RetrogeneDB ID: retro_alyr_4

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 6:13296051..13297284(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: fgenesh2_kg.6__2753__AT5G27570.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh2_kg.7__793__AT4G33270.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_4
ATGGATTTCGACTATGCTCCCTACGCTCTTACCGAAGGAAGAAAACCTAAAGTTGAGGTAACTTCAGCGTCAAGGAAAGC
GTACATGAACCAATTGGCTGAGACTATGAATCAGAATCGAACCCGGATTCTCGCTTTCAGAAACAAACCTAAAGCTCTGC
TTTCTAGTAATCACTCTGATTCTCCTCATGAACAATCTAAATCCGTAAAGCGTCGTAGATACATTCCTCAGAATAGTGAG
AAAATCTTGGATGCACCTGGCATTGTGGATGACTTCTACCTTAACTTGTTGGACTGGGGTAGTTCTAATGTCTTAGCCCT
AGCTTTGGGCCACTCTATTTACTTGCGGGATGCTTCTAGTGATTCTACATCTATGCTTGTGACTATTGATGAAGAGAAGG
GACCTGTCACAAGTATTAACTGGATGCAAGATGGTTGTACTCTCGCAATTGGTCTTGACAACTCTGAAGTGCAGATTTGG
GATTCTGCTTCGAATAGTCAACTGAGAACATTGAGAGGTGGTCACCAGACAAGAGTAGGATCATTAGCATGGAACAATCA
CATCCTAACAACTGGAGGAAGGGATGGAAAAATCATCAACAATGATGTGAGGATCAGATCATCAATTGTGGGAAGTTACT
TGGGTCACACTGATGAGGTTTGTGGTCTTAAGTGGTCAGAATCTGGGAAACAATTAGCAAGTGGTGGTAACGACAAGGTA
GTACACATATGGGATCGTTCTCTCGCATCCTCAAACTCAACTAGGAAATGGTTGCAGAGGTTTGAGGGACATACAGCTGC
TACGAAAGCTCTTGCATGGTGTCCATTCCAAGCGAATTTGCTTGCAACTGGTGGTGGTGTAGGAGATAGGACTATTAAGT
TCTGGAATACACACACTGGTGCTTGCTTGAATTCAGTAGAAACTGGCTCTCAAGTTTGTTCATTGTTATGGAGTAATAAG
GAAAGAGAGTTGCTTAGTTCACATGGGTTTACACAGAACCAGCTTACACTTTGGAAGTATCCATCTATGTTGAAAATAGC
TGAACTCAATGGTCATACATCAAGAGTTCTTTATATGGCACAGAGTCCGGATGGTTGTACTGTGGCTTCAGCAGCAGGAG
ACGAGACTCTTAGGCTTTGGAATGTTTTTGGAGTACCACCACCAAAGACCACCAAAAAAGCTGCTCCAAAAGCATATCTG
CAGATATTTTCTCATGTGAATTGTATTCGTTGA

Alignment

ORF - retro_alyr_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.09 %
• Parental protein coverage: 90.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDFDYAHFALTEGRKGNDQTAAVSSPSKEAYRKQLAETMNLNHTRILAFRNKPQAPVELLPSNHSASLHQ
          MDFDYA..ALTEGRK.......V.S.S..AY..QLAETMN.N.TRILAFRNKP.A...LL.SNHS.S.H.
Retrocopy MDFDYAPYALTEGRKPKVE---VTSASRKAYMNQLAETMNQNRTRILAFRNKPKA---LLSSNHSDSPHE

Parental  QPKSVKPRRYIPQTSERTLDAPDIVDDFYLNLLDWGSANVLAIALDHTVYLWDASTGSTSELVTIDEEKG
          Q.KSVK.RRYIPQ.SE..LDAP.IVDDFYLNLLDWGS.NVLA.AL.H..YL.DAS..STS.LVTIDEEKG
Retrocopy QSKSVKRRRYIPQNSEKILDAPGIVDDFYLNLLDWGSSNVLALALGHSIYLRDASSDSTSMLVTIDEEKG

Parental  PVTSINWAPDGRHVAVGLNNSEVQLWDSASNRQLRTLKGGHQSRVGSLAWNNHILTTGGMDGLIINNDVR
          PVTSINW..DG...A.GL.NSEVQ.WDSASN.QLRTL.GGHQ.RVGSLAWNNHILTTGG.DG.IINNDVR
Retrocopy PVTSINWMQDGCTLAIGLDNSEVQIWDSASNSQLRTLRGGHQTRVGSLAWNNHILTTGGRDGKIINNDVR

Parental  IRSPIVETYRGHTQEVCGLKWSGSGQQLASGGNDNVVHIWDRSVASSNSNTQWLHRLEEHTSAVKALAWC
          IRS.IV..Y.GHT.EVCGLKWS.SG.QLASGGND.VVHIWDRS.ASSNS...WL.R.E.HT.A.KALAWC
Retrocopy IRSSIVGSYLGHTDEVCGLKWSESGKQLASGGNDKVVHIWDRSLASSNSTRKWLQRFEGHTAATKALAWC

Parental  PFQANLLATGGGGGDRTIKFWNTHTGACLNSVDTGSQVCSLLWSKNERELLSSHGFTQNQLTLWKYPSMV
          PFQANLLATGGG.GDRTIKFWNTHTGACLNSV.TGSQVCSLLWS..ERELLSSHGFTQNQLTLWKYPSM.
Retrocopy PFQANLLATGGGVGDRTIKFWNTHTGACLNSVETGSQVCSLLWSNKERELLSSHGFTQNQLTLWKYPSML

Parental  KMAELTGHTSRVLYMAQSPDGCTVASAAGDETLRFWNVFGV--PETAKKAAPKAVSEPFSHVNRIR
          K.AEL.GHTSRVLYMAQSPDGCTVASAAGDETLR.WNVFGV..P.T.KKAAPKA....FSHVN.IR
Retrocopy KIAELNGHTSRVLYMAQSPDGCTVASAAGDETLRLWNVFGVPPPKTTKKAAPKAYLQIFSHVNCIR

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_4 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	Bo1g008280	1 retrocopy	retro_bole_31,
Arabidopsis lyrata	fgenesh2_kg.7__793__AT4G33270.1	1 retrocopy	retro_alyr_4 ,
Prunus persica	PRUPE_ppa019777mg	1 retrocopy	retro_pper_34,