RetrogeneDB ID: retro_atha_6

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 5:7955993..7956632(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT5G23600
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT2G45330
• Aliases: None
• Description: None

Sequence

>retro_atha_6
ATGATCTTTGTGGATAGAATCGATGCCCTTGGACGAATCTTGACGAGAATATTGCGACATATGGCTACTGAGCTGAGATT
GAACATGAGAGGTGATGGTTTTGTTAAAGTTGAAGATTTACTCAACCTGAATTTGAAAACTTGTGCAAATATTCAGTTAA
ATTCACACACGATTGATGAAATTAGAGAGGCTGTGACAAGGGACAATAAAAAACGGTTTAGCCTCATCGATGAGGATGGA
GAGCTCTTGATTCGCGCTAATCAAGGCCACTCAATCACGACGGTTGAGTCAGAGAAGTTACTTAAACCAATATTGTCACC
AGAAGAAGCTCCAGTGTGTGTACATGGAACTTATAGGAAGAATTTAGAATCCATCTTAGCATCGGGCTTAAAGCGTATGA
ATAGAATGCATGTTCACTTCTCTTGTGGATTACCTACAGATGGTGAAGTGATTAGTGGCGTGAGAAGAAATGTAAATGTT
ATCATCTTCCTCCACATCAAGAAAGCTCTTGAAGATGGGATTGCGTTCTACATTTCAGACAACAAAGTGATTTTGACTCA
AGGCATTGTTGGTGTCTTGCCTGTCGATTACTTCCAGAAGATCGAGTCTTGGCCTGATCGGCAATCCATACCTTTCTGA

Alignment

ORF - retro_atha_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.19 %
• Parental protein coverage: 71.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DRIDALGRLLTRILRHMATELRLNMRGDGFVKVEDLLNLNLKTSANIQLKSHTIDEIREAVRRDNKQRFS
          DRIDALGR.LTRILRHMATELRLNMRGDGFVKVEDLLNLNLKT.ANIQL.SHTIDEIREAV.RDNK.RFS
Retrocopy DRIDALGRILTRILRHMATELRLNMRGDGFVKVEDLLNLNLKTCANIQLNSHTIDEIREAVTRDNKKRFS

Parental  LIDENGELLIRANQGHSITTVESEKLLKPILSPEEAPVCVHGTYRKNLESILASGLKRMNRMHVHFSCGL
          LIDE.GELLIRANQGHSITTVESEKLLKPILSPEEAPVCVHGTYRKNLESILASGLKRMNRMHVHFSCGL
Retrocopy LIDEDGELLIRANQGHSITTVESEKLLKPILSPEEAPVCVHGTYRKNLESILASGLKRMNRMHVHFSCGL

Parental  PTDGEVISGMRRNVNVIIFLDIKKALEDGIAFYISDNKVILTEGIDGVLPVDYFQKIESWPDRQSIPF
          PTDGEVISG.RRNVNVIIFL.IKKALEDGIAFYISDNKVILT.GI.GVLPVDYFQKIESWPDRQSIPF
Retrocopy PTDGEVISGVRRNVNVIIFLHIKKALEDGIAFYISDNKVILTQGIVGVLPVDYFQKIESWPDRQSIPF

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_6 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	AT2G45330	1 retrocopy	retro_atha_6 ,
Solanum tuberosum	PGSC0003DMG402025960	1 retrocopy	retro_stub_121,