RetrogeneDB ID: retro_atri_15

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00065:1394989..1396105(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMTR_s00065p00110200
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00078p00164770
• Aliases: None
• Description: None

Sequence

>retro_atri_15
ATGTCTTGCGCTGTAGTTGCAGGTTCACCAGTCTTCAAGGCCGGTTCTCCATTAAAAATTGACCATCACCTTCAACCTGG
TTATCCAGGCTCTCCGTTACGATGTGGGTTTGTTGGTTTCAGAGAAGAGAGCCAAGGTGGAAGCCCTTCTTTGCGACAGA
TGAGCAATGGAATTAGGGTTTGGGAGGAAGAAGGGTTAGGGTTTTCTCGTGGGGAAGAAGCGGTTAAGGGGATTTTGAAG
AGGAAGAGGCCTGCAAGGCTTCAGATCCCCTCTTCTTCTCCTTGTGCTTCTGGTTTTGAGCCGATTGAGCAGGGACCTGA
ACTTGTTCATGTAGAAAGCGACAGATATTCTGTCATTTGTAAGAGAGGAAGGAGATCAGTCATGGAGGATTGTTATGCTG
CGAACCTGGACCTTTACGGTGATTCGAAACAGGCTTTCTTGGGTGTTTTTGATGGCCATGGAGGAAAACGAGCAGCAGAG
TTTGCTGCACAAAATATGGGGAAGAACATAATGGAGCTCGCGACCAACTGTGATGGTGTAGAAGGAATTGGAGATGCTGT
TAAGAATGGATACTTAGTCACTGATTCAGAATTCTTGCGAGATAAAGCTCGAGGTGGCGCTTGTTGTGTAACAGCATTAA
TCCGAGAAGGCAATTTGGTGGTCTCAAATGCCGGCGACTGTCGCGCCGTAATGAGCAGAGGTGGAACTGCTGAAGCCCTC
ACCTCTGATCACAGGCCTGCAAGAGAAGACGAGAGAGAGAGAATTGAAAGCTTGGGTGGGTATGTGGATCTCCGCCGTGG
GGTGTGGAGGTTACAGGGATGCCTAGCCGTGTCACGAGGGATTGGAGATCAGCATTTGAAACAATGGGTATCTGCAGAAC
CAGAGACAGAGATCCTAAGGATAACCCCCGAATGCGAATTCTTGATCTTAGCTTCAGATGGGCTATGGGAGAAGGTTGGT
AACCAGGAGGCGATCGACTTGGCTCGACCCCTATGTGCGACTACTGATAAGCCATCTCCATTATCAGCCTGTAAAAAGCT
TGTGGATTTATCCTTAAGCAGAGGATCATTGGATGATATCAGTGTGATGATAATCCAGTTGAGCCGGTTTGTATGA

Alignment

ORF - retro_atri_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.52 %
• Parental protein coverage: 91.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LNIHHHLQPGYPGSPLRCG-VGFREESQGGSPSLRQKSNGIRVWEEEGLGFCGGEEGVKGVLKRKRPARL
          L.I.HHLQPGYPGSPLRCG.VGFREESQGGSPSLRQ.SNGIRVWEEEGLGF..GEE.VKG.LKRKRPARL
Retrocopy LKIDHHLQPGYPGSPLRCGFVGFREESQGGSPSLRQMSNGIRVWEEEGLGFSRGEEAVKGILKRKRPARL

Parental  KIPSTSPCTSRRFEPIEQGPEEVHAESDRFSVFCKRGRRAVMEDCYAANLDLYSDSKQAFLGVFDGHGGK
          .IPS.SPC.S..FEPIEQGPE.VH.ESDR.SV.CKRGRR.VMEDCYAANLDLY.DSKQAFLGVFDGHGGK
Retrocopy QIPSSSPCASG-FEPIEQGPELVHVESDRYSVICKRGRRSVMEDCYAANLDLYGDSKQAFLGVFDGHGGK

Parental  RAAEFAAENMGKNIMEHVTKCDGVEGIGDAVKNGYLVTDSEFSREKARGGACCVTALLREGNLVVSNAGD
          RAAEFAA.NMGKNIME..T.CDGVEGIGDAVKNGYLVTDSEF.R.KARGGACCVTAL.REGNLVVSNAGD
Retrocopy RAAEFAAQNMGKNIMELATNCDGVEGIGDAVKNGYLVTDSEFLRDKARGGACCVTALIREGNLVVSNAGD

Parental  CRAVMSRGGTAEALTSDHRPSREDEKERIESLGGYVDLCRGVWRLQGCLAVSRGIGDQHLKQWVSAEPET
          CRAVMSRGGTAEALTSDHRP.REDE.ERIESLGGYVDL.RGVWRLQGCLAVSRGIGDQHLKQWVSAEPET
Retrocopy CRAVMSRGGTAEALTSDHRPAREDERERIESLGGYVDLRRGVWRLQGCLAVSRGIGDQHLKQWVSAEPET

Parental  EILRITPECEFLILGSDGLWDKVGNQEAIDLARPLCATTDKPSPLSA
          EILRITPECEFLIL.SDGLW.KVGNQEAIDLARPLCATTDKPSPLSA
Retrocopy EILRITPECEFLILASDGLWEKVGNQEAIDLARPLCATTDKPSPLSA

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_15 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_s00078p00164770	1 retrocopy	retro_atri_15 ,
Brachypodium distachyon	BRADI1G65520	1 retrocopy	retro_bdis_27,