RetrogeneDB ID: retro_atha_17

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 1:25763622..25764105(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT1G68610
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT1G14870
• Aliases: None
• Description: None

Sequence

>retro_atha_17
ATGAACCTTTCCTCTAACGACCAACCAAGCCAAGGCCGTATCAAGGCCAAGGATTGGTCGACTGATTTGTGTGAATGTTG
GATGGACATAAACTCATGCTGCTTGACTTGTTGGTGCCCTTGTGTTGCCTTTGGACGCATCGCGGAGGTTGTAGACAGAG
GTTCCACATCGTGTGGTGTGAGCGGAGCGATGTACATGATCATATTCATGTTGACCGGGTATGGAGGAAGCAGTCTCTAC
TCTTGCTTTTACCGAACCAAACTTAGAGCCCAATACAATCTCAAGGAGAGACCTTGTTGTGACTGTTGTGTCCACTTTTG
TTGCGAGCCATGCGCTCTTTGTCAAGAGTATAGGCAACTTCAACACAACCGCGATTTGGACTTGGTCATCGGGTGGCATG
GGAATATGGAACGACATGCACGACTTGCTGCCTCTACACCTTCGGCTCCTCCACTTCAAGCACCCATGTCTAGATTGGTT
TAA

Alignment

ORF - retro_atha_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.77 %
• Parental protein coverage: 90.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EWSTGFCDCFSDCKNCCITFWCPCITFGQVAEIVDRGSTSCGTAGALYALIAVVTGC--ACIYSCFYRGK
          .WST..C.C..D...CC.T.WCPC..FG..AE.VDRGSTSCG..GA.Y..I...TG......YSCFYR.K
Retrocopy DWSTDLCECWMDINSCCLTCWCPCVAFGRIAEVVDRGSTSCGVSGAMYMIIFMLTGYGGSSLYSCFYRTK

Parental  MRAQYNIKGDDCTDCLKHFCCELCSLTQQYRELKH-RGYDMSLGWAGNVERQQNQGGVAMGAPVFQGGMT
          .RAQYN.K...C.DC..HFCCE.C.L.Q.YR.L.H.R..D...GW.GN.ER..........AP..Q..M.
Retrocopy LRAQYNLKERPCCDCCVHFCCEPCALCQEYRQLQHNRDLDLVIGWHGNMERHARLAASTPSAPPLQAPMS

Parental  R
          R
Retrocopy R

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_17 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 lyrata	Al_scaffold_0001_1541	1 retrocopy	retro_alyr_27,
Arabidopsis thaliana	AT1G14870	1 retrocopy	retro_atha_17 ,