RetrogeneDB ID: retro_alyr_24

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 6:7275963..7277217(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: scaffold_601818.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: scaffold_802017.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_24
ATGATCTCCCTGAATCTATCTCCTTCCTTAAATCCGGGTCTCCTCCACAAGACCCGGAGCCGTCAACAACCGACCCGTCT
CTCTGCTCTTCTCGTCACCAACCCTAAACCCTTCAATCACAGATACCCACTAGGGCTTTCACCGATTCCCAGTCTCCAGA
TTCGTGATGCCGCCGCAAAACCATTGCTTTCACTCACAAACCCTGAGTCCTCATCTGGGTTCTCGAGAAAACCCAGATCC
ATCGCCGCCGTTGGCTCATCGGATTCAAATCCAGACGAAAAATCCGATCTTGGCGAAGCGGAGAAGAAAGAGAAGAAAGC
TAAGACTCTTCAGCTAGGGATTGTGTTTGGTCTTTGGTATTTCCAGAACATCGTCTTCAACATCTTCAACAAAAAGGCAC
TCAATGTCTTCCCTTATCCATGGCTTCTCGCTTCGTTTCAGCTCTTCGCAGGTTCTATTTGGATGCTTATCTTATGGTCC
TTTAAGCTTTATCCTTGCCCTAAAATCTCCAAACCTTTCATCATTGCTCTCCTTGGTCCTGCATTGTTTCACACTATTGG
ACACATCTCAGCTTGTGTCTCGTTCTCCAAAGTCGCTGTTTCTTTCACTCATGTTATCAAATCAGCAGAGCCTGTCTTCT
CTGTTATCTTCTCGTCTTTACTCGGTGATTCGTACCCGTTAGCTGTCTGGTTATCGATTCTTCCGATTGTTATGGGTTGT
TCTTTAGCTGCAGTCACTGAAGTCTCATTCAATTTAGGTGGATTATCAGGAGCTATGATTAGTAATGTTGGTTTCGTCTT
AAGAAACATTTACTCTAAAAGAAGTCTACAGAGCTTCAAAGAGATTGATGGATTGAATCTATACGGTTGCATTAGTATAC
TCTCTCTGCTTTATCTGTTTCCCGTGGCGATTTTCGTTGAAGGATCACATTGGGTTCAAGGTTACCATAAAGCCATTGCA
TCTGTTGGGACACCATCAACGTTCTACTTTTGGGTTTTGCTCTCTGGTGTCTTCTACCATCTGTACAACCAATCTTCTTA
CCAGGCACTCGACGAGATCAGTCCATTGACTTTCTCTGTAGGGAACACAATGAAGCGAGTCGTGGTGATTGTCTCCACGG
TTTTGGTGTTTAGGAATCCTGTTAGACCTCTGAATGCTCTTGGATCAGCCATTGCGATTTTCGGTACCTTCTTGTATTCT
CAGGCCACCGCAAAAAAGAAGAAGATTGAAGTGGGAGGTGATAAGAAGAACTAA

Alignment

ORF - retro_alyr_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.13 %
• Parental protein coverage: 97.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PTKIG-LFRRNPSSSLRRSPVSLS-FPSTEL---PKRTVLAVSKPLHLSSLRAKSPVVRCEAYEADRSEP
          PT....L...NP.....R.P..LS..PS...........L....P...S....K.......A.....S.P
Retrocopy PTRLSALLVTNPKPFNHRYPLGLSPIPSLQIRDAAAKPLLSLTNPESSSGFSRKPRSIA--AVGSSDSNP

Parental  QPIDDAAAAETKSEAAKKLKIGIYFATWWALNVVFNIYNKKVLNAYPYPWLTSTLSLAAGSLMMLISWAV
          ....D...AE.K...AK.L..GI.F..W...N.VFNI.NKK.LN..PYPWL.....L.AGS..MLI.W..
Retrocopy DEKSDLGEAEKKEKKAKTLQLGIVFGLWYFQNIVFNIFNKKALNVFPYPWLLASFQLFAGSIWMLILWSF

Parental  GIVETPKTDFDFWKTLFPVAVAHTIGHVAATVSMSKVAVSFTHIIKSGEPAFSVLVSRFLLGETFPTSVY
          .....PK....F...L...A..HTIGH..A.VS.SKVAVSFTH.IKS.EP.FSV..S..LLG...P..V.
Retrocopy KLYPCPKISKPFIIALLGPALFHTIGHISACVSFSKVAVSFTHVIKSAEPVFSVIFSS-LLGDSYPLAVW

Parental  LSLIPIIGGCALSALTELNFNMIGFMGAMISNLAFVFRNIFSKKGMKG-KSVSGMNYYACLSMLSLLILT
          LS..PI..GC.L.A.TE..FN..G..GAMISN..FV.RNI.SK......K...G.N.Y.C.S.LSLL.L.
Retrocopy LSILPIVMGCSLAAVTEVSFNLGGLSGAMISNVGFVLRNIYSKRSLQSFKEIDGLNLYGCISILSLLYLF

Parental  PFAIAVEGPQMWVDGWQTALATVG--PQFVWWVAAQSVFYHLYNQVSYMSLDQISPLTFSVGNTMKRISV
          P.AI.VEG...WV.G...A.A.VG....F..WV....VFYHLYNQ.SY..LD.ISPLTFSVGNTMKR..V
Retrocopy PVAIFVEGSH-WVQGYHKAIASVGTPSTFYFWVLLSGVFYHLYNQSSYQALDEISPLTFSVGNTMKRVVV

Parental  IVSSIIIFRTPVQPVNALGAAIAILGTFLYSQA
          IVS....FR.PV.P.NALG.AIAI.GTFLYSQA
Retrocopy IVSTVLVFRNPVRPLNALGSAIAIFGTFLYSQA

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_24 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00062p00036220	1 retrocopy	retro_atri_14,
Brassica oleracea	Bo9g118840	1 retrocopy	retro_bole_30,
Musa acuminata	GSMUA_Achr7G03380_001	1 retrocopy	retro_macu_2,
Populus trichocarpa	POPTR_0001s44610	1 retrocopy	retro_ptri_19,
Physcomitrella patens	PP1S70_177V6	1 retrocopy	retro_ppat_10,
Arabidopsis lyrata	scaffold_802017.1	1 retrocopy	retro_alyr_24 ,
Theobroma cacao	TCM_030978	1 retrocopy	retro_tcac_18,