RetrogeneDB ID: retro_ptri_10

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 14:12463400..12465503(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0014s16350
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0002s22260
• Aliases: None
• Description: None

Sequence

>retro_ptri_10
ATGGAACCAAACACAGAGGAGGCTGTCATGGCAAAAGAGATTGCTGAGAAGCGATTTGCTGAAAGAGATTTTACTGGTGC
AAAGAATTATGCTTTGAAGGCAAAAACTTTGTGTCCTGGATTAGAGGGTATATCTCAGATGGTGGCCACTTTTGAAGTTT
ATATTGCATCTCAGGCCAAATGCAATGGTGAAATTGACTATTTCTCTGTTCTTGGATTGAAGCCTTCTGCAGATAAAGAT
GCAGTGAAAAGGCAGTATCGAAAGATGGCTGTGTTGCTCCATCCTGATAAGAATAAAACTGTGGGAGCTGATGGAGCATT
TAAACTAGTATCTGAAGCATGGACTATGTTGTCAGATAGTCTTAAGAAAAACTCTTATGATGTAAAGAGAAACAAAAAGA
TGGCATCTTGTGTTGTTCAGACAAACCTATCTTCAGTTCATGCTGCTGGGGTTACAGGATACAGCCATTGTTCCAATTCA
CCAACTGCTCACGGACTTGATACTTTCTGGACAGTTTGCACCTCTTGCAAAGTTCAGTATGAGTATCTACGGAAGTATGT
GAATAAGAGACTTTCTTGTAAGAACTGCCGGGGTACTTTCATTGCTGTGGAAACTGGGGCAGCTCCAGTCAGTGGTTCTT
TCCCCTACTGTCCTTGGTCATATGTCCCTGGTAATGGGCATAGAAGTCATGGATATGATGGGGTTGCATATGTCCCAACC
ACCTCTACCTTATACTCAGGAAATGGGGTCTCAGGATTGCATACTGGACATGGGTACGAGTATGTTTCAAATTTATCATT
TCAATGGAGCTCATTTTCTGGAACTCCAGGGAGTGTTGTTGGTCCCAATGGATCATGTGCATTATCTGCTGATACTGTTT
ATCAGGCTAATGGAAGTGCCAGTGCAGCAAAGGTTAAACCAGCAGCCAATGGAAGGCGATCCATGAAAACTGCCACAGCA
AAGATAAACTCTGATGTATCTGCAAGCTGTAACGAGTCTTCAGGCTCCAAGACTGGTAGACCTGATAAGAAAAGGAAGGT
TGCTGTTGGATCCGGTTTTAGAAATGGGTGTGAAGAAAAAGAACCAAAGTCCGGTTCTGAAGTTGGATTAGCTAATGGAT
ATAAAAATGTTGAGCATGATGCCAAGCTTTCCAGTCCAATTGAAGTTCCAACAAGACACAGCTCGATTGCTCCGGCTTTT
GATGCTAGAAAGTTGTTGATTGACAAGGCAAGGACTGACATCAGGAAGAAATTGGAGGAGATGAGATTAGCTTCAGCTGC
AGCAGTTAAAGAGAACATGGAAGATCAATCCACAGAGGCAGGAGAGGCTCCTAAACAAGCAAATTCAGATGTTGCTGGCC
ATCAAACAAAGTCAAACAAAATAGGGCCAATCTCGATAACAGTCCCTGATCCTGATTTCCATGATTTTGACAAAGATAGA
GCTGAGGAATGCTTCAAGCCAAAACAAATATGGGCATTGTATGATGAAGATGATGGTATGCCTCGCTTATACTGTTTGAT
TCGCCAGGTGGTCTCAGTTAAACCCTTTAAGATTCTCATCACTTACTTGAACTCTAAAACTGATGGTGAATTTGGGGCAG
TGAATTGGATAGATTCTGGGTTTACTAAATCTTGTGGACACTTCAGAGCACAGAATTCTGATGTTGTTGATCAAGTGAAC
ATTTTCTCTCATGTTTTGAAAGGTGAAAAGGCTGGTAGAGGTGGCTGTGTTCGGATATACCCCAAAAGTGGAGATGTTTG
GGCTGTTTATCGAAACTGGTCACCTGATTGGAACATATCAACCCCAGATGATGTGAGGCACCAGTATGAGATGGTAGAGG
TCCTTGATAAGTACTCTGAAGAGCTTGGAGTTTGTGTTGCTCCTCTGAACAAGCTAGCTGGTTTCAAAACAGTATACCAA
AGGAACGCAGGCAAGGATGCCATGAGATGGATTCCAAGAAGAGAGATGGTACGCTTTTCTCACCAGGTGCCTTCTTGGTC
ACTTGAAGGAGAAGCTAGTAATTTGCCAGGAAAGTGTTGGGATCTGGACCCCGCCGCTACTCCAGACGAGCTACTTCATG
CTGCAACAGAAGCGAAGGCTTAG

Alignment

ORF - retro_ptri_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.7 %
• Parental protein coverage: 59.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SNVSFQWSSFSGTSGDAQRPDKKRKVSIGSTSRNGHEENEPKLGSEVRLANGCANVEHDTKLSIPSEVPT
          S.VS......SG......RPDKKRKV..GS..RNG.EE.EPK.GSEV.LANG..NVEHD.KLS.P.EVPT
Retrocopy SDVSASCNESSGSK--TGRPDKKRKVAVGSGFRNGCEEKEPKSGSEVGLANGYKNVEHDAKLSSPIEVPT

Parental  RRSLIAPAFDARKLLIDKARTDIRKKLEEMRLASAAAVTKNIEDLFTKAGEAPKQSNSDITGHHTKPNKI
          R.S.IAPAFDARKLLIDKARTDIRKKLEEMRLASAAAV..N.ED..T.AGEAPKQ.NSD..GH.TK.NKI
Retrocopy RHSSIAPAFDARKLLIDKARTDIRKKLEEMRLASAAAVKENMEDQSTEAGEAPKQANSDVAGHQTKSNKI

Parental  EPISITVPDPDFHDFDKDRAEECFKPKQIWALYDEDDGMPRLYCLIRQVVSVKPFKIHITYLNSKTDSEF
          .PISITVPDPDFHDFDKDRAEECFKPKQIWALYDEDDGMPRLYCLIRQVVSVKPFKI.ITYLNSKTD.EF
Retrocopy GPISITVPDPDFHDFDKDRAEECFKPKQIWALYDEDDGMPRLYCLIRQVVSVKPFKILITYLNSKTDGEF

Parental  GVVNWIDSGFAKSCGHFRAWNSDVVDQVNIFSHVMKGEKPGRGGCVRIYPKSGDVWAVYQNWSPDWNRST
          G.VNWIDSGF.KSCGHFRA.NSDVVDQVNIFSHV.KGEK.GRGGCVRIYPKSGDVWAVY.NWSPDWN.ST
Retrocopy GAVNWIDSGFTKSCGHFRAQNSDVVDQVNIFSHVLKGEKAGRGGCVRIYPKSGDVWAVYRNWSPDWNIST

Parental  PDDVRHQYEMVEVLDNYSEELGVCVTPLIKLTGFKTVYQRNTDKGAIRWIPRREMVRFSHQVPSWSLEGE
          PDDVRHQYEMVEVLD.YSEELGVCV.PL.KL.GFKTVYQRN..K.A.RWIPRREMVRFSHQVPSWSLEGE
Retrocopy PDDVRHQYEMVEVLDKYSEELGVCVAPLNKLAGFKTVYQRNAGKDAMRWIPRREMVRFSHQVPSWSLEGE

Parental  ASNLPEKCWDLDPAATPDELLHAATEAKA
          ASNLP.KCWDLDPAATPDELLHAATEAKA
Retrocopy ASNLPGKCWDLDPAATPDELLHAATEAKA

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_10 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_0002s22260	1 retrocopy	retro_ptri_10 ,