RetrogeneDB ID: retro_alyr_10

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 8:13800174..13801989(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: scaffold_801434.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: scaffold_202963.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_10
ATGGATATGCAATCGAGAATCGAGTCAGAAGATGTTAGGGTTAGGGTTTCTAATGATGAAGATCGTCAGAGCTCTCGACG
TCATCTGCAGATTGGTGGTGTCGCTGATGGAGACAAGATCAGAAAACAGACCTCCTCTAATGAAGAATTAGCCAGGCCAT
CGAAAAAGGAGGTAGATAGGGATGCTTTGGGAAAACCTAGTGGAGTTTATATTCCTCCGTTCAAGCTAGCAAGCATGTTG
AATGATGAGAAAGATAAGAGCAGCGTAGAGTATCAACGTCTTACATGGGATGCTTTTCGTAAAAGTATTAACGGGCTCGT
TAACAAGGTTAACGCAAACAACATCAAGAACATAATCCCTGAACTGTTTGCTGAAAATCTCATCAGAGGAAGAGGACTTT
TTTGTCGTGCTTGTATCAAGTCTCAAATGGAATCACCTGGATTCACTGACGTTTTTGCAGCGTTAGTCGCGGTTATCAAC
TCTAAATTCCCTCAAGTTGCTCTGCTTTTAGTGAAAAGAGTTGTTTTGATACTAAAGAGAGCTTATATGCGTAACGATAA
GCCTCAGTTTCTTGCTGCTGTTAAATTCGTAGCGCATTTAGTAAACCAGCAAGTCGCTGATGAGATCATTGCTTTTGAAT
TACTCACTGTGCTTTTGGAAAACCCGACTGATGCCAGAGTAGAGATGGCTGTTGCGTTTGTGATTGAGTGTGGCGCGTTG
CTGCAAGACGTTGCACCAAAAGGATTACATGGGATTTTTGATCGGTTTCGCGGTATATTGCATGAAGGAGAGATAGATAA
GAGAACTCAGTACTTGATTGAACGTCTCTTTGCTATTGGGAGAGCGAAATTTCAGGGATATCCCGCGGTTCGCGCTGAGC
TTGATCTCGTGGAAGAAAAGTATTCACATGATGTCTCTCTTGATGAGGAAATTGATCCTGAAACTGCTCTTGATGTTTTC
AAACTTGATCCTGACTTCGTAGACAAGGAACAGAAATACGAGGCGCTGAAGAAAGAGTTACTTGGTGAGGAGGAATCCGA
GGATGAAGATGGCGGCGGCTGTGATGCTAGTTCAGAGGATAACGATGCGGAGGAAGAAGAAATGAGAATAAGCGATGAGA
CAGCGACTAATCTTGTTAATCTTAGGAGGACAATTTACCTAACCATTATGTCCACCGTAGATTTCGAGGAAGCAGGTCAC
AAGTTACCTAAAATTAAGCTTGAACCAGGTCAAGAGATGGAACTATGCATAATGCTCTTGGAATGTTGCTCTCAAGAGAA
AACTTATCTTCCTTACTACGGTTTGTTGGGTCAGCGTTTCTGTATGCTCAAAAAGATCCATCAAGCGAATTTCGAGAAAT
GCTTTGTTCAACAGTATTCAATGAGTCACCGTCTTGAGACAACCAAGTTGCATAACGTTGCTACGTTTTTTGCTCATTTA
CTTTGCAGAGATGCTCTCCCTTGGCATGTTCTTGGCTACATTCGGTTAACGGAAGACTACACAACTTCCTCGTCGCGTAT
CTTCGTTAAGATCCTTTTCTTGAAATTGTCAGATGACTTGGGGATTAAGATACTTAATGAGAGGCTTCAGGATCCAACAA
TGGAGGAGTCACTTGAATCTATCTTCCCTAAAGATAATCCAAAGAACACTAGATTTGCAATCAACTTCTTTACTGCTATT
GGTCTTGGAGGCATTACAGAGAATCTTAGAGAGTATTTGAAGAACATGCGACATCAGAAGCAAGTTGCGGAATCATCATC
TTCTTCTAGTTCGGATAGCGACATAGAGAAGCAGAAGCGAACAAGAAGATCTTGA

Alignment

ORF - retro_alyr_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.08 %
• Parental protein coverage: 61.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLAELNPSENNAMALGKTGGVYIPPFKLARMMKEVEDKSSVEYQRLTWDALRKSINGLVNKVNASNIKNI
          .LA.....E....ALGK..GVYIPPFKLA.M.....DKSSVEYQRLTWDA.RKSINGLVNKVNA.NIKNI
Retrocopy ELARPSKKEVDRDALGKPSGVYIPPFKLASMLNDEKDKSSVEYQRLTWDAFRKSINGLVNKVNANNIKNI

Parental  IPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAVINAKFPEVAELLLKRVILQLKRAYKRNDKP
          IPELFAENLIRGRGLFCR.C.KSQM.SPGFTDVFAALVAVIN.KFP.VA.LL.KRV.L.LKRAY.RNDKP
Retrocopy IPELFAENLIRGRGLFCRACIKSQMESPGFTDVFAALVAVINSKFPQVALLLVKRVVLILKRAYMRNDKP

Parental  QLLAAVKFIAHLVNQQVAEEIIALELVEVLLDEPTDDSVEVAVGFVRDCGAMLQDVTPKGLNGIFERFRG
          Q.LAAVKF.AHLVNQQVA.EIIA.EL..VLL..PTD..VE.AV.FV..CGA.LQDV.PKGL.GIF.RFRG
Retrocopy QFLAAVKFVAHLVNQQVADEIIAFELLTVLLENPTDARVEMAVAFVIECGALLQDVAPKGLHGIFDRFRG

Parental  ILHEGEIDKRVQYLIESLHATRKAKFQGYPAVRPELDLVEEKYSHDLSLNQEIDPETALDVFKPDPDFVE
          ILHEGEIDKR.QYLIE.L.A...AKFQGYPAVR.ELDLVEEKYSHD.SL..EIDPETALDVFK.DPDFV.
Retrocopy ILHEGEIDKRTQYLIERLFAIGRAKFQGYPAVRAELDLVEEKYSHDVSLDEEIDPETALDVFKLDPDFVD

Parental  NEKKYEALKKELLGDEESEDDDGSDASSEDNDEDEDESDEEDEEQMRIRDETETNLVNLRRTIYLTIMSS
          .E.KYEALKKELLG..E.E..D..........ED........EE.MRI.DET.TNLVNLRRTIYLTIMS.
Retrocopy KEQKYEALKKELLG--EEESEDEDGGGCDASSED----NDAEEEEMRISDETATNLVNLRRTIYLTIMST

Parental  VDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINKIHQENFEKCFVQQYSMI
          VDFEEAGHKL.KIKLEPGQEMELCIMLLECCSQE.TYL.YYGLLGQRFCM..KIHQ.NFEKCFVQQYSM.
Retrocopy VDFEEAGHKLPKIKLEPGQEMELCIMLLECCSQEKTYLPYYGLLGQRFCMLKKIHQANFEKCFVQQYSMS

Parental  HRLETNKLRNVAKFFAHLLGTDALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLQDP
          HRLET.KL.NVA.FFAHLL..DALPWHVL.YIRLTE..TTSSSRIF.KILF..LS..LGI..LNERLQDP
Retrocopy HRLETTKLHNVATFFAHLLCRDALPWHVLGYIRLTEDYTTSSSRIFVKILFLKLSDDLGIKILNERLQDP

Parental  TMQESLESIFPKDNPKNTRFAINFFTSIGLGGITENLREYLKNMPSLIMQQQKQVAESESGSSS
          TM.ESLESIFPKDNPKNTRFAINFFT.IGLGGITENLREYLKNM.....Q.Q.....S.S.S.S
Retrocopy TMEESLESIFPKDNPKNTRFAINFFTAIGLGGITENLREYLKNMRH---QKQVAESSSSSSSDS

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_10 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G39400	1 retrocopy	retro_bdis_57,
Medicago truncatula	MTR_3g434840	1 retrocopy	retro_mtru_18,
Sorghum bicolor	Sb03g029810	1 retrocopy	retro_sbic_32,
Arabidopsis lyrata	scaffold_202963.1	1 retrocopy	retro_alyr_10 ,
Solanum lycopersicum	Solyc04g079920.2	1 retrocopy	retro_slyc_47,