RetrogeneDB ID: retro_atha_18

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 3:18983710..18984952(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT3G51110
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT5G41770
• Aliases: None
• Description: None

Sequence

>retro_atha_18
ATGATGATGATTCCAAGGATGGTTAAGAACAAAACCCCTGCTCCGGTTCAAATCACGGCGGAGCAGGTTTTGAAGGAGGC
GAGAGAGAGAGAGGACAGTCGCATCCTGCGGCCGCCTAAACAGAAGATCACAGATTCGGATGAGCTTGCCGAGTACAGAC
TCCGACGTCGGAAGGAGTTTGAGGACCAGATCCGCGGCGCAAAAACGAACTCACAAGTTTGGGTGAGGTATGCTGATTGG
GAAGAGTCTCAGAAGGATCACGATCGTGCTCGGAGCGTGTGGGAACGAGCTTTGGAAGACGAGAGTTACAGGAACCATAC
GCTCTGGCTCAAATACGCAGAGTTCGAGATGAGGAACAAATCCGTCAACCATGCGAGGAACGTTTGGGATCGAGCCGTGA
AGATTCTACCTCGCGTGGACCAGTTTTGGTATAAGTATATTCACATGGAGGAGATACTTGGTAATATCGACGGAGCTAGA
AAGATTTTTGAACGGTGGATGGATTGGTCACCAGATCAACAAGCTTGGCTCTGTTTTATCAAATTCGAACTTAGGTATAA
CGAAATCGAACGGTCAAGATCGATTTACGAGAGATTTGTGCTTTGCCATCCTAAAGCTTCTTCCTTTATTCGATACGCAA
AGTTTGAGATGAAGAACAGTCAAGTTTCGCTTGCGAGGATTGTGTACGAACGCGCCATTGAGATGCTTAAAGACGTCGAA
GAAGAAGCTGAGATGATCTTTGTGGCCTTTGCTGAGTTTGAAGAACTATGTAAAGAAGTGGAACGGGCTAGGTTTCTTTA
CAAGTATGCTCTTGATCATATCCCTAAAGGAAGAGCTGAGGATTTGTACAAGAAGTTTGTGGCGTTTGAGAAGCAGTATG
GGAATAAGGAAGGTATTGATGATGCCATTGTTGGCAGGAGAAAGTTACAGTATGAAGGTGAAGTGAGGAAGAACCCTTTG
AACTACGATTCTTGGTTCGATTACATTAGCTTAGAGGAGACTTTGGGGGATAAAGATAGGATCAGAGAAGTCTATGAGAG
GGCTATTGCTAATGTTCCACTCGCTGAGGAGAAACGATACTGGCAGAGATATATCTACTTGTGGATTGATTATGCACTGT
TTGAAGAGATTCTAGCTGAAGACGTGGAGCGTACTCGAGCTGTGTACAGAGAATGCCTCAATCTTATCCCCTCACTCCAA
ATTCTCTTTTGCCAAGATATGGTTGCTCGCTGCACAGTTTGA

Alignment

ORF - retro_atha_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.55 %
• Parental protein coverage: 56.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PTRVKNKTPAPIQITAEQILREARERQEAEI-RPPKQKITDSTELSDYRLRRRKEFEDQIRRARWNIQVW
          P..VKNKTPAP.QITAEQ.L.EARER....I.RPPKQKITDS.EL..YRLRRRKEFEDQIR.A..N.QVW
Retrocopy PRMVKNKTPAPVQITAEQVLKEAREREDSRILRPPKQKITDSDELAEYRLRRRKEFEDQIRGAKTNSQVW

Parental  VKYAQWEESQKDYARARSVWERAIEGD-YRNHTLWLKYAEFEMKNKFVNSARNVWDRAVTLLPRVDQLWY
          V.YA.WEESQKD..RARSVWERA.E...YRNHTLWLKYAEFEM.NK.VN.ARNVWDRAV..LPRVDQ.WY
Retrocopy VRYADWEESQKDHDRARSVWERALEDESYRNHTLWLKYAEFEMRNKSVNHARNVWDRAVKILPRVDQFWY

Parental  KYIHMEEILGNIAGARQIFERWMDWSPDQQGWLSFIKFELRYNEIERARTIYERFVLCHPKVSAYIRYAK
          KYIHMEEILGNI.GAR.IFERWMDWSPDQQ.WL.FIKFELRYNEIER.R.IYERFVLCHPK.S..IRYAK
Retrocopy KYIHMEEILGNIDGARKIFERWMDWSPDQQAWLCFIKFELRYNEIERSRSIYERFVLCHPKASSFIRYAK

Parental  FEMKGGEVARCRSVYERATEKLAD-DEEAEILFVAFAEFEERCKEVERARFIYKFALDHIPKGRAEDLYR
          FEMK...V...R.VYERA.E.L.D..EEAE..FVAFAEFEE.CKEVERARF.YK.ALDHIPKGRAEDLY.
Retrocopy FEMKNSQVSLARIVYERAIEMLKDVEEEAEMIFVAFAEFEELCKEVERARFLYKYALDHIPKGRAEDLYK

Parental  KFVAFEKQYGDKEGIEDAIVGKRRFQYEDEVRKSPSNYDSWFDYVRLEESVGNKDRIREIYERAIANVPP
          KFVAFEKQYG.KEGI.DAIVG.R..QYE.EVRK.P.NYDSWFDY..LEE..G.KDRIRE.YERAIANVP.
Retrocopy KFVAFEKQYGNKEGIDDAIVGRRKLQYEGEVRKNPLNYDSWFDYISLEETLGDKDRIREVYERAIANVPL

Parental  AEEKRYWQRYIYLWINYALFEEIETEDIERTRDVYRECLKLIPHSKFSFAK
          AEEKRYWQRYIYLWI.YALFEEI..ED.ERTR.VYRECL.LIP.....F..
Retrocopy AEEKRYWQRYIYLWIDYALFEEILAEDVERTRAVYRECLNLIPSLQILFCQ

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_18 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT5G41770	1 retrocopy	retro_atha_18 ,
Brassica oleracea	Bo6g066460	1 retrocopy	retro_bole_29,
Triticum aestivum	Traes_7DL_41F6E8FC4	1 retrocopy	retro_taes_37,