RetrogeneDB ID: retro_atha_2

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 1:24906450..24907236(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT1G66770
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT4G10850
• Aliases: None
• Description: None

Sequence

>retro_atha_2
ATGGTGCATGAACAGTTGAATCTTATTCGGAAGATTGTTGGTATATTAGGAAACTTCATCTCTCTATGTTTGTTTCTATC
GCCAACGCCAACGTTTATACACATAGTGAAAAAGAAGTCAGTGGAAAAATACTCACCATTGCCATATTTAGCGACTCTCC
TAAACTGTTTGGTTCGTGCTCTTTATGGACTTCCTATGGTTCATCCTGATAGCACCTTGCTCGTTACAATAAGCGGTATA
GGAATCACGATCGAAATCGTTTTCCTTACAATCTTTTTTGTATTTTGTGGTCGTCAACAACATCGGTTGGTAATATCCGC
TGTTTTAACCGTTCAAGTTGTGTTTGTGGCTACCCTTGCGGTTTTGGTCTTAACTCTCGAACACACTACCGATCAACGGA
CGATAAGCGTTGGGATTGTATCTTGCGTTTTCAACGCTATGATGTATGCTTCTCCATTGTCTGTCATGAAAATGGTAATA
AAAACAAAAAGTTTGGAGTTCATGCCGTTTTTGTTATCGGTAGTTGGTTTTCTAAACGCAGGTGTTTGGACAATTTATGG
CTTTGTGCCTTTTGATCCATTCCTGGCTATACCAAATGGGATTGGGTGTGTTTTTGGACTAGTACAGTTAATATTGTATG
GTACCTACTACAAATCTACCAAAGGGATAATGGAGGAAAGGAAGAACCGACTCGGTTACGTTGGTGAAGTCGGATTATCC
AATGCGATCGCTCAAACTGAACCCGAGAACATCCCATATTTAAACAAAAGAGTTAGCGGCGTTTGA

Alignment

ORF - retro_atha_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVFAHLNLLRKIVGIIGNFIALCLFLSPTPTFVRIVKKKSVEEYSPIPYLATLINCLVWVLYGLPTVHPD
          MV...LNL.RKIVGI.GNFI.LCLFLSPTPTF..IVKKKSVE.YSP.PYLATL.NCLV..LYGLP.VHPD
Retrocopy MVHEQLNLIRKIVGILGNFISLCLFLSPTPTFIHIVKKKSVEKYSPLPYLATLLNCLVRALYGLPMVHPD

Parental  STLVITINGTGILIEIVFLTIFFVYCGRQKQRLIISAVIAAETAFIAILAVLVLTLQHTTEKRTMSVGIV
          STL..TI.G.GI.IEIVFLTIFFV.CGRQ..RL.ISAV......F.A.LAVLVLTL.HTT..RT.SVGIV
Retrocopy STLLVTISGIGITIEIVFLTIFFVFCGRQQHRLVISAVLTVQVVFVATLAVLVLTLEHTTDQRTISVGIV

Parental  CCVFNVMMYASPLSVMKMVIKTKSVEFMPFWLSVAGFLNAGVWTIYALMPFDPFMAIPNGIGCLFGLAQL
          .CVFN.MMYASPLSVMKMVIKTKS.EFMPF.LSV.GFLNAGVWTIY...PFDPF.AIPNGIGC.FGL.QL
Retrocopy SCVFNAMMYASPLSVMKMVIKTKSLEFMPFLLSVVGFLNAGVWTIYGFVPFDPFLAIPNGIGCVFGLVQL

Parental  ILYGAYYKSTKRIMAERENQPGYVG---LSSAIARTGSEKTANTNQEPNNV
          ILYG.YYKSTK.IM.ER.N..GYVG...LS.AIA.T..E.....N.....V
Retrocopy ILYGTYYKSTKGIMEERKNRLGYVGEVGLSNAIAQTEPENIPYLNKRVSGV

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_2 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT4G10850	1 retrocopy	retro_atha_2 ,
Arabidopsis lyrata	fgenesh2_kg.6__3062__AT4G10850.1	1 retrocopy	retro_alyr_16,