RetrogeneDB ID: retro_atha_27

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 3:22403463..22404627(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT3G60610
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT1G60170
• Aliases: None
• Description: None

Sequence

>retro_atha_27
GATGATCATGAGTATAAGCTTATTGTGGATTGTAATAAGCTTTCGGTTGATATTGAGGATGAAATCGTTATTGTCCACAA
CTTTATCAAAGAAAAGTACAAGCTTAGGTTTCAAGAGCTTGAGTCGTTGGTTCATCACCCTATTGACTATGCATGTGTTG
TCAAGAAGATTGGCAATGAGACGGATTTGACTCTTGTTGATTTTGCTGGCCTTGATCTTACTCCAGCTATTATCATGGCT
ATTTCAGTTACTGCTTCAACTACGAAAGGGAGTGCACTGCCAGAGGATGTTTAGCAAAAGGTGTTAGAGGCTTGTGATCG
GGATTTAGATCTTGATTCCGCAAGAAAGAAGGTCCTTGAGTTTGTTGAAAGTAAGATGGGTTCTATTGCTCCTAATCTTT
CCGCCATTGTTGGGAGTGCTGTTGCAGCCAAACTCATGGGGACAGCTGGAGGTTTGTCAGCACTTGCTAAAATGCCTGCC
TGTAATGTTCAAGTTCTTGGCCACAAGAGGAAGAACCTTGTTGGGTTTTCTTCTGCAACGTCTCAGTCCCGTGTGGGTTA
TCTGGAGCAGACAGAGATTTTCCAAAGCACGCCTCCTGGACTTGAGGCTCGCGCTGGCAGGCTCGTGGCTGCAAAATCAA
CTTTGGCAGCTAGAGTTGATGCTACTAGAGAGGATCCGTTAGGGATAAGTGGAAAAGCTTTCAGGGAGGAGATCCGTAAG
AAGATTGACAAGTGGCAAGAACCTCCTCCTGCAAGGCAGCCTAAGCCACTTCCTATTCCTCATTCTGAGCCGAAGAAAAG
AAGGGGTGGTCGCCGTCTAAGAAAACTGAAAGCAAGGTATCAAGTAACAGATATGAGGAAGCTGGCCAACAGGACGGCCT
TTGGTACACCTGAAGAGAGCTCCCTCGGTGATGGACTAGGAGAAGGTTATGGAATGCTTGGACAGGCAGGAAGCAAGAGG
CTGCGAGTATCCAGTGTTCAGAGCAAGCTTAAAATTAATGCCAAGGTCGCCAAAAAGCTTAAAGAAAGGCAGTATGCGGG
TGGTGCAACTACCTCTGGTTTGACATCAAGCTTGGCTTTCACTTCTATGCAGGGAATAGAGTTGTGCAATCCTCAGCAAG
CTTTAGGATTAGGAAGTGGGGCTCAAAGCACTTCTCAGAGTCAG

Alignment

ORF - retro_atha_27 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.24 %
• Parental protein coverage: 79.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDPEYKLIVDCNQLSVDIENEIVIVHNFIKDKYKLKFQELESLVHHPIDYACVVKKIGNETDLALVDLAD
          DD.EYKLIVDCN.LSVDIE.EIVIVHNFIK.KYKL.FQELESLVHHPIDYACVVKKIGNETDL.LVD.A.
Retrocopy DDHEYKLIVDCNKLSVDIEDEIVIVHNFIKEKYKLRFQELESLVHHPIDYACVVKKIGNETDLTLVDFAG

Parental  L-LPSAIIMVVSVTALTTKGSALPEDVLQKVLEACDRALDLDSARKKVLEFVESKMGSIAPNLSAIVGSA
          L.L..AIIM..SVTA.TTKGSALPEDV.QKVLEACDR.LDLDSARKKVLEFVESKMGSIAPNLSAIVGSA
Retrocopy LDLTPAIIMAISVTASTTKGSALPEDV*QKVLEACDRDLDLDSARKKVLEFVESKMGSIAPNLSAIVGSA

Parental  VAAKLMGTAGGLSALAKMPACNVQVLGHKRKNLAGFSSATSQSRVGYLEQTEIYQSTPPGLQARAGRLVA
          VAAKLMGTAGGLSALAKMPACNVQVLGHKRKNL.GFSSATSQSRVGYLEQTEI.QSTPPGL.ARAGRLVA
Retrocopy VAAKLMGTAGGLSALAKMPACNVQVLGHKRKNLVGFSSATSQSRVGYLEQTEIFQSTPPGLEARAGRLVA

Parental  AKSTLAARVDATRGDPLGISGKAFREEIRKKIEKWQEPPPARQPKPLPVPDSEPKKRRGGRRLRKMKERY
          AKSTLAARVDATR.DPLGISGKAFREEIRKKI.KWQEPPPARQPKPLP.P.SEPKKRRGGRRLRK.K.RY
Retrocopy AKSTLAARVDATREDPLGISGKAFREEIRKKIDKWQEPPPARQPKPLPIPHSEPKKRRGGRRLRKLKARY

Parental  QVTDMRKLANRMAFGTPEESSLGDGLGEGYGMLGQAGSNRLRVSSVPSKLKINAKVAKKLKERQYAGGAT
          QVTDMRKLANR.AFGTPEESSLGDGLGEGYGMLGQAGS.RLRVSSV.SKLKINAKVAKKLKERQYAGGAT
Retrocopy QVTDMRKLANRTAFGTPEESSLGDGLGEGYGMLGQAGSKRLRVSSVQSKLKINAKVAKKLKERQYAGGAT

Parental  TSGLTSSLAFTPVQGIELCNPQQALGLGSGTQSTYFSE
          TSGLTSSLAFT..QGIELCNPQQALGLGSG.QST..S.
Retrocopy TSGLTSSLAFTSMQGIELCNPQQALGLGSGAQSTSQSQ

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_27 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G60170	1 retrocopy	retro_atha_27 ,
Brassica oleracea	Bo1g091740	1 retrocopy	retro_bole_6,
Brassica rapa	Bra031522	1 retrocopy	retro_brap_23,
Solanum tuberosum	PGSC0003DMG400004771	1 retrocopy	retro_stub_45,