RetrogeneDB ID: retro_atri_1

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00022:1554275..1555130(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMTR_s00022p00118880
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00040p00218420
• Aliases: None
• Description: None

Sequence

>retro_atri_1
ATGGCTGAGCATTTGGCTTCAATATTTGGTACAGAGAAGGACAGGGTTAACTGCCCCTTCTATTTCAAGATTGGAGCTTG
CAGGCATGGTGATCGATGTTCTCGTCTTCATAATCGCCCAACCATAAGCCCCACTCTCCTTCTCTCTAACATGTATCAGA
GACCCGACATGATGACACCAGGTGTTGATCCCCAAGGCCAAGCCATGGAACCCCAAAAAATCCAAGAACACTTTGAAGAT
TTCTATGAAGACATATACGAGGAATTAAGCAAGTTTGGTGAGATCGAAAGCCTCAATGTGTGCGACAATTTAGCAGATCA
CATGGTGGGTAATGTCTATGTTCAGTTCAAAGAAGAGGAGCAAGCAGCTGCCGCTCTGCAAGCTATGCAATATCGATACT
ATTCAGGTCGACCCATAATCATTGATTTCTCGCCTGTTACTGATTTTCGAGAAGCGACTTGTAGGCAATACGAAGAGAAC
AACTGTAACAGAGGTGGGTATTGCAATTTCATGCATGTGAAGCAAATTGGAAGGGAATTACGGAGAAAGCTGTTCGGAAG
GAACAGGAGATACAGGAGGAGCAGGAGTAGGAGTAGGAGTGTGAGCCCTGGTCACAGGAGGGAATCAGAGAGAAAGGGCT
ATGGGGATCATGGTAGAAGGAGCTATGATAGATATGATAAGCACGGAAGCCATGATAGGCATGGGAGCTATGACAAGTAT
GATAGGCATGGGAGGCATGACAGGCATGGAAGGCATGGGAGTCCAAAGAGAACGAGGAGTCCAGTTCGCGAAGGAAGTGA
GGAAAGGAGGGCGAGGATCGAACAGTGGAACAAGGAGCGAGAGGAGAATCATTAA

Alignment

ORF - retro_atri_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.99 %
• Parental protein coverage: 97.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEHLASIFGTEKDRVNCPFYFKIGACRHGDRCSRLHTKPSISPTLLLSNMYQRPDMVTPGMDPQGQAMD
          MAEHLASIFGTEKDRVNCPFYFKIGACRHGDRCSRLH..P.ISPTLLLSNMYQRPDM.TPG.DPQGQAM.
Retrocopy MAEHLASIFGTEKDRVNCPFYFKIGACRHGDRCSRLHNRPTISPTLLLSNMYQRPDMMTPGVDPQGQAME

Parental  PRKIQEHFEDFYEDLFEELSKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRALSNRFYAGRPII
          P.KIQEHFEDFYED..EELSK.GEIESLN.CDNLADHMVGNVYVQF.EEE.AA.AL.A...R.Y.GRPII
Retrocopy PQKIQEHFEDFYEDIYEELSKFGEIESLNVCDNLADHMVGNVYVQFKEEEQAAAALQAMQYRYYSGRPII

Parental  VDFSPVTDFREATCRQYEENTCNRGGYCNFMHLKKISRELRRQLFGRYRRRHSRSRSRSRSHSPYRPRIH
          .DFSPVTDFREATCRQYEEN.CNRGGYCNFMH.K.I.RELRR.LFGR..RR..RSRSRSRS.SP...R..
Retrocopy IDFSPVTDFREATCRQYEENNCNRGGYCNFMHVKQIGRELRRKLFGR-NRRYRRSRSRSRSVSPGHRRES

Parental  DERPHGGRGRGRRYDDRDFHHER-RPRSRSPGRRRGRSRSPGLRRNRSPVREGSAERRAKIEQWNREREQ
          .....G..GR.R.YD..D.H....R..S.....R.GR....G..R..SP.R..S..R....E...R....
Retrocopy ERKGYGDHGR-RSYDRYDKHGSHDRHGSYDKYDRHGRHDRHG--RHGSPKRTRSPVREGSEERRARIEQW

Parental  KSTDNEN
          .....EN
Retrocopy NKEREEN

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_1 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00040p00218420	1 retrocopy	retro_atri_1 ,
Theobroma cacao	TCM_041518	1 retrocopy	retro_tcac_16,
Vitis vinifera	VIT_08s0007g03950	1 retrocopy	retro_vvin_15,