RetrogeneDB ID: retro_atri_13

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00029:849581..850328(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMTR_s00029p00077410
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00045p00165520
• Aliases: None
• Description: None

Sequence

>retro_atri_13
ATGTTCAGGGCAGCACTAAGATCCGCCATTGGAGCCAAGTCCCGTCTCCAAACCCTGGACCCAACCCAAATGAGATCTTA
TGGCCTCATCCCCATGGTCATCGAGCAAACGTCGCGAGGCGAGCGGGCCTACGACATATTTTCTCGCCTCCTGAAAGAGC
GCATCGTGTGCATCACAGGTCCCATCGCCGACGACACAGCCTCGCTGGTGATGGCGCAGCTCCTATATCTCGAATCGGAG
AACCCCTCGAAACCGATAAACATGTATATCAACTCCCCTGGCGGGGTCGTGACTGCGGGCCTGGCCATATATGACACTAT
GCAGTATATTCACTCTCCGATCAGGACGATATGCGTTGGGCAGGCGGCCTCGATGGGATCGTTCCTGCTGGCGGCTGGGG
CACCAGGAGAGCGGCGGGCACTCCCAAACGCACGAATAATGGTGCACCAGCCTTCGGGTGGGGCCCAGGGGCAGGCGAGC
GATATCGCGATACACGCAGAGGAGATTTTGAAGACCAAGGACAGGTTGAATGCCTTGTATGCAAAGCACACAGGGCAGGA
TGCAGAGGTGATAAGGCAGCGTCTGGAGAGGGACACTTTCATGTCGGCGGAGGAGGCATGCAAGTTCGGGATTGTGGATG
AGGTAATTCAGCGGAGACCGGTGTGGTTGGTGTCAGATGCGGTGGGATCCGCGCCGTCTTCTTCATCATTGGAGGGGAAG
GCAAATGATAAAGAGGGCTCCAAATGA

Alignment

ORF - retro_atri_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.57 %
• Parental protein coverage: 59.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERFQSVISQLFQHRIIRCGGAVDDDMANVIVAQLLYLDAVDPYKDIVIYVNSPGGSVTAGMAIFDTMKHI
          ER.....S.L...RI....G...DD.A....AQLLYL....P.K.I..Y.NSPGG.VTAG.AI.DTM..I
Retrocopy ERAYDIFSRLLKERIVCITGPIADDTASLVMAQLLYLESENPSKPINMYINSPGGVVTAGLAIYDTMQYI

Parental  RPDVSTVCVGLAASMGAFILSSGTKGKRYSLPNSRIMIHQPLGGAQGGQTDIDIQANEMLHHKANLNGYL
          .....T.CVG.AASMG.F.L..G..G.R..LPN.RIM.HQP.GGAQG...DI.I.A.E.L..K..LN...
Retrocopy HSPIRTICVGQAASMGSFLLAAGAPGERRALPNARIMVHQPSGGAQGQASDIAIHAEEILKTKDRLNALY

Parental  SYHTGQSLDKINQDTDRDFFMSAKEAKDYGLIDGII
          ..HTGQ....I.Q...RD.FMSA.EA...G..D..I
Retrocopy AKHTGQDAEVIRQRLERDTFMSAEEACKFGIVDEVI

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_13 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00045p00165520	1 retrocopy	retro_atri_13 ,
Oryza brachyantha	OB03G24650	1 retrocopy	retro_obra_19,
Oryza glaberrima	ORGLA03G0142400	1 retrocopy	retro_ogla_20,
Triticum aestivum	Traes_4AS_C67AE6944	1 retrocopy	retro_taes_83,