RetrogeneDB ID: retro_atri_11

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00040:4332680..4333955(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMTR_s00040p00217260
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00080p00093010
• Aliases: None
• Description: None

Sequence

>retro_atri_11
ATGAAGGCCATCCCATTAAACTCCAGCTTGCACAGCTCCGCCCTAGCCGAGCCCCATCATTCCCTGCAATGTCCACTGGT
GGCGCCATCCCGCCTCCTGCATCCCCGCCACCGCCTGCGTCCCATCATCCACTGCAGCAGTGTCAATGGCGTTCACGGCG
CCGCCACCCACAGCCGTGCCGCCTGGCAGAGCTCCTGCGCTATCCTCTCGAGCAAGGTCGTCGCCGAGCAGCAGAAGGTC
GATAAAGGTACCGACATGGTCTCCCCCGCCATCAATGGCCACAAGTCCCTTGACCTTGTCCCTGTCGGGAATGCTGGCGT
AAACCTCCCGAAGCCCCTCTCGATCTCGGACCTTGCGCCCGCCCCGATGCATGGCTCCAGTCTGCGCGTCGCATACCAGG
GCGTCCCCGGGGCATACAGCGAGGCCGCCGCCGGCAAGGCATATCCTGACTGTGAGGCGATCCCCTGTGACCAGTTTGAG
GTGGCCTTCCAGGCGGTGGAGCTTTGGCTGGCAGACCGCGCCGTGCTTCCCGTCGAGAACTCCCTCGGCGGCAGCATCCA
CCGCAACTACGACCTCCTGCTCCGCCACCGCCTCCACATCGTTGGCGAGGTCCAGTTGCCGGTCCACCACTGTCTCCTCG
CCCTCCCCGGCATCCGCAAGGAGTACCTCACCCGCGTCATCAGCCACCCCCAGGCCCTCGCCCAGTGCGAGCACACCCTC
ACCAAGCTCGGCCTCTCTGTCGCCCGCGAGGCCGTCGATGATACCGCTGGTGCTGCAGAGTTTGTCGCCGCAAACGGCCT
CCGCGACACCGCCGCAATCGCCAGCGCCCGTGCCGCCGAGCTCTACGGCCTCTCCATCCTCGCCGATGGCATCCAGGACG
ACTCCAGCAACGTCACCCGGTTCGTCATGCTTGCCCGCGAGCCGATCGTGCCCCGCACAGATCGGCCGTTCAAGACCAGC
ATCGTCTTCGCCCATGATAAGGGCACCTCGGTGCTCTTCAAGGTCCTCTCCGCCTTCGCCTTTCGGAACATCAGCCTGAC
CAAGATCGAGAGCCGGCCGCACCGCAACCGGCCGATCCGGCTCGTCGACGACGCCAATGTTGGTACTGCCAAGCACTTCG
AGTACTTGTTTTATGTGGATTTTGAGGCCTCCATGGCCGATGTGAGAGCTCAGAATGCCTTGGCCGAGGTCCAGGAATTT
ACAACTTTCTTGAGGGTATTAGGGTCATATCCCATGGACATGACCCCATGGATCCCATCTCGTGAAAACTCCTAA

Alignment

ORF - retro_atri_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.77 %
• Parental protein coverage: 79.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PAPKESVSLPRPLSVTDLSGSVNRGSRLRVAYQGVPGAYSEAAAAKAYPNCEAVPCEQFETAFGAVERWL
          P.....V.LP.PLS..DL......GS.LRVAYQGVPGAYSEAAA.KAYP.CEA.PC.QFE.AF.AVE.WL
Retrocopy PVGNAGVNLPKPLSISDLAPAPMHGSSLRVAYQGVPGAYSEAAAGKAYPDCEAIPCDQFEVAFQAVELWL

Parental  VDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVQFAVRHCLLAVPGVKIENLKRVLSHPQALSQCENKL
          .DRAVLP.ENSLGGSIHRNYDLLLRHRLHIVGEVQ..V.HCLLA.PG...E.L.RV.SHPQAL.QCE..L
Retrocopy ADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGIRKEYLTRVISHPQALAQCEHTL

Parental  TKLG--VVREAVDDTAGAAHLVATHELQDAGAVASARAAEIYGLDILAQDIQDDSDNVTRFLMLAREPII
          TKLG..V.REAVDDTAGAA..VA...L.D..A.ASARAAE.YGL.ILA..IQDDS.NVTRF.MLAREPI.
Retrocopy TKLGLSVAREAVDDTAGAAEFVAANGLRDTAAIASARAAELYGLSILADGIQDDSSNVTRFVMLAREPIV

Parental  PGVDRPFKTSIVFSLEEGSGVLFKALAVFAMRQINLTKIESRPRRKHSLHIPIPEECSNGSPKYFDYLFY
          P..DRPFKTSIVF....G..VLFK.L..FA.R.I.LTKIESRP.R.....I........G..K.F.YLFY
Retrocopy PRTDRPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRP--IRLVDDANVGTAKHFEYLFY

Parental  VDFDASMADERAQNALRHLREFATFLRVLGSYPKDIS
          VDF.ASMAD.RAQNAL....EF.TFLRVLGSYP.D..
Retrocopy VDFEASMADVRAQNALAEVQEFTTFLRVLGSYPMDMT

Legend:

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

Expression

RNA-Seq

Amborella trichopoda was not studied using RNA-Seq expression data.

ChIP-Seq

Amborella trichopoda was not studied using ChIP-Seq data.

EST

Amborella trichopoda was not studied using EST data.

TSS

Amborella trichopoda was not studied using FANTOM5 data.

Lab

retro_atri_11 was not experimentally validated.

Homology

Retrocopy orthology:

Amborella trichopoda 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00080p00093010	1 retrocopy	retro_atri_11 ,
Oryza brachyantha	OB07G32920	1 retrocopy	retro_obra_27,
Oryza nivara	ONIVA03G14420	1 retrocopy	retro_oniv_4,
Oryza glaberrima	ORGLA03G0127300	1 retrocopy	retro_ogla_17,
Oryza rufipogon	ORUFI03G13820	1 retrocopy	retro_oruf_22,