RetrogeneDB ID: retro_atha_1

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 5:19947795..19949055(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT5G49200
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT5G40880
• Aliases: None
• Description: None

Sequence

>retro_atha_1
ATGGATTACAAAGCGCCAAGGAGATACTACTCACACGGAGTTGTTGCGAGACAGCAAGATTTCGCAACAGATATAGTTAC
GAGAAGAAGACCTTATGTCCCTTACGACCGTCCAAATAAGTTTTCAAGGAGTCTGGTTTGGACGTCAAAAGAGTACAAAT
CACCCGAGGGCAATAATATGCCAAGGACCAATGATGTGTCACCGAAACCACCAGTTTTAGGTTTGGCGAGGAAGAATGCT
GCTTGTGGGCCAATGAGATCTTCTAGTCTCAGAAAATGGGTATGTAAGTATTGGAAAGATGGAAAGTGCAAGAGGGGTGA
GCAGTGCCAGTTCTTACACTCTTGGTCTTGTTTCCCTGGATTGGCCATGGTAGCTTCTCTTGAAGGGCACAATAAGGAAC
TAAAGGGGATCGCTCTCCCTGAGGGTTCAGATAAACTCTTTTCAGTCAGTATTGATGGTACATTGCGAGTTTGGGACTGC
AATTCTGGTCAGTGTGTACATTCCATCAACCTTGACGCAGAAGCAGGGTCTCTAATCAGTGAAGGCCCTTGGGTTTTCCT
TGGCTTGCCAAACGCTATAAAGGCTTTTAACGTTCAAACCAGTCAAGATTTGCATCTTCAAGCAGCAGGGGTGGTTGGTC
AGGTGAATGCAATGACTATTGCAAACGGAATGCTTTTTGCTGGAACAAGTTCTGGTAGTATCTTAGTCTGGAAAGCTACT
ACAGACTCTGAGTCTGATCCATTCAAATACTTGACATCTCTTGAGGGACATAGTGGTGAAGTCACTTGTTTTGCTGTTGG
AGGTCAAATGCTATACTCTGGTTCTGTCGATAAAACAATCAAGATGTGGGATCTCAACACCCTGCAATGTATAATGACCC
TGAAGCAACATACCGGCACTGTCACTTCACTCTTATGTTGGGATAAATGTTTGATATCGTCTTCCTTGGATGGGACCATA
AAAGTTTGGGCTTATTCTGAAAACGGAATCTTGAAAGTTGTTCAAACTCGCAGACAAGAACAGAGTAGTGTTCATGCTCT
TTCTGGTATGCATGATGCAGAAGCCAAACCGATAATATTCTGCTCTTACCAAAACGGAACCGTTGGCATTTTCGACCTAC
CATCTTTTCAAGAAAGAGGAAGGATGTTCTCTACGCACACGATCGCCACACTCACAATTGGTCCTCAAGGATTGTTATTC
AGTGGAGACGAGAGTGGTAACTTGCGTGTATGGACCTTAGCTGCTGGCAACAAAGTTTAG

Alignment

ORF - retro_atha_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.85 %
• Parental protein coverage: 75.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SNQPRKNAVYGPRSSSLSDTR---GCGPRLNGSPKKSVCNFWKDGNCKKGEKCQFLHSWSCFPGLAMVAA
          .N.PR.N.V..P....L...R....CGP....S..K.VC..WKDG.CK.GE.CQFLHSWSCFPGLAMVA.
Retrocopy NNMPRTNDV-SPKPPVLGLARKNAACGPMRSSSLRKWVCKYWKDGKCKRGEQCQFLHSWSCFPGLAMVAS

Parental  LEGHKNDIKGIALPQGSDKLFSVSGDGTLLIWDCNSGQCVRSINLQAEAGSLISEGPWVFLGLPNAVKAF
          LEGH....KGIALP.GSDKLFSVS.DGTL..WDCNSGQCV.SINL.AEAGSLISEGPWVFLGLPNA.KAF
Retrocopy LEGHNKELKGIALPEGSDKLFSVSIDGTLRVWDCNSGQCVHSINLDAEAGSLISEGPWVFLGLPNAIKAF

Parental  NVQNSKDVHLE--GVVGQVHAMTAANGMLFAGTSSGSILVWKA-TDSESDPFKYLTSLEGHHSGEVTCFV
          NVQ.S.D.HL...GVVGQV.AMT.ANGMLFAGTSSGSILVWKA.TDSESDPFKYLTSLEG.HSGEVTCF.
Retrocopy NVQTSQDLHLQAAGVVGQVNAMTIANGMLFAGTSSGSILVWKATTDSESDPFKYLTSLEG-HSGEVTCFA

Parental  VGGEVLYSGSVDKTIKVWDLNTLQCRMTLKQHIGTVTSLLCWDKCLISSSLDGTIKLWACSENESLKVVQ
          VGG..LYSGSVDKTIK.WDLNTLQC.MTLKQH.GTVTSLLCWDKCLISSSLDGTIK.WA.SEN..LKVVQ
Retrocopy VGGQMLYSGSVDKTIKMWDLNTLQCIMTLKQHTGTVTSLLCWDKCLISSSLDGTIKVWAYSENGILKVVQ

Parental  TRKQE-LSVHTLCGMHDAEAKPIMFCSYQNGAVGIFDLPSFEERGKMFSTQTICTLTIGPGGLLFSGDKS
          TR.QE..SVH.L.GMHDAEAKPI.FCSYQNG.VGIFDLPSF.ERG.MFST.TI.TLTIGP.GLLFSGD.S
Retrocopy TRRQEQSSVHALSGMHDAEAKPIIFCSYQNGTVGIFDLPSFQERGRMFSTHTIATLTIGPQGLLFSGDES

Parental  GNLRVWSLASGTKV
          GNLRVW.LA.G.KV
Retrocopy GNLRVWTLAAGNKV

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_1 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT5G40880	1 retrocopy	retro_atha_1 ,