RetrogeneDB ID: retro_atri_14

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00048:4904276..4905485(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMTR_s00048p00229560
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00062p00036220
• Aliases: None
• Description: None

Sequence

>retro_atri_14
ATGTCTTCCATGCCACCTTTACTTTCTCTCTTCACCCCAAAATCTTGCCTGAAACCCCCAAAAAAATCTCATTTATCCCC
AAATCTTCCCAAAAATCCCCTTCTGTCTCACCAAATATTGCAAATAAAACATGCCCAATATGTGTCTGAGGTCCACGGCC
TTCAATATCAATATGCATCACATAGTTTTTATCCCCAAAATTACTCAACAAAATATCTAAAGAGACCCAAACTCCATATC
CCTAGAGCTAGTGCAAGCTCTGATCCAATTACAAATGCAGAGAAGAGAAAAGGCATAGGAACCCTAAAACTTGGCCTTGT
ATTTGGGCTCTGGTATTTATACAATGTCATCTTCAACATATACAACAAGAAGGTGCTCATTCTCTTCCCTTATCCCTGGT
TTCTGGCCTCTTTCCAGCTATTCACTGGCTCTCTATGGATGCTTTTTCTCTGGTTTTTTAAGTTTCAACCATGCCCAACA
ATCTCCAAGGGCTTCATTCTTGCCCTGCTTGGCCCTGCCTTCTTCCACACAGTGGGTCACATATCTGCCTGTGTTTCTTT
ATCTAGAGTTGCAGTCTCATTTACCCATGTCATAAAATCATCAGAGCCTGTGTTTTCGGTGGTTTTCTCGGCCTTTTTAG
GAGAAAGATACCCATTTCTAGTATGGCTCTCTCTCTTCCCAATTGTATTTGGCTGTTCTTTGGCAGCCATTACTGAACTC
AGCTTTAATTTGCAGGGATTTTATGGGGCAGTTATCAGTAATATTGGGTTTGTTCTTAGGAATATTTATTCCAAGAAGAG
TTTGGGAGAATTTAAGGATATTGATGGACTTAATCTTTATGGAGTGATCAGTATTTTGTCATTTTTTTACCTGTTTCCAG
TGTCCATTGTTGTGGAGGGATCACAGTGGGTAGAGGGTTTTAACAGTGCAGTAAAAGCAATTGGGAAGCCATGGATTTTC
TTACTTTGGGTGTTAATTTCTGGGGTTTTTTACCATTTATATAACCAGTCTTCATATGAAGCTCTTGATGAGATAAGTCC
ATTGAGCTTTTCAGTTGGGAATACCATGAAGAGGGTTGTGGTTATTGTGGCCAGTCTTTTGGTGTTTAGGAATCCTATTA
GACCTCTCAATGCATTGGGATCTGCTGTAGCTATTCTGGGTACCTTCCTATATTCTCAGGCCACACAAAAGATCAAAGCA
AAAAGATGA

Alignment

ORF - retro_atri_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.47 %
• Parental protein coverage: 74.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKIGIYFATWWALNVVFNIYNKKVLNAFPYPWLTSTLSLATGSLMMILSWATRIAEAPKTDFDFWKALAP
          LK.G..F..W...NV.FNIYNKKVL..FPYPW......L.TGSL.M...W.......P.....F..AL..
Retrocopy LKLGLVFGLWYLYNVIFNIYNKKVLILFPYPWFLASFQLFTGSLWMLFLWFFKFQPCPTISKGFILALLG

Parental  VAIAHTIGHVAATVSMSKVAVSFTHIIKSAEPAFSVLVSRFLLGETFPVPVYLSLLPIIGGCALAAVTEL
          .A..HT.GH..A.VS.S.VAVSFTH.IKS.EP.FSV..S.F.LGE..P..V.LSL.PI..GC.LAA.TEL
Retrocopy PAFFHTVGHISACVSLSRVAVSFTHVIKSSEPVFSVVFSAF-LGERYPFLVWLSLFPIVFGCSLAAITEL

Parental  NFNMIGFMGAMISNLAFVFRNIFSKRGM-KGKSVSGMNYYACLSILSLLILTPFAIAVEGPKMWAAGWQK
          .FN..GF.GA.ISN..FV.RNI.SK......K...G.N.Y...SILS...L.P..I.VEG...W..G...
Retrocopy SFNLQGFYGAVISNIGFVLRNIYSKKSLGEFKDIDGLNLYGVISILSFFYLFPVSIVVEG-SQWVEGFNS

Parental  ALVDIGPH--FVWWVAAQSVFYHLYNQVSYMSLDEISPLTFSVGNTMKRISVIVSSIIIFHTPVQPINAL
          A...IG....F..WV....VFYHLYNQ.SY..LDEISPL.FSVGNTMKR..VIV.S...F..P..P.NAL
Retrocopy AVKAIGKPWIFLLWVLISGVFYHLYNQSSYEALDEISPLSFSVGNTMKRVVVIVASLLVFRNPIRPLNAL

Parental  GAAIAILGTFFYSQRERERERER
          G.A.AILGTF.YSQ........R
Retrocopy GSAVAILGTFLYSQATQKIKAKR

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_14 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00062p00036220	1 retrocopy	retro_atri_14 ,
Brassica oleracea	Bo9g118840	1 retrocopy	retro_bole_30,
Musa acuminata	GSMUA_Achr7G03380_001	1 retrocopy	retro_macu_2,
Populus trichocarpa	POPTR_0001s44610	1 retrocopy	retro_ptri_19,
Physcomitrella patens	PP1S70_177V6	1 retrocopy	retro_ppat_10,
Arabidopsis lyrata	scaffold_802017.1	1 retrocopy	retro_alyr_24,
Solanum lycopersicum	Solyc07g064270.2	1 retrocopy	retro_slyc_32,
Theobroma cacao	TCM_030978	1 retrocopy	retro_tcac_18,
Vitis vinifera	VIT_10s0116g00760	1 retrocopy	retro_vvin_26,