RetrogeneDB ID: retro_atri_6

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00069:3596057..3597095(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMTR_s00069p00197560
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00080p00074790
• Aliases: None
• Description: None

Sequence

>retro_atri_6
ATGACAGAAGGCCATGGCTGGACAACGCGACGAGGAAGCAACCCTAAACTCGAAGAAGCCATAGACATTCCCCCGACACC
AACTGGTGACATCAAATATGGAGCCAGTTTCCCTGCAACTCAAGACCTAACCACTGGTTTGATCATTGCTTCATGGTATG
CTTCGAACATAGGAGTCCTCCTCCTCAACAAATACCTTCTAAGCTTCTATGGCTTTCGATATCCCATCTTCTTAACCATG
CTACATATGGTCGCCTGCTCTGTCTATAGCTCCATAGCCATTCACTGGCTCGCGATTGTCCCCCCTCAAAACTTAGTTTC
TCGACGCCAATTCCTCAAAATTTTTGCGCTCTCTCTCATATTCTGCTTCTCTGTAGTTTGTGGGAACACATCGCTTCGGT
ATTTACCTGTCTCTTTTAACCAGGCAATTGGGGCCACTACCCCATTTTTCACTGCTGTTTTTGCGTTCATTATCACTTGT
AAAAGAGAGTCACCTGGTGTTTATCTAGCTCTGTTACCTGTGGTTTTAGGCATCGTTGTAGCAAGCAATAGTGAGCCCCT
TTTCCATCTGTTTGGATTCATTGTTTGCCTTGGCTCCACAGCTGGTCGAGCTTTGAAATCAGTGGTTCAAGGCCTATTGC
TCACCTCTGAGGCTGAAAAATTACACTCTATGAATTTGCTCTTGTATATGGCTCCAATGGCTGCTTTGTTATTGCTTCCG
TTCTCTCTCTTTGTAGAGGGAGATGTAGCGAGTGTAGCTTTGGCAAAAGCAAGGGTTGATCCCATGATTGTAGTTCTTTT
GTTGGGCAATATGACTGTTGCTTATCTTGTGAATTTGACGAATTTTTTGGTAACAAAGCATACAAGTGCGCTTACTTTGC
AAGTTCTTGGTAATGCAAAGGCAGCAGTAGCAGCTGTGGTTTCGGTGTTGATTTTTAGGAACCCAGTTACCGTGATGGGA
ATGACAGGTTTTGCAGTGACAATCATGGGTGTGGTTCTTTACAGTGAAGCAAAGAAGAGGTCGAAGGTTCCACATTAG

Alignment

ORF - retro_atri_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.89 %
• Parental protein coverage: 96.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSSKMFTLGLV-GAWYSSNIGVLLLNKYLLSNYGFRFPIFLTMCHMTACSLLSYVAIAWMKIVPMQTIRS
          P.....T.GL....WY.SNIGVLLLNKYLLS.YGFR.PIFLTM.HM.ACS..S..AI.W..IVP.Q...S
Retrocopy PATQDLTTGLIIASWYASNIGVLLLNKYLLSFYGFRYPIFLTMLHMVACSVYSSIAIHWLAIVPPQNLVS

Parental  RIQFVKIAALSAIFCASVVSGNVSLRYLPVSFNQAIGATTPFFTAVFAYIMTVKREAWLTYVTLIPVVAG
          R.QF.KI.ALS.IFC.SVV.GN.SLRYLPVSFNQAIGATTPFFTAVFA.I.T.KRE....Y..L.PVV.G
Retrocopy RRQFLKIFALSLIFCFSVVCGNTSLRYLPVSFNQAIGATTPFFTAVFAFIITCKRESPGVYLALLPVVLG

Parental  VIIASGGEPSFHLFGFLMCIAATAARALKSVLQGILLSSEGEKLNSMNLLLYMAPIAVVLLLPATLLMEP
          ...AS..EP.FHLFGF..C...TA.RALKSV.QG.LL.SE.EKL.SMNLLLYMAP.A..LLLP..L..E.
Retrocopy IVVASNSEPLFHLFGFIVCLGSTAGRALKSVVQGLLLTSEAEKLHSMNLLLYMAPMAALLLLPFSLFVEG

Parental  NVLGITVAQARHDVKVVWYLLFNSSLAYFVNLTNFLVTKHTSALTLQVLGNAKGAVAVVVSILLFRNPVS
          .V.....A.AR.D...V..LL.N...AY.VNLTNFLVTKHTSALTLQVLGNAK.AVA.VVS.L.FRNPV.
Retrocopy DVASVALAKARVDPMIVVLLLGNMTVAYLVNLTNFLVTKHTSALTLQVLGNAKAAVAAVVSVLIFRNPVT

Parental  VVGMLGYSITVFGVILYSEVKKRSK
          V.GM.G...T..GV.LYSE.KKRSK
Retrocopy VMGMTGFAVTIMGVVLYSEAKKRSK

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_6 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00080p00074790	1 retrocopy	retro_atri_6 ,
Musa acuminata	GSMUA_Achr10G05900_001	1 retrocopy	retro_macu_3,
Medicago truncatula	MTR_3g070000	1 retrocopy	retro_mtru_1,
Solanum tuberosum	PGSC0003DMG401027186	1 retrocopy	retro_stub_37,
Prunus persica	PRUPE_ppa009115mg	1 retrocopy	retro_pper_41,
Solanum lycopersicum	Solyc05g052790.2	1 retrocopy	retro_slyc_35,
Theobroma cacao	TCM_042615	1 retrocopy	retro_tcac_6,
Vitis vinifera	VIT_13s0019g03270	1 retrocopy	retro_vvin_10,