RetrogeneDB ID: retro_alyr_1

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 8:12479503..12480007(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: scaffold_801255.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: scaffold_403747.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_1
ATGGCTAGTGGAAGTGAGCGTGTGGTGGTCGTAGGAGTAGATGATTCAGCCCATAGCTACCATGCACTCGAGACGGCTCT
TGATCTCTTTTTCATACCTTTCAAGGCCAACCCACAATTCAAACTTGTCGTTGTTCACGGACGACCAACAGCGACCTCCT
TCCTCGGTGTTGCTGGTCCTGGAACGGTGGATATTATACCAATGGTGGAACAAGATTTAAACAAGACCGCAGAATTGGTT
AAGAAGAAGTGCTCCGAAGTGTGCTCGGCTAAGTCCGTTGAGATCTCGTCTTTGGAGGTGATTGAAGGAGATCCAAGGAA
TATTATGTTGGAAGCCGTGGAGAGACATCATGCATGTGTTATTGTCCTTGGTAGCCATGGTTATGGAGCTGTCAAGAGGG
TGTTTTTGGGGAGTGTGAGTGATTATTTAGCTCATCACGCACATTGCTCCGTTATGATCGTCAAGAAACCTAAGGCTAAA
CCTACTTCTACGGAAACACACTAA

Alignment

ORF - retro_alyr_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.76 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATGDEKSVMVVGVDDSEQSTYALEWTLDRFFAPYAPNYPFKLFIVHAKPNAVSAVGLAGPGTAEVVPYV
          MA.G.E..V.VVGVDDS..S..ALE..LD.FF.P...N..FKL..VH..P.A.S..G.AGPGT....P.V
Retrocopy MASGSER-VVVVGVDDSAHSYHALETALDLFFIPFKANPQFKLVVVHGRPTATSFLGVAGPGTVDIIPMV

Parental  DADLKHTAAKVVEKAKAICQSKSVHGAVIEVFEGDARNILCEVVDKHHASILVVGSHGYGAIKRAVLGST
          ..DL..TA..V..K....C..KSV.....EV.EGD.RNI..E.V..HHA...V.GSHGYGA.KR..LGS.
Retrocopy EQDLNKTAELVKKKCSEVCSAKSVEISSLEVIEGDPRNIMLEAVERHHACVIVLGSHGYGAVKRVFLGSV

Parental  SDYCAHHAHCSVMIVKKPKIK
          SDY.AHHAHCSVMIVKKPK.K
Retrocopy SDYLAHHAHCSVMIVKKPKAK

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Arabidopsis lyrata was not studied using ChIP-Seq data.

EST

Arabidopsis lyrata was not studied using EST data.

TSS

Arabidopsis lyrata was not studied using FANTOM5 data.

Lab

retro_alyr_1 was not experimentally validated.

Homology

Retrocopy orthology:

Arabidopsis lyrata 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo3g039740	1 retrocopy	retro_bole_20,
Brassica rapa	Bra000458	1 retrocopy	retro_brap_16,
Arabidopsis lyrata	scaffold_403747.1	1 retrocopy	retro_alyr_1 ,