RetrogeneDB ID: retro_atri_2

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00013:2993386..2994400(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMTR_s00013p00179280
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00025p00110680
• Aliases: None
• Description: None

Sequence

>retro_atri_2
ATGCCTGCTCTACCAGAAGAACCCATGTCTGCTCTGCCAGAAGAACCCCTTCTTGCTTCGAACCCTGATCGATTTTGCAT
GTTTCCCATAAAATATCCCCAAATTTGGGAGATGTATAAGAAAGCAGAGGCCTCTTTCTGGACTGCTGAAGAGGTCGATC
TCTCTCAAGACCTTCAGCACTGGGATTCTCTCACTTCTGGGGAAAAACACTTCATAACCCATGTCCTTGCTTTCTTTGCA
GCTTCTGATGGTATAGTCCTTGAAAACCTTGCGGGTCGATTCATGAAGGAGGTTCAAGTTGCAGAGGCTAGGGCTTTCTA
TGGCTTCCAGATCGCCATTGAAAACATCCACTCTGAGATGTACAGCCTCTTGCTTGAATCTTACATCAAGGATTCCAGTG
AGAAGAGTCGATTGTTCAGGGCTGTTGAAACGGTTCCCTGTGTTGCCAAAAAAGCAGACTGGGCGCTAAAATGGATCAAT
TCCTCTGAATCTTTTGCAGAGAGGTTGATTGCTTTTGCCTGTGTTGAAGGTATCTTCTTTTCTGGTAGTTTTTGTTCCAT
ATTTTGGCTAAAAAAAAGGGGTTTAATGCCTGGTTTAACCTTCTCTAATGAACTCATTTCAAGAGATGAAGGTTTACACT
GTGATTTTGCTTGCCTTCTCTATGATCTTCTAAACCACAAGCTCCCTCAACAAAGCGTTCAAAATATAGTAAGGGAATCT
GTAGAGATAGAGAGAGAATTTGTTTGTGATGCCTTGCCCTGTGCTCTAGTGGGAATGAACGGCAATCTGATGAGCCAGTA
CATCGAATTTGTGGCTGATAGGCTGTTGAATGCTTTGGGGTGTGATAAAATCTATGGGGTTCAAAACCCATTTGATTGGA
TGGAACTCATTTCACTGCAGGGGAAGACTAATTTCTTTGAGAAGAGGGTTGGAGAATACCAAAAGGCTTCAGTGATGAAC
AGTATTAATGGAGATGGGAAGAATCATGTGTTTAGGTTGGATGAGGACTTCTGA

Alignment

ORF - retro_atri_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.04 %
• Parental protein coverage: 99.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AMKPEEEREREEEEILTEKCDRFCMFPIRHKQLWEMYKKAQASFWTAEEVDLSADINQWESLSGNEKHFI
          A...E......EE..L....DRFCMFPI...Q.WEMYKKA.ASFWTAEEVDLS.D...W.SL...EKHFI
Retrocopy ALPEEPMSALPEEPLLASNPDRFCMFPIKYPQIWEMYKKAEASFWTAEEVDLSQDLQHWDSLTSGEKHFI

Parental  SHVLAFFASSDGIVLENLAARFLNDIQLPEARAFYGFQIAMENIHSEMYSLLLETYIKDSREKQRLFNAI
          .HVLAFFA.SDGIVLENLA.RF....Q..EARAFYGFQIA.ENIHSEMYSLLLE.YIKDS.EK.RLF.A.
Retrocopy THVLAFFAASDGIVLENLAGRFMKEVQVAEARAFYGFQIAIENIHSEMYSLLLESYIKDSSEKSRLFRAV

Parental  ESISCVARKAKWAIDWIQCSNSFAERLVAFSCIEGIFFSGSFCAIFWLKKRGLMPGLTFSNELISRDEGL
          E...CVA.KA.WA..WI..S.SFAERL.AF.C.EGIFFSGSFC.IFWLKKRGLMPGLTFSNELISRDEGL
Retrocopy ETVPCVAKKADWALKWINSSESFAERLIAFACVEGIFFSGSFCSIFWLKKRGLMPGLTFSNELISRDEGL

Parental  HCDFACLLYSLLRRPLSEQRVHQIVHDSVEIETEFVCEALPCDLIGMNSVLMSQYIKFVADRLLVSLGYH
          HCDFACLLY.LL...L..Q.V..IV..SVEIE.EFVC.ALPC.L.GMN..LMSQYI.FVADRLL..LG..
Retrocopy HCDFACLLYDLLNHKLPQQSVQNIVRESVEIEREFVCDALPCALVGMNGNLMSQYIEFVADRLLNALGCD

Parental  KKYNVENPFEWMDFISLQGKANFFERRVGDYQKASVMSNIHNGVDNHVFTTDEDF
          K.Y.V.NPF.WM..ISLQGK.NFFE.RVG.YQKASVM..I.....NHVF..DEDF
Retrocopy KIYGVQNPFDWMELISLQGKTNFFEKRVGEYQKASVMNSINGDGKNHVFRLDEDF

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_2 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00025p00110680	1 retrocopy	retro_atri_2 ,
Brassica rapa	Bra014962	1 retrocopy	retro_brap_7,
Prunus persica	PRUPE_ppa008063mg	1 retrocopy	retro_pper_7,
Solanum lycopersicum	Solyc01g080210.2	1 retrocopy	retro_slyc_6,
Theobroma cacao	TCM_020494	1 retrocopy	retro_tcac_4,
Vitis vinifera	VIT_05s0020g02560	1 retrocopy	retro_vvin_20,