RetrogeneDB ID: retro_atha_10

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 3:17513656..17514868(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT3G47520
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT5G09660
• Aliases: None
• Description: None

Sequence

>retro_atha_10
ATGGCAACAGCAACATCAGCTTCTCTGTTTTCAACTGTTTCTTCATCTTACTCCAAAGCTAGCTCCATACCACATTCAAG
ACTCCAATCTGTGAAATTCAACTCAGTCCCTAGCTTCACCGGTCTCAAATCAACCTCTCTCATCTCCGGATCTGATTCCT
CTTCCTTAGCCAAGACTCTACGCGGTTCCGTAACGAAAGCACAAACATCTGACAAGAAGCCTTACGGATTCAAAATCAAC
GCTTCATACAAAGTAGCTGTTCTTGGTGCTGCTGGTGGTATAGGTCAGCCTTTATCACTTCTCATCAAGATGTCTCCGTT
AGTCTCTACGCTTCATCTTTACGATATCGCCAATGTTAAAGGAGTTGCTGCTGATCTAAGTCATTGTAACACTCCTTCTC
AAGTTCGTGATTTCACTGGTCCTTCTGAGTTAGCTGATTGTTTGAAAGATGTTAACGTTGTTGTCATCCCTGCTGGTGTG
CCGAGGAAACCCGGTATGACTCGTGACGATCTTTTCAACATCAATGCCAATATTGTCAAGACTCTTGTTGAAGCTGTTGC
TGAGAATTGCCCTAATGCTTTCATTCATATTATTAGTAACCCGGTTAACTCTACGGTACCTATTGCTGCTGAAGTGTTGA
AGAAGAAAGGTGTTTATGATCCTAAGAAGCTGTTTGGTGTCACTACTTTGGATGTTGTGAGGGCTAACACTTTTGTTTCT
CAGAAGAAGAATCTTAAGCTTATTGATGTTGATGTTCCGGTTATTGGTGGACATGCTGGAATCACCATTTTGCCTCTCCT
CTCGAAGACAAAACCGTCTGTTAACTTTACTGATGAAGAGATCCAAGAGCTCACTGTTAGGATTCAGAACGCTGGTACTG
AGGTTGTTGATGCTAAGGCAGGTGCAGGTTCAGCTACTTTGTCAATGGCTTATGCTGCTGCTAGATTTGTAGAGTCATCT
CTTCGTGCTCTTGATGGAGACGGAGATGTCTACGAGTGCTCGTTTGTGGAGTCGACTCTGACTGATCTTCCTTTCTTTGC
ATCACGGGTTAAGATAGGGAAGAACGGTCTTGAAGCTGTGATTGAGTCAGACCTTCAGGGATTGACTGAGTATGAGCAGA
AAGCACTAGAAGCTCTTAAGGTAGAATTGAAAGCTAGCATTGACAAGGGTGTCGCATTTGCAAACAAACCAGCTGCTGCA
GCAGCTAACTAG

Alignment

ORF - retro_atha_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.35 %
• Parental protein coverage: 88.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NPGFKVAILGAAGGIGQSLSLLMKMNPLVSLLHLYDVVNAPGVTADVSHMDTGAVVRGFLGAKQLEDALT
          N...KVA.LGAAGGIGQ.LSLL.KM.PLVS.LHLYD..N..GV.AD.SH..T...VR.F.G...L.D.L.
Retrocopy NASYKVAVLGAAGGIGQPLSLLIKMSPLVSTLHLYDIANVKGVAADLSHCNTPSQVRDFTGPSELADCLK

Parental  GMDLVIIPAGIPRKPGMTRDDLFKINAGIVKTLCEGVAKCCPNAIVNLISNPVNSTVPIAAEVFKKAGTY
          ....V.IPAG.PRKPGMTRDDLF.INA.IVKTL.E.VA..CPNA....ISNPVNSTVPIAAEV.KK.G.Y
Retrocopy DVNVVVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVAENCPNAFIHIISNPVNSTVPIAAEVLKKKGVY

Parental  DPKKLLGVTTLDVARANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQVKPPSSFTPQEIEYLTNRIQ
          DPKKL.GVTTLDV.RANTFV.....L....VDVPV.GGHAG.TILPLLS..KP...FT..EI..LT.RIQ
Retrocopy DPKKLFGVTTLDVVRANTFVSQKKNLKLIDVDVPVIGGHAGITILPLLSKTKPSVNFTDEEIQELTVRIQ

Parental  NGGTEVVEAKAGAGSATLSMAYAAAKFADACLRGLRGDANVVECSFVASQVTELAFFATKVRLGRTGAEE
          N.GTEVV.AKAGAGSATLSMAYAAA.F....LR.L.GD..V.ECSFV.S..T.L.FFA..V..G..G.E.
Retrocopy NAGTEVVDAKAGAGSATLSMAYAAARFVESSLRALDGDGDVYECSFVESTLTDLPFFASRVKIGKNGLEA

Parental  VYQ--LGPLNEYERIGLEKAKDELAGSIQKGVEFIRK
          V....L..L.EYE...LE..K.EL..SI.KGV.F..K
Retrocopy VIESDLQGLTEYEQKALEALKVELKASIDKGVAFANK

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_10 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT5G09660	1 retrocopy	retro_atha_10 ,
Brassica rapa	Bra009397	1 retrocopy	retro_brap_19,
Brachypodium distachyon	BRADI4G00910	1 retrocopy	retro_bdis_5,
Triticum aestivum	Traes_5AL_31CDB68F2	1 retrocopy	retro_taes_27,