RetrogeneDB ID: retro_atri_8

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00055:1347311..1349585(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMTR_s00055p00107870
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00129p00121180
• Aliases: None
• Description: None

Sequence

>retro_atri_8
ATGGCTGCTCTGGTTCTGCTTCTCTTCTTATTCTCTCTCGAACTCTCTTCCTGTAGCGCCCAACAAAAGACCTTCATATT
CCTGGTGGATGAGCACTCCAAGCCCTCAGTTTTCTCCTCCCACCAGCTCTGGTACACCTCTGCCTTCATCCACCCTACGC
GTATGGTCCAAGTGTACGATACCGCATTCCATGGCTTCGCGGCACGGCTAGCTGCCGATGAGGCGGCTGAGATTGGAGAG
CACCCTGCAATCCTTGTGGTGCTGGAAGACCAGCCCCGCCAACTCCATACCACTCGCTCCCCACAGTTCTTAGGGCTCAG
CAACCGGCGGGGCCTTTGGTCTGACTCCGACTATGGCTCTGATGCCATCATTGGTGTTCTTGATACCGGTATATGGCCGG
AGCGCCGCAGCTTCGCCGACCACAACATGGGCCCTATCCCTGCTCGATGGAAGGGTGAATGTGAAACCGGCCCTGGCTTT
ACCACAGCCCACTGTAACCGCAAGCTAATTGGAGCTCGATTTTTCGCCAGGGGTTATGAGGCCACTGCTGGCGCTGTGAA
CGACACTGCTGAGTTCCGGTCGCCCAGGGACGCCGATGGACACGGTTCACATACCGCATCGACAGCCGCCGGGAGGTATG
TTTTTCAGGCAAATATGTCTGGATATGCATCTGGAATAGCCCGGGGTGTAGCCCCAAAGGGGCGACTGGCGGTCTACAAG
GTCTGCTGGAAAGCAGGCTGCTTCGACTCAGACATCCTTGCCGCCTTCGATCGAGCAATTGCAGACGGCGTGGATGTCAT
CTCTGTATCAATTGGCGGGGGATCGGTGCCTTATTACCTTGACTGCATCGCTCTCGGATCCTTTGGGGCCACTGCTAAAG
GGGTCTTTGTGGCGTCTTCGGCCGGGAATGATGGCCCAACCGGACTTTCAGTCACGAACCTTGCCCCTTGGCTAACAACC
GTTGGAGCCGGCAGCATCGACCGGAATTTCCCTGCCGATGTCACCCTCGGCAATGGTAAGACTCTGCATGGTGTTTCCCT
CTACTCGGGGAGCTCGCTTGCAGGAAAAATGTACCCCGTGGTCTACCCTGGGAAAGCAGGCGGGCTCTCGACTGCCCTTT
GCATGGACAACTCCTTGAGTCCGGGTGCCGTCAAGGGGAAGATCGTGGTATGCGATAGAGGCAACAATCCCCGTGTGGCA
AAGGGCTTGGTCGTGAAGAACGCTGGCGGAGTAGGGATGATCCTTGCCAATGCCGCTTCCAATGGTGAGGGCCTCGTCGG
TGATGCCCACCTCCTCCCTGCGTGCACCGTTGGGGCAGATGAAGGCGAAGCCATCAAATCCTACATATCATCCGCCAACA
ACCCAATCGCAACCCTTGGCTTCAAGGGCACCGTCCTCGGAGTGAAACCGGCGCCGGTGGTGGCCTCCTTCTCAGCCCGC
GGCCCCAACGGCCAGACACCTGAAATCCTGAAGCCCGACCTCGTTGCCCCAGGCGTCAACATACTCGCTGCTTGGACCGA
CGCCGTAGGCCCAACAGGCCTGAGCTCCGACTTCAGGAAGACGGAATTCAACATCCTTTCAGGCACATCCATGGCCTGTC
CCCACGTTGCTGGGGCGGCCGCCCTGCTAAAGGGCGCCCACCCTGGCTGGAGCCCTGCCGCCATCCGCTCCGCCCTAATG
ACCACAGCGACTGTCACCGACAACCGCGGGCAGTCCATGACCGATGAGTCCACCCAGAAACCCTCAAACCCCTTCGATTA
CGGAGCCGGCCATGTCGAACTGGACCGGGCCATGGATCCCGGCCTCATATACGACATCACCACAGAAGACTATGTCAACT
TCCTATGCGCCATCAAATACAGCCCCAAGGCCATCCAGGTGATCACGAGGAAATCAGTGAGCTGCCCGAGACGAATAAGC
GGGCCCGAGAGCTTGAATTACCCATCTATCATGGCATTCATGGAGGGGAACAGGTCGGGTTACCTCAGAAAAGTGTTTCT
GAGGACGGCAACAAACGTCGGTGCCACAGTGTCGACGTACAGAGTGAGCGTTACGATGCCGGCGAAGGGCATCGCCGTGT
CGGTGAAACCGTCGACTCTCGTTTTCACGGGACTGGGGCAGAAGCAGAGCTACGCCGTGACAGTGGTGGCCGACCGCCGG
AGCTTCATGTCGGGCGGGGGAGGCTCAGCATTCGGGTACATGGTGTGGTCTGACGGCAAGCATGAGGTTCGGAGCCCCAT
CGTGGTGGCTCTAACTCAGAGCGTCGGCGACTGA

Alignment

ORF - retro_atri_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.46 %
• Parental protein coverage: 76.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIHTYSTVFHGFSAKITPSMAKKLEKMAGILSVIPDKARQLQTTRSPQFLGLKRKDTMGLLAESDFGSNL
          ....Y.T.FHGF.A......A........IL.V..D..RQL.TTRSPQFLGL......GL...SD.GS..
Retrocopy MVQVYDTAFHGFAARLAADEAAEIGEHPAILVVLEDQPRQLHTTRSPQFLGLSNR--RGLWSDSDYGSDA

Parental  IIGVLDTGIWPERRSFSDRGLGPVPSSWKGECVEGRGFSASSCNRKLVGARYFSGGYEAMSGPMNETAEY
          IIGVLDTGIWPERRSF.D...GP.P..WKGEC..G.GF....CNRKL.GAR.F..GYEA..G..N.TAE.
Retrocopy IIGVLDTGIWPERRSFADHNMGPIPARWKGECETGPGFTTAHCNRKLIGARFFARGYEATAGAVNDTAEF

Parental  RSPRDSDGHGTHTASIAAGRYVYPADMLGYAHGVAAGMAPKARLAAYKVCWTSGCFDSDILAAFDRAVLD
          RSPRD.DGHG.HTAS.AAGRYV..A.M.GYA.G.A.G.APK.RLA.YKVCW..GCFDSDILAAFDRA..D
Retrocopy RSPRDADGHGSHTASTAAGRYVFQANMSGYASGIARGVAPKGRLAVYKVCWKAGCFDSDILAAFDRAIAD

Parental  GVNVISLSVGGGVVPFYLDSIAIGAFAAAQHNIFVSASAGNEGPAESTVTNVAPWITTVGAGTLDRNFPA
          GV.VIS.S.GGG.VP.YLD.IA.G.F.A.....FV..SAGN.GP....VTN.APW.TTVGAG..DRNFPA
Retrocopy GVDVISVSIGGGSVPYYLDCIALGSFGATAKGVFVASSAGNDGPTGLSVTNLAPWLTTVGAGSIDRNFPA

Parental  EISLGNGVKFSGVSLYSGPHLSQKPEIPLVYAGNAPATGGDGYSSSLCMENSLDPEMVRGKIVLCDRGSN
          ...LGNG....GVSLYSG..L..K...P.VY....P...G.G.S..LCM.NSL.P..V.GKIV.CDRG.N
Retrocopy DVTLGNGKTLHGVSLYSGSSLAGKM-YPVVY----PGKAG-GLSTALCMDNSLSPGAVKGKIVVCDRGNN

Parental  ARVNKGIVVKEAGGVGMILANGAGDGEGLVADSHVLPAAAIGANAGDLVRSYVNSVKNPTATIRFQGTQL
          .RV.KG.VVK.AGGVGMILAN.A..GEGLV.D.H.LPA...GA..G....SY..S..NP.AT..F.GT.L
Retrocopy PRVAKGLVVKNAGGVGMILANAASNGEGLVGDAHLLPACTVGADEGEAIKSYISSANNPIATLGFKGTVL

Parental  GVRPAPVVASFSARGPNPVAPEILKPDVIAPGVNILAAWTDDVGPAGVTSDRRKTEFNILSGTSMACPHV
          GV.PAPVVASFSARGPN...PEILKPD..APGVNILAAWTD.VGP.G..SD.RKTEFNILSGTSMACPHV
Retrocopy GVKPAPVVASFSARGPNGQTPEILKPDLVAPGVNILAAWTDAVGPTGLSSDFRKTEFNILSGTSMACPHV

Parental  SGLAALLMGAHPDWTPSMIRSALMTTAYVRDNRGGPHMLDEATWNASSPLDYGAGHVDPNRAMVPGLVYD
          .G.AALL.GAHP.W.P..IRSALMTTA.V.DNR.G..M.DE.T...S.P.DYGAGHV...RAM.PGL.YD
Retrocopy AGAAALLKGAHPGWSPAAIRSALMTTATVTDNR-GQSMTDESTQKPSNPFDYGAGHVELDRAMDPGLIYD

Parental  LTIQDHVDFLCSSNYSAKNIEIITRKPEKCSQKVTHAGNLNYPAISAVFE
          .T..D.V.FLC...YS.K.I..ITRK...C.........LNYP.I.A..E
Retrocopy ITTEDYVNFLCAIKYSPKAIQVITRKSVSCPRRISGPESLNYPSIMAFME

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_8 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00129p00121180	1 retrocopy	retro_atri_8 ,