RetrogeneDB ID: retro_atri_9

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00047:1613694..1614315(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMTR_s00047p00121790
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00080p00025480
• Aliases: None
• Description: None

Sequence

>retro_atri_9
ATGGCAGACTCAGACAACGAATCGGGGGGCCAGATGAACAGCGGACCGGGAAACAGTGAATTCTCTCCTCGAGAGCAAGA
CCGCTTCCTCCCCATCGCCAACGTGAGCCGAATTATGAAGAAAGCTCTCCCTGCAAATGCAAAGATCTCCAAAGACGCAA
AAGAAACAGTTCAAGAATGCGTCTCCGAGTTCATAAGCTTCATAACAGGGGAAGCCTCTGATAAATGTCAGAGAGAGAAG
AGGAAGACTATTAATGGGGATGATTTGCTTTGGGCCATGACCACTCTCGGGTTTGAAGAGTATGTTGAGCCATTGAAGAG
TTACCTGCAAAAGTTTAGAGAGATGGAGGGGGAGAAGAGCAATATGGGGAGGAGTGAGAAAGAGGGAGGTGGGGGCAATG
GAGCCAATAGTAACAGTAGTGGTGGCAATCCAATGGGGAACAATAATGGGGGTGGGTATAATGGGGGAATGTATACTGGT
GTGCCATTGATGATGTTTGAGCAGCAACAACAACAGCAACAGCAACAAAGCAATAGGTTATTGGGTTCTTCCTCTTCTTA
TCAGATGGGTGGGAAGAGTGGGTCTTCTGGTGTTCCTGGTCATGCAAGGCATGGGAGGTGA

Alignment

ORF - retro_atri_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.46 %
• Parental protein coverage: 62.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADASASPGSPESPNSGEQSPHSNVREQDRFLPIANISRIMKKALPPNGKIAKDAKETVQECVSEFISFI
          MAD.....G.....NSG........REQDRFLPIAN.SRIMKKALP.N.KI.KDAKETVQECVSEFISFI
Retrocopy MADSDNESGG--QMNSGPGNSEFSPREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFI

Parental  TSEASDKCQREKRKTINGDDLLWAMSTLGFEDYIDPLKVYLQMYREMEGDSKGTKGGDQSAKKESAGVQA
          T.EASDKCQREKRKTINGDDLLWAM.TLGFE.Y..PLK.YLQ..REMEG..K...G...S.K....G..A
Retrocopy TGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVEPLKSYLQKFREMEGE-KSNMG--RSEKEGGGGNGA

Parental  GSSTQQVSHQGSFNQG
          .S........G..N.G
Retrocopy NSNSSGGNPMGNNNGG

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_9 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00080p00025480	1 retrocopy	retro_atri_9 ,
Zea mays	GRMZM5G804893	1 retrocopy	retro_zmay_28,