RetrogeneDB ID: retro_atha_22

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 1:23655715..23657379(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT1G63760
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT1G05890
• Aliases: None
• Description: None

Sequence

>retro_atha_22
ATGGATTCCGATGATGATATGCTCGATGCCCACGATATGGACTCGGTAGATTATGATTTTGACAGCGGCGGCACCGATGA
TGACAACGATATTGATGAAACTGATTACGTGTTTGGTGAGGCTGACACGGACGATGCCGCCATCATCGCCTACCATCGCT
CTCAGATAAATTATGTTGTTCTCAAGGAAGAAGATATTCGCAGGCATCAGAAGGATGACGTTGGGCGAGTTTCCGTTGTC
CTCTCCATAACCGATGTCCAAGCAAGTCTTTTGCTTCTTCACTATCACTGGAGTGTCAGTAAAGTTAATGATGAATGGTT
TGCGGATGAGGACAGAGTTCGTAGAACTGTTGGCATATTAGAGGGACCTGCACCTGATGGCAGAGAGTTTACATGTGGAA
TATGCTTTGAATCCTACCCTCTTGAGGAAACTATATCGGTTTCTTGTGGTCACCCATTCTGCGCTACATGTTGGACGGGT
TATATAAGCACAAGCATCAATGATGGCCCAGGATGTTTGATGCTAAAATGTCCCTACCCTTGTTGTCCTGCGGCCATTGG
TCGAGATATGATCGATAACTTGTGTTCCAAGGAAGACAAGTAGAGGTATTATAGATATTTTCTTAGGTCTTATGTTGAAG
TCAACAGAGAGATGAAGTGCTGTCCTGCCCCAGGATGTGAGCATGCAATTAGTTTTGCTGCTGGGACCGAAAGTAATTAT
GATGTTTCGTGCTTGTGTTCGCATAGCTTTTGCTGGAATTGCAGTGAAGAGGCTCACCGTCCTGTGGATTGTGACACAGT
TGGAAAATGGATACTAAAGAACAGCACTGAATCTGAAAATATGAATTGGATACTTGCCAATTCGAAGCCTTGTCCAAAGT
GTAAGAGGCCAATAGAAAAGAATCATGGATGTATGCACATGACATGCACACCACCTTGTAAGTTTGAGTTTTGTTGGCTC
TGCCTTAACGCATGGACAGAACACGGGGAAAGTAGTGGTGGGTATTATGCCTGCAACCGGTATGAGGCGGCTAAGAAACA
AGGGTTGTATGATGAGGCTGAAAGGAGGCGAGAGATGGCAAAAAACTCGCTAGAGAAATACACTCATTACTATAAACGAT
GGGCAAGCAATCAAGTGTCGAGGCAAAAAGCTATGGGGGATCTGCAGAAAATGCAATCAGAGAAGCTTAGGAAGCTTAGT
GACATACAGTGCACATCAGAATCTCAGCTCAAGTTTATCGCAGAGGCTTGGCTCCAGATCATTGAATGCAGACGGGTACT
CAAATGGACATATGCATATGGATACTATGTACCAGATGATCATACTAAGAAACAATTTTTTGAGTATTTGCAAGGGGAGG
CTGAGTCAGGTTTGGAGAGGCTCCACGAATGCATAGAGAATGATATTGAGGTGTTTGAATTTGGTGAGGGCCCTTCAGAG
GAATTCAATCATTTCCGGACAAAATTAACTGATTTAACCAGCATAACAAAAACCTTCTTCCAAAATCTGGTCAAAGCTCT
GGAGAATGGTCTTGCTGACGTGGATTCACATGCTGCTAGCAGCAAACCAGCAAACTGTAAACCTTCTAGCAATACAAAAG
ACGGTGGGAAAGGTAAAAAGGAAGCTCTAACGATGGCGGGTTCAGCAGAAACCTAGATGGCAAT

Alignment

ORF - retro_atha_22 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDSDDDM---HDMDSVDYDYYSGGTYDDNDSDETDFGFGEADTDDAAIIASYRSKSNYVVLKEEDIRRHQ
          MDSDDDM...HDMDSVDYD..SGGT.DDND.DETD..FGEADTDDAAIIA..RS..NYVVLKEEDIRRHQ
Retrocopy MDSDDDMLDAHDMDSVDYDFDSGGTDDDNDIDETDYVFGEADTDDAAIIAYHRSQINYVVLKEEDIRRHQ

Parental  NDDVGRVSAVLSITDVEASTLLLHYHWSVSKVNDEWFADEERVRRTVGILEGPVVTTPDGREFTCGICFD
          .DDVGRVS.VLSITDV.AS.LLLHYHWSVSKVNDEWFADE.RVRRTVGILEGP....PDGREFTCGICF.
Retrocopy KDDVGRVSVVLSITDVQASLLLLHYHWSVSKVNDEWFADEDRVRRTVGILEGPA---PDGREFTCGICFE

Parental  SYTLEEIVSVSCGHPFCATCWTGYISTTINDGPGCLMLKCPDPSCPAAIGRDMIDKLASKEDKEKYYRYF
          SY.LEE..SVSCGHPFCATCWTGYIST.INDGPGCLMLKCP.P.CPAAIGRDMID.L.SKEDK..YYRYF
Retrocopy SYPLEETISVSCGHPFCATCWTGYISTSINDGPGCLMLKCPYPCCPAAIGRDMIDNLCSKEDK*RYYRYF

Parental  LRSYVEVNREMKWCPAPGCEHAIDFAGGTES-YDVSCLCSHSFCWNCTEEAHRPVDCDTVGKWILKNSAE
          LRSYVEVNREMK.CPAPGCEHAI.FA.GTES.YDVSCLCSHSFCWNC.EEAHRPVDCDTVGKWILKNS.E
Retrocopy LRSYVEVNREMKCCPAPGCEHAISFAAGTESNYDVSCLCSHSFCWNCSEEAHRPVDCDTVGKWILKNSTE

Parental  SENMNWILANSKPCPKCKRPIEKNHGCMHMTCTPPCKFEFCWLCLNAWTEHGERTGGFYACNRYEAAKQE
          SENMNWILANSKPCPKCKRPIEKNHGCMHMTCTPPCKFEFCWLCLNAWTEHGE..GG.YACNRYEAAK..
Retrocopy SENMNWILANSKPCPKCKRPIEKNHGCMHMTCTPPCKFEFCWLCLNAWTEHGESSGGYYACNRYEAAKKQ

Parental  GLYDEAERRREMAKNSLERYTHYYERWASNQVSRQKAMGDLQKMQSEKLGKLSDIQCTPESQLKFIAEAW
          GLYDEAERRREMAKNSLE.YTHYY.RWASNQVSRQKAMGDLQKMQSEKL.KLSDIQCT.ESQLKFIAEAW
Retrocopy GLYDEAERRREMAKNSLEKYTHYYKRWASNQVSRQKAMGDLQKMQSEKLRKLSDIQCTSESQLKFIAEAW

Parental  LQIIECRRVLKWTYAYGYYL-QDHAKKPFFEYLQGEAESGLERLHKCVEKDIEVFELAEGPSEEFNHFRT
          LQIIECRRVLKWTYAYGYY...DH.KK.FFEYLQGEAESGLERLH.C.E.DIEVFE..EGPSEEFNHFRT
Retrocopy LQIIECRRVLKWTYAYGYYVPDDHTKKQFFEYLQGEAESGLERLHECIENDIEVFEFGEGPSEEFNHFRT

Parental  KLTGLTSITKTFFENLVKALENGLADVDSQAASSKPANSKPSSKTKGGGKGK-GSSKN-GGSSRNPDGN
          KLT.LTSITKTFF.NLVKALENGLADVDS.AASSKPAN.KPSS.TK.GGKGK...S.N.GG.SRN.DGN
Retrocopy KLTDLTSITKTFFQNLVKALENGLADVDSHAASSKPANCKPSSNTKDGGKGK<KGSSNDGGFSRNLDGN

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_22 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G05890	1 retrocopy	retro_atha_22 ,
Brassica oleracea	Bo5g007100	1 retrocopy	retro_bole_13,
Brassica oleracea	Bo8g005850	1 retrocopy	retro_bole_12,
Brassica rapa	Bra015463	1 retrocopy	retro_brap_11,
Oryza sativa japonica	OS04G0492100	1 retrocopy	retro_osat_31,