RetrogeneDB ID: retro_atha_9

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 5:7741978..7742827(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT5G23070
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT3G07800
• Aliases: None
• Description: None

Sequence

>retro_atha_9
ATGTTTGGTGTTTCGATGAGAACATTAATCTCACCATCTCTTGCTCCCTTCTCTCTTCATCTCCATAAACCCTCTCTCTT
CTCCACCGCTCTTCGCTTCTCCTTCTCAATCAACAACATAACCCCCACAAATTCACCTCCTTCCACCATTTCCACCAGAA
AGCTACAAACGAAAGCGACGAGGGTAACATCATCATCATCATCTCAGCCGCTCTCCTCCTCATCTCCCGGCGAAATCCAC
GTCGTAGTCGGTCCAATGTTCTCCGGTAAAACAACAACACTTCTCCGCCGTATACTCGCCGAAAGAGAAACCGGTAAAAG
AATCGCAATCATCAAATCCAACAAAGACACAAGATACTGCACCGAATCAATAGTTACTCACGACGGTGAGAAATACCCTT
GCTGGTCACTCCCCGATCTCTCGTCCTTCAAAGAGAGATTCGGATTCGACGACTACGAGAATCGATTAGATGTGATTGGA
ATCGACGAAGCTCAATTCTTCGGAGATCTTTACGAGTTTTGCCGTGAAGCTGCTGATAAAGAGGGTAAAACTGTAATTGT
TGCTGGATTGGATGGTGATTTTATGAGGAGGAGGTTTGGTTCGGTTCTTGATTTGATTCCGATTGCGGATACGGTTACGA
AGCTGACGTCACGGTGTGAGGTTTGTGGGAAGAGAGCTTTGTTTACGATGAGGAAGACGGAGGAGAAAGAGACGGAGTTG
ATCGGTGGTGCTGAAGTTTATATGCCTGTGTGTAGGAGTCATTACGTTTGCGGTCAAAACGTTTTGGAAACCGCTCGTGC
CGTTTTGGATTCAAGCAATAATCATAGTGTTGTAGCAAGTTCACTTTAG

Alignment

ORF - retro_atha_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.05 %
• Parental protein coverage: 84.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LERRGSGAVHVIMGPMFSGKSTSLLRRIKSEISDGRSVAMLKSSKDTRYAKDSVVTHDGIGFPCWALPDL
          L.....G..HV..GPMFSGK.T.LLRRI..E...G...A..KS.KDTRY...S.VTHDG...PCW.LPDL
Retrocopy LSSSSPGEIHVVVGPMFSGKTTTLLRRILAERETGKRIAIIKSNKDTRYCTESIVTHDGEKYPCWSLPDL

Parental  MSFPEKFGLDAY-NKLDVIGIDEAQFFGDLYEFCCKVADDDGKIVIVAGLDGDYLRRSFGAVLDIIPIAD
          .SF.E.FG.D.Y.N.LDVIGIDEAQFFGDLYEFC...AD..GK.VIVAGLDGD..RR.FG.VLD.IPIAD
Retrocopy SSFKERFGFDDYENRLDVIGIDEAQFFGDLYEFCREAADKEGKTVIVAGLDGDFMRRRFGSVLDLIPIAD

Parental  SVTKLTARCEVCGHKAFFTLRKNCDTRTELIGGADVYMPVCRKHYITNHIVIKASKKVLEDSD
          .VTKLT.RCEVCG..A.FT.RK.....TELIGGA.VYMPVCR.HY.....V......VL..S.
Retrocopy TVTKLTSRCEVCGKRALFTMRKTEEKETELIGGAEVYMPVCRSHYVCGQNVLETARAVLDSSN

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_9 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT3G07800	1 retrocopy	retro_atha_9 ,
Brassica oleracea	Bo3g061430	1 retrocopy	retro_bole_16,
Brassica rapa	Bra001266	1 retrocopy	retro_brap_33,
Arabidopsis lyrata	fgenesh2_kg.3__818__AT3G07800.1	1 retrocopy	retro_alyr_19,