RetrogeneDB ID: retro_alyr_18

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 8:3071372..3072896(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: fgenesh2_kg.8__336__AT5G44640.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: scaffold_403368.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_18
ATGAGAACTAAATATCTTTCTTTACTAGTAGTCCTTGTTGTTTTGGCTTCCAATGAAGTTATTGCCAAGAAACACTCTTC
AACACCTAAACTAAGAAGAAGTGATTTCCCAAAAGATTTTCTTTTTGGAGCTGCAACATCTGCTTACCAAGTCGAAGGAG
CTGCTCATGAAGATGGTAGAGGACCAAGTATTTGGGATACATTCTCTGAAAAATATCCGGAAAAGATAAAAGATGGTAGC
AATGGATCTATTGCAAGTGATTCTTACCATCTTTACAAAGAAGATGTGGGTTTACTACATCAAATTGGTTTTGGTGCCTA
TAGATTCTCCATCTCGTGGTCGAGGATTTTGCCACGTGGGAATCTAAAAGGAGGAATCAACCAAGCTGGTATTGACTATT
ACAACAACTTGATCAATGAGCTTTTGTCTAAAGGAATTAAGCCTTTCGCCACCATTTTCCATTGGGACACACCACAAGAT
ATTGAAGATGCTTACGGAGGATTTCTTGGTGCGGAGATTGTGAATGATTTCCGTGATTATGCGGATATTTGTTTCAAGAA
TTTTGGAGATCGAGTTAAGCATTGGATGACATTAAACGAGCCATTAACTGTGGTGCAACAAGGATATGTTGCTGGTGTAA
TGGCTCCAGGAAGGTGCTCAAAATTCACAAATCCTAATTGCACTGCGGGAGATGGAGCTACAGAGCCTTATATTGTTGGT
CACAACCTAATCCTTGCACACGGAGAAGCGGTCAGGGTATACAGAGAAAAATATAAAGCATCTCAAAATGGTCAAGTTGG
TATCGCTTTGAACGCGGGTTGGAACTTACCTTATACAGAATCAGCCGAAGATAGGTTAGCTGCGGCACGAGCCATGGCCT
TCACATTCGACTATTTCATGGAGCCGCTTGTGACCGGTAAATACCCGGTTGACATGGTCAATAACGTAAAAGGCGGTCGC
TTACCTACATTTACTGCTAAACAATCTAAAATGCTAAAGGGATCATATGATTTCATTGGCATCAATTATTACTCATCGTC
TTACGCTAAGGATGTTCCTTGCTCAAGCGAAAACGTTACACAATTCTCTGATCCTTGTGCTAGCGTCACAGGTGAAAGAG
AAGGAGTTCCCATCGGTCCAAAGGCAGCATCGGATTGGCTTTTGATATATCCAAAGGGAATTCGTGATCTCCTCCTCTAT
GCAAAATACAAGTTCAAGGATCCTGTCCTGTACATAACCGAGAACGGGAGAGATGAAGCTAGTACCGGTAAAATCGACCT
TAAAGATAGTGAGAGGATCGATTACTATGCTCGACATTTGAAGATGGTTCAAGACGCTATCTCAATTGGAGCCAATGTGA
AGGGATTCTTTGCATGGTCTTTGCTAGATAACTTTGAATGGGCAACAGGTTACGCGGTCCGGTTCGGACTAGTTTACGTG
GATTTCAATGATGGACGTAAGAGATATCCTAAGAAATCAGCAAAATGGTTCACAAAATTGTTGAGCGAAAAGAAAAGGAA
TTGA

Alignment

ORF - retro_alyr_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKGDHLSLLVVLIVLASNEVLANNNSSTPKLRRSDFPEDFIFGSATSAYQVEGAAHEDGRGPSIWDTFSE
          M....LSLLVVL.VLASNEV.A...SSTPKLRRSDFP.DF.FG.ATSAYQVEGAAHEDGRGPSIWDTFSE
Retrocopy MRTKYLSLLVVLVVLASNEVIAKKHSSTPKLRRSDFPKDFLFGAATSAYQVEGAAHEDGRGPSIWDTFSE

Parental  KYPEKIKDGSNGSVADNSYHLYKEDVALLHQIGFNAYRFSISWSRILPRGNLRGGINQAGIDYYNNLINA
          KYPEKIKDGSNGS.A..SYHLYKEDV.LLHQIGF.AYRFSISWSRILPRGNL.GGINQAGIDYYNNLIN.
Retrocopy KYPEKIKDGSNGSIASDSYHLYKEDVGLLHQIGFGAYRFSISWSRILPRGNLKGGINQAGIDYYNNLINE

Parental  LLSKGIKPFATMFHWDTPQALEDAYGGFRGAEIVNDFRDYADICFKSFGDRVKHWMTLNEPLTVVQQGYV
          LLSKGIKPFAT.FHWDTPQ..EDAYGGF.GAEIVNDFRDYADICFK.FGDRVKHWMTLNEPLTVVQQGYV
Retrocopy LLSKGIKPFATIFHWDTPQDIEDAYGGFLGAEIVNDFRDYADICFKNFGDRVKHWMTLNEPLTVVQQGYV

Parental  AGVMAPGRCSKFTNPNCTGGNGATEPYIVGHNLILAHGAAVQVYREKYKASQNGQVGIALNAGWNLPYTE
          AGVMAPGRCSKFTNPNCT.G.GATEPYIVGHNLILAHG.AV.VYREKYKASQNGQVGIALNAGWNLPYTE
Retrocopy AGVMAPGRCSKFTNPNCTAGDGATEPYIVGHNLILAHGEAVRVYREKYKASQNGQVGIALNAGWNLPYTE

Parental  SPEDRLAAARAMAFTFDYFMEPLVTGKYPVDMVNNVKGGRLPIFTAQQSKMLKGSYDFIGINYYSSTYAK
          S.EDRLAAARAMAFTFDYFMEPLVTGKYPVDMVNNVKGGRLP.FTA.QSKMLKGSYDFIGINYYSS.YAK
Retrocopy SAEDRLAAARAMAFTFDYFMEPLVTGKYPVDMVNNVKGGRLPTFTAKQSKMLKGSYDFIGINYYSSSYAK

Parental  DVPCSTKDVTMFSDPCASVTGERDGVPIGPKAASDWLLIYPKGIRDLVLYAKYKFKDPVMYITENGRDEF
          DVPCS...VT.FSDPCASVTGER.GVPIGPKAASDWLLIYPKGIRDL.LYAKYKFKDPV.YITENGRDE.
Retrocopy DVPCSSENVTQFSDPCASVTGEREGVPIGPKAASDWLLIYPKGIRDLLLYAKYKFKDPVLYITENGRDEA

Parental  STNKIFLQDGDRIDYYARHLEMVQDAISVGANVKGFFAWSLLDNFEWATGYTVRFGLVYVDFKDGCKRYP
          ST.KI.L.D..RIDYYARHL.MVQDAIS.GANVKGFFAWSLLDNFEWATGY.VRFGLVYVDF.DG.KRYP
Retrocopy STGKIDLKDSERIDYYARHLKMVQDAISIGANVKGFFAWSLLDNFEWATGYAVRFGLVYVDFNDGRKRYP

Parental  KKSAEWFKKLLNEKKNN
          KKSA.WF.KLL.EKK.N
Retrocopy KKSAKWFTKLLSEKKRN

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_18 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis lyrata	scaffold_403368.1	1 retrocopy	retro_alyr_18 ,
Triticum aestivum	Traes_2AL_D3D671F67	1 retrocopy	retro_taes_38,