RetrogeneDB ID: retro_alyr_31

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 1:24567030..24567843(+)
• Located in intron of: fgenesh2_kg.1__3931__AT1G48410.2

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh2_kg.7__854__AT4G32840.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_31
CAGGTGTATATAATAGGAGGAGACGGCACAATGCGTGGGGCTGTCGAGATCTTCAAGGAAATCAGCCTCAGGAAACTGGA
GGTGGGAATCACAGGTATTCCCAAAACCGTGGACAACGATGTCGGCATCATTGATAGATCATTCGGCTTTCAAACGGCTG
TAGAGATGGCTCAGCAGGCTATATCTGCTGCTCACGTGGAGGCCGAGAGCGCAGTCAATGGCATTGGACTTGTGAAGCTT
ATGGGCAGAAGTACTGGCCACATTGCTCTACATGCCACTCTTAGCAGCCGTGATGTGGACTGTTGTTTGATCCCTGAGAT
GGACTTCTACCTTGAAGGCAAAGGTGGGCTCTTTGAGTTTCTGGAGAAAAGACTTAAAGAACGCGGGCATGCTGTTCTTG
TTGTGGCTGAAGGGGCAGGCCAAGAGATGATCCCAAGAAATGAATCACAGAAACAAGAGAGGGATGAATCTGGCAACCCT
GTTTTCTTGGATGTCGGAGTCTGGTTTAAGTCAGTGCTCAAGGACTGGTGGGGCCGAGAGCATCCAGACGAGCTCTTCAC
CGTCAAGTATATCGATCCCACTTACATGATAAGAGCTGTACCTGCAAATGCTACGGACAACTTGTATTGTACACTCTTGG
CCCACTCGGCCATCCATGGAGTCATGGCTGGTTACACAGGGTTCGTGCCTGGCCCAATCAATGGGAACTATGCTTATATC
CCCTTAGAGGAGGTGGCACTGACTAAGAACAAAGTTAACACGAGTGACCACAAGTGGGCGTGGGTGCGCTCAGTCACAAA
CCAGCCTGATTTT

Alignment

ORF - retro_alyr_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.52 %
• Parental protein coverage: 58.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVYIIGGDGTQKGASAIYKEIRRRGLKVSVAGIPKTIDNDIPVIDKSFGFDTAVEEAQRAINAAHVEANS
          QVYIIGGDGT..GA..I.KEI..R.L.V...GIPKT.DND...ID.SFGF.TAVE.AQ.AI.AAHVEA.S
Retrocopy QVYIIGGDGTMRGAVEIFKEISLRKLEVGITGIPKTVDNDVGIIDRSFGFQTAVEMAQQAISAAHVEAES

Parental  VENGIGLVKLMGRYSGFIAMYATLASRDVDCCLIPESPFYLEGKGGLYEFIAKRLRENGHMVIVIAEGAG
          ..NGIGLVKLMGR..G.IA..ATL.SRDVDCCLIPE..FYLEGKGGL.EF..KRL.E.GH.V.V.AEGAG
Retrocopy AVNGIGLVKLMGRSTGHIALHATLSSRDVDCCLIPEMDFYLEGKGGLFEFLEKRLKERGHAVLVVAEGAG

Parental  QDLVAESTDQ---QDASGNKLLKDVGLWMSLKIKEHFAKQSVMDI-TLKYIDPTYMIRAIPANASDNVYS
          Q........Q....D.SGN....DVG.W.....K............T.KYIDPTYMIRA.PANA.DN.Y.
Retrocopy QEMIPRNESQKQERDESGNPVFLDVGVWFKSVLKDWWGREHPDELFTVKYIDPTYMIRAVPANATDNLYC

Parental  TLLAQSAVHGAMAGYTGFVSGLVNGRHTYIPFNRITERQNKVVITDRMWARMLSSTNQPSF
          TLLA.SA.HG.MAGYTGFV.G..NG...YIP........NKV...D..WA...S.TNQP.F
Retrocopy TLLAHSAIHGVMAGYTGFVPGPINGNYAYIPLEEVALTKNKVNTSDHKWAWVRSVTNQPDF

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_31 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis lyrata	fgenesh2_kg.7__854__AT4G32840.1	1 retrocopy	retro_alyr_31 ,
Oryza longistaminata	KN540365.1_FG001	1 retrocopy	retro_olon_23,