RetrogeneDB ID: retro_atha_12

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: Pt:52659..54156(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ATCG00480
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT5G08670
• Aliases: None
• Description: None

Sequence

>retro_atha_12
ATGAGAACAAATCCTACTACTTCAAATCCAGAGGTTTCGATACGTGAAAAAAAAAACCTGGGACGTATCGCCCAAATCAT
TGGTCCGGTACTGGATGTAGCCTTCCCCCCGGGCAAAATGCCTAATATTTACAATGCTCTGGTGGTTAAGGGTCGAGATA
CTCTTGGTCAAGAAATTAATGTGACTTGTGAAGTACAGCAATTATTAGGAAATAATCGAGTTAGAGCTGTAGCTATGAGT
GCGACAGAGGGTTTAAAGAGAGGAATGGACGTGGTTGATATGGGAAATCCTCTAAGTGTTCCAGTCGGCGGAGCGACTCT
AGGACGAATTTTCAACGTGCTTGGGGAACCCGTTGATAATTTAGGTCCTGTCGATACTCGCACAACATCTCCTATCCATA
AATCCGCGCCTGCTTTTATAGAATTAGATACAAAATTATCGATTTTTGAAACAGGAATTAAAGTAGTAGATCTTTTGGCC
CCTTATCGTCGTGGGGGAAAAATTGGACTATTCGGTGGGGCTGGCGTGGGTAAAACAGTACTAATTATGGAATTGATCAA
CAACATTGCTAAAGCTCATGGTGGTGTATCCGTATTTGGTGGAGTAGGCGAACGGACTCGTGAAGGAAATGATCTTTACA
TGGAAATGAAAGAATCTGGAGTCATTAATGAACAAAATCTTGCGGAATCCAAAGTGGCCCTAGTTTATGGTCAGATGAAT
GAACCGCCAGGAGCTCGTATGAGAGTTGGTCTGACTGCCTTAACTATGGCAGAATATTTCCGAGATGTTAATGAGCAAGA
CGTACTTCTATTTATCGACAATATCTTCCGTTTCGTACAAGCAGGATCCGAGGTATCCGCCTTATTGGGTAGAATGCCTT
CTGCTGTGGGTTATCAACCCACCCTTAGTACCGAAATGGGTACTTTACAAGAAAGAATTACTTCTACGAAAAAGGGGTCC
ATAACCTCTATTCAAGCAGTTTATGTACCTGCAGATGATTTGACTGACCCCGCACCTGCCACCACATTTGCACATTTAGA
TGCGACTACCGTACTATCAAGAGGATTAGCTGCCAAAGGTATCTATCCAGCGGTAGATCCTTTAGATTCAACGTCAACTA
TGCTACAACCTCGAATCGTTGGCGAGGAACATTATGAAACTGCGCAACAAGTAAAACAAACTTTACAACGTTACAAGGAG
CTTCAGGACATTATAGCTATCCTGGGGTTGGATGAATTATCCGAAGAGGATCGCTTAACCGTAGCAAGAGCACGAAAAAT
TGAGCGTTTCTTATCACAACCCTTTTTCGTAGCAGAAGTATTTACAGGTTCTCCGGGAAAATATGTTGGTCTAGCGGAAA
CAATTAGAGGGTTTAATTTGATCCTTTCCGGAGAATTTGATTCTCTTCCCGAACAGGCCTTTTACTTAGTGGGTAACATC
GATGAAGCTACTGCGAAGGCTACGAACTTAGAAATGGAGAGTAAATTGAAGAAATGA

Alignment

ORF - retro_atha_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.45 %
• Parental protein coverage: 77.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVSHHLGQNVVRTIAMDGTEGLVRGRKVLNTGAPITVPVGRATLGRIMNVLGEPIDERGEIKTEHYLPIH
          EV...LG.N.VR..AM..TEGL.RG..V...G.P..VPVG.ATLGRI.NVLGEP.D..G...T....PIH
Retrocopy EVQQLLGNNRVRAVAMSATEGLKRGMDVVDMGNPLSVPVGGATLGRIFNVLGEPVDNLGPVDTRTTSPIH

Parental  RDAPALVDLATGQEILATGIKVVDLLAPYQRGGKIGLFGGAGVGKTVLIMELINNVAKAHGGFSVFAGVG
          ..APA...L.T...I..TGIKVVDLLAPY.RGGKIGLFGGAGVGKTVLIMELINN.AKAHGG.SVF.GVG
Retrocopy KSAPAFIELDTKLSIFETGIKVVDLLAPYRRGGKIGLFGGAGVGKTVLIMELINNIAKAHGGVSVFGGVG

Parental  ERTREGNDLYREMIESGVIKLGEKQSESKCALVYGQMNEPPGARARVGLTGLTVAEYFRDAEGQDVLLFI
          ERTREGNDLY.EM.ESGVI.......ESK.ALVYGQMNEPPGAR.RVGLT.LT.AEYFRD...QDVLLFI
Retrocopy ERTREGNDLYMEMKESGVIN-EQNLAESKVALVYGQMNEPPGARMRVGLTALTMAEYFRDVNEQDVLLFI

Parental  DNIFRFTQANSEVSALLGRIPSAVGYQPTLASDLGALQERITTTKKGSITSVQAIYVPADDLTDPAPATT
          DNIFRF.QA.SEVSALLGR.PSAVGYQPTL....G.LQERIT.TKKGSITS.QA.YVPADDLTDPAPATT
Retrocopy DNIFRFVQAGSEVSALLGRMPSAVGYQPTLSTEMGTLQERITSTKKGSITSIQAVYVPADDLTDPAPATT

Parental  FAHLDATTVLSRQISELGIYPAVDPLDSTSRMLSPHILGEEHYNTARGVQKVLQNYKNLQDIIAILGMDE
          FAHLDATTVLSR.....GIYPAVDPLDSTS.ML.P.I.GEEHY.TA..V...LQ.YK.LQDIIAILG.DE
Retrocopy FAHLDATTVLSRGLAAKGIYPAVDPLDSTSTMLQPRIVGEEHYETAQQVKQTLQRYKELQDIIAILGLDE

Parental  LSEDDKLTVARARKIQRFLSQPFHVAEIFTGAPGKYVDLKENINSFQGLLDGKYDDLSEQSFYMVGGIDE
          LSE.D.LTVARARKI.RFLSQPF.VAE.FTG.PGKYV.L.E.I..F...L.G..D.L.EQ.FY.VG.IDE
Retrocopy LSEEDRLTVARARKIERFLSQPFFVAEVFTGSPGKYVGLAETIRGFNLILSGEFDSLPEQAFYLVGNIDE

Parental  VVAKAEKIAKES
          ..AKA.....ES
Retrocopy ATAKATNLEMES

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Arabidopsis thaliana was not studied using RNA-Seq expression data.

ChIP-Seq

Arabidopsis thaliana was not studied using ChIP-Seq data.

EST

Arabidopsis thaliana was not studied using EST data.

TSS

Arabidopsis thaliana was not studied using FANTOM5 data.

Lab

retro_atha_12 was not experimentally validated.

Homology

Retrocopy orthology:

Arabidopsis thaliana 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00006p00059970	1 retrocopy	retro_atri_7,
Arabidopsis thaliana	AT5G08670	1 retrocopy	retro_atha_12 ,
Oryza sativa indica	BGIOSGA017602	2 retrocopies	retro_oind_104, retro_oind_87,
Brassica rapa	Bra006013	2 retrocopies	retro_brap_51, retro_brap_57,
Chlamydomonas reinhardtii	CHLREDRAFT_78348	1 retrocopy	retro_crei_1,
Aegilops tauschii	F775_32946	1 retrocopy	retro_atau_18,
Hordeum vulgare	MLOC_70791	1 retrocopy	retro_hvul_13,
Oryza glaberrima	ORGLA01G0220100	1 retrocopy	retro_ogla_47,