RetrogeneDB ID: retro_alyr_13

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 5:4030734..4032315(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: scaffold_500729.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh1_pm.C_scaffold_7000531
• Aliases: None
• Description: None

Sequence

>retro_alyr_13
ATGAACTACGAGGAGGAGGATGAGAATTACTCGCTGGATGATGATGAGCAGGAGGATGAGAATTACAACGAGGCAGAAGT
CGATGTGCAACACGTGACCTCGACAAAATCTACGAGCCAGGTGATCACAAAAAAATCTCTAGTAGCAGCACAAAAAGAAA
GTCTGGTTAGGGTTATGGAATTGTTATCGGTTAAGGAGAACCAAGCTAGGACTCTTCTTATTTATTACCAATGGAACGTT
GATAAGTTGTTATCTGTGTATATTGATCAAGGCAAAGATCATATGTTTTCTTGTGCTGGTCTTACTGTTTTTGACCCTTC
TTTAGTTACTTTAAAGAAGACGATGAACTGTGATGTCTGCATGGAAGATGATTTACCAAGTGATGTGATGACGAGAATGG
AGTGTGGTCATAGCTTTTGCAATGATTGTTGGAAGGAACATTTTACTGTGAGGATTAATGAAGGTGAAAGCAAAAGGATT
CTATGTATGGCTCATAAATGTAAAGCGATTTGCGATGAAGATGTTGTTAGGAAGCTAGTTAGTCCGGAATTAGCTGAGAA
GTATGATCGTTTCCTTATTGAATCTTATGTGGAAGATAACAAGATGGTGAAGTGGTGTCCAAGTATACCGCATTGCGGGA
GTGCGATACGAAAGATCGAAGATGATGACGTCGTTGAGGTTGAATGTTCATGTGGACTTCAGTTCTGTTTCAGTTGTTTG
AGCGAGTCTCACTCTCCTTGCTCTTGTTTGATGTGGAAGCTATGGAAAAAGAAGTGTGTAGACGAGTCTGAGACGGTTAA
TTGGATAACGGTTAATACGAAGCTGTGTCCCAAATGTTACAAACCTATTTCAAAACAAGATGGTTGCAATCTCATGACTT
GTAAGTGTGGGCAGCATTTTTGTTGGCTGTGTGGTGAAGCTACTGGGGCAAGTCATACTGTGCAGAGTATTGCTGGTCAT
AGTTGTGGTCGGTACAAAGATGACAAAGTAAGGCAAATGGAGAGAGCCAAAAGGGATTTAGACAGGTATACGCATTACCA
TTACCGCTACAAAGCACATACCGATTCTTTAAAGCTCGAGGATAAACTTAGGAAGAGTATCCTTGAGAAGGCAGTGTCAA
ATGCTGAAACCAAGGATCAACAAGTGTTTAAAGAATACAGCTGGGTTATAGATGCAGTCAACAGGTTATTCAGATCAAGA
AAGATTCTTTCGTATTCTTATCCTTTCGCGCTCTACATGTTTGGTGAAGAGTTGTTTAAAGATGAGATGAGCGACGAAGA
GAGAGAGATGAAGAAGAATCTGTTTGAAGATCAGCAGCAACAACTTGAAGGTAATGTTGAGAAACTTTCTAAGATTTTAG
AAGAGCCTTTTGATGAGTATGATCATGAGAAAGTTGTGGATATGAAGAGACACCTCAACAATTTGAGTAATGCGGTTGAT
AACCTCTGCAAGAAAATGTATGAGTGCATTGAGAATGAATTACTAGGTCCAATACAATTTGGAATCCACAACATTGCACC
TTACAGATCAAAGGGAATAGAACAAGCAACTGAGTTTTGTGCTGAAATATGCCAAACTTAA

Alignment

ORF - retro_alyr_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.41 %
• Parental protein coverage: 68.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSCDVCIED-VPGDQMTRMDCGHCYCNNCWTEHFTVQINEGQSKRIRCMAHQCNAICDEDIVRNLVSKKR
          M.CDVC.ED..P.D.MTRM.CGH..CN.CW.EHFTV.INEG.SKRI.CMAH.C.AICDED.VR.LVS...
Retrocopy MNCDVCMEDDLPSDVMTRMECGHSFCNDCWKEHFTVRINEGESKRILCMAHKCKAICDEDVVRKLVS---

Parental  PDLAEKFDRFLLESYIEDNKMVKWCPSTPHCGNAIRA-EDDKLCEVECSCGLQFCFSCLCQAHSPCSCLM
          P.LAEK.DRFL.ESY.EDNKMVKWCPS.PHCG.AIR..EDD...EVECSCGLQFCFSCL...HSPCSCLM
Retrocopy PELAEKYDRFLIESYVEDNKMVKWCPSIPHCGSAIRKIEDDDVVEVECSCGLQFCFSCLSESHSPCSCLM

Parental  WELWRKKCRDESETINWITVHTKLCPKCYKPVEKNGGCNLVRCICGQCFCWLCGGATGSDHTYRSIAGHS
          W.LW.KKC.DESET.NWITV.TKLCPKCYKP..K..GCNL..C.CGQ.FCWLCG.ATG..HT..SIAGHS
Retrocopy WKLWKKKCVDESETVNWITVNTKLCPKCYKPISKQDGCNLMTCKCGQHFCWLCGEATGASHTVQSIAGHS

Parental  CGRYQDDKEKQMERAKRDLDRYTHYHHRYKAHTDSSKLEDKLRDTIHEK-VSKSEKRELKL-KDFSWVTN
          CGRY.DDK..QMERAKRDLDRYTHYH.RYKAHTDS.KLEDKLR..I.EK.VS..E.......K..SWV..
Retrocopy CGRYKDDKVRQMERAKRDLDRYTHYHYRYKAHTDSLKLEDKLRKSILEKAVSNAETKDQQVFKEYSWVID

Parental  GLDRLFRSRRVLSYSYAFAYYMFGEELFKDEMTPEEREMKKNLFEDQQQQLESNVEKLSQFLEEPFDEFS
          ...RLFRSR..LSYSY.FA.YMFGEELFKDEM..EEREMKKNLFEDQQQQLE.NVEKLS..LEEPFDE..
Retrocopy AVNRLFRSRKILSYSYPFALYMFGEELFKDEMSDEEREMKKNLFEDQQQQLEGNVEKLSKILEEPFDEYD

Parental  DDKVMAIRIQIINLSVAVDTLCKKMYECIENDLLGSLQLGIHNISPYRSKGIEQAAQFYA
          ..KV........NLS.AVD.LCKKMYECIEN.LLG..Q.GIHNI.PYRSKGIEQA..F.A
Retrocopy HEKVVDMKRHLNNLSNAVDNLCKKMYECIENELLGPIQFGIHNIAPYRSKGIEQATEFCA

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_13 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Arabidopsis lyrata	fgenesh1_pm.C_scaffold_7000531	1 retrocopy	retro_alyr_13 ,