RetrogeneDB ID: retro_atha_5

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 2:8464532..8465531(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT2G19550
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT3G47590
• Aliases: None
• Description: None

Sequence

>retro_atha_5
ATGAAGCCAACGAAGATCGTGATTCCGAACCGCCGCAACGAGAAGCTCGTGGGTCTGCTTCACGAAACTGGATCAAAAGA
AGTTGTGGTCTTATGCCATGGCTTTAGATCGGACAAGACCAACAAGATTCTCAAAAACGTGGCTACAGCTTTGGAGAAAG
AAAAAATCAGCTCTTTTCGTTTCGATTTCTCTGGTAACGGAGATAGTGAAGGAACTTTCTATTATGGTAACTTCAACAGT
GAAGCAGAGGATGATCTGCATTACGTTATTCAACACTTGTCCTCCTCTAACATCATGAACCGTCTAGTTCCTGTCATTCT
TGGTCATAGTAAAGGTGGTGATGTCGTTCTTCTCTATGCTTCCAAGTTTCCCGATTATATCCGCAATGTCGTCAATATCT
CTGGACGTTTTGATCTTAAGAATGATGTGCGTCTCGGAGATGGTTATATAGAAAAGATTAAGGAACAGGGGTTTATTGAT
GCTACAGAGGGCAAATCTTGTTTTCGTGTTACTCAAGAGTCTTTAATGGATAGGTTAAACACTGATATGCATCAAGCTTG
TCTCAATATTGATAAACAATGCAAAGTTTTGACAGTTCATGGTTCGGATGATACCGTGGTACCTGGGGAAGATGCTAAGG
AGTTTGCAAAGGTTATACCGAATCATAAGCTGGAGATTGTGGAAGGAGCTAATCATGGTTACACCAAACATCAGAAGGAA
TTGGTTTCCATAGCGGTGGAGTTTACCAAGACTGCGATTGTTGAACAACACAATTTGTTAGTTGTCTTTGGGAGATGGCT
CATCATCGTCATGATAGTTGTTACATTCTACATGAGTGTTTTCGATCATTTAATCAAAGTTTATCCACTACTTGTAATTT
TCAAATTGGAGAATGTTATGAGCAGAATTCAACAATTAATCTACTTGATTTTTTTTTACTTGTTAAGGATTAAACTATTA
TTAGGCTTGTGGCTTCTGTTACTGGAGAGGAGAATGTAA

Alignment

ORF - retro_atha_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.41 %
• Parental protein coverage: 80.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RIVIPNRHNEKLVGLLHETGSTDIVVLCHGFRSNKSNQIMNNVAAAIQKEGISAFRFDFSGNGESEGSFY
          .IVIPNR.NEKLVGLLHETGS...VVLCHGFRS.K.N.I..NVA.A..KE.IS.FRFDFSGNG.SEG.FY
Retrocopy KIVIPNRRNEKLVGLLHETGSKEVVVLCHGFRSDKTNKILKNVATALEKEKISSFRFDFSGNGDSEGTFY

Parental  YGNYNHEA-DDLHSVVQYFSNK---NRVVPIILGHSKGGDVVLLYASKYHD-VRNVINLSGRYDLKKGIR
          YGN.N.EA.DDLH.V.Q..S.....NR.VP.ILGHSKGGDVVLLYASK..D..RNV.N.SGR.DLK...R
Retrocopy YGNFNSEAEDDLHYVIQHLSSSNIMNRLVPVILGHSKGGDVVLLYASKFPDYIRNVVNISGRFDLKNDVR

Parental  ERLGEDFLERIKQQGFIDVGDGKSGYRVTEKSLMDRLSTDIHEACLKIDKECRVLTVHGSEDEVIPVEDA
          ..LG....E.IK.QGFID...GKS..RVT..SLMDRL.TD.H.ACL.IDK.C.VLTVHGS.D.V.P.EDA
Retrocopy --LGDGYIEKIKEQGFIDATEGKSCFRVTQESLMDRLNTDMHQACLNIDKQCKVLTVHGSDDTVVPGEDA

Parental  KEFAKIIPNHKLEIVEGANHGYTEHQSQLVSTVMEFIKTVIVKNN
          KEFAK.IPNHKLEIVEGANHGYT.HQ..LVS...EF.KT.IV...
Retrocopy KEFAKVIPNHKLEIVEGANHGYTKHQKELVSIAVEFTKTAIVEQH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Arabidopsis thaliana was not studied using RNA-Seq expression data.

ChIP-Seq

Arabidopsis thaliana was not studied using ChIP-Seq data.

EST

Arabidopsis thaliana was not studied using EST data.

TSS

Arabidopsis thaliana was not studied using FANTOM5 data.

Lab

retro_atha_5 was not experimentally validated.

Homology

Retrocopy orthology:

Arabidopsis thaliana 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT3G47590	1 retrocopy	retro_atha_5 ,
Oryza sativa indica	BGIOSGA001352	1 retrocopy	retro_oind_81,
Brassica rapa	Bra019508	1 retrocopy	retro_brap_47,
Hordeum vulgare	MLOC_20645	1 retrocopy	retro_hvul_20,
Oryza sativa japonica	OS01G0579900	1 retrocopy	retro_osat_70,
Populus trichocarpa	POPTR_0018s06860	1 retrocopy	retro_ptri_17,