVSKPKSKTLQLALVFGLWYFQNVVFNIYNKKALNVFPFPWFLASFQLFVGSIWMLI

Parental  SWATRIAETPKTDFEFWKTLFPVAVAHTIGHVAATVSMSKVAVSFTHIIKSGEPAFSVLVSRFILGETFP
          .W.......PK....F...L...A..HTIGH..A.VS.SKVAVSFTH.IKS.EP.FSV..S.F.LG.T.P
Retrocopy LWSLKLQPCPKISKPFIIALLGPALFHTIGHISACVSFSKVAVSFTHVIKSSEPVFSVVFSSF-LGDTYP

Parental  SSVYLSLVPIIGGCALAAVTELNFNMIGFMGAMISNLAFVFRNIFSKKGMKG-KSVSGMNYYACLSMLSL
          ..V.LS..PI..GC.LAAVTE..FN..G..GA.ISN..FV.RNI.SK......K.V.G.N.Y...S..SL
Retrocopy LKVWLSILPIVLGCSLAAVTEVSFNFQGLWGALISNVGFVLRNIYSKRSLQNFKEVDGLNLYGWISIISL

Parental  LILTPFAIAVEGPQMWAAGWQTALSEIGPN--FVWWIAAQSVFYHLYNQVSYMSLDEISPLTFSIGNTMK
          ..L.P.A...EG.Q.W..G...A....G....F..W.....VFYHLYNQ.SY..LDEISPLTFS.GNTMK
Retrocopy FYLFPVAVVIEGSQ-WIQGYHKAIEAVGKSSTFYIWVLLSGVFYHLYNQSSYQALDEISPLTFSVGNTMK

Parental  RISVIVSSIIIFHTPVQPVNALGAAIAVLGTFLYSQV
          R..VI.S....F..PV.P.NALG.AIA..GTFLYSQV
Retrocopy RVVVIISTVLVFGNPVRPLNALGSAIAIFGTFLYSQV

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_19 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00062p00036220	1 retrocopy	retro_atri_14,
Brassica oleracea	Bo9g118840	1 retrocopy	retro_bole_30,
Musa acuminata	GSMUA_Achr7G03380_001	1 retrocopy	retro_macu_2,
Populus trichocarpa	POPTR_0001s44610	1 retrocopy	retro_ptri_19 ,
Physcomitrella patens	PP1S70_177V6	1 retrocopy	retro_ppat_10,
Arabidopsis lyrata	scaffold_802017.1	1 retrocopy	retro_alyr_24,
Theobroma cacao	TCM_030978	1 retrocopy	retro_tcac_18,