AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene059623

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059623.t1 MTR_6g087770 93.617 47 3 0 1 47 1 47 2.56e-27 94.0
MS.gene059623.t1 MTR_2g101850 72.340 47 13 0 1 47 1 47 9.20e-21 77.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059623.t1 AT1G52245 74.468 47 12 0 1 47 1 47 2.96e-21 78.6
MS.gene059623.t1 AT3G16120 70.213 47 14 0 1 47 1 47 3.24e-17 68.6
MS.gene059623.t1 AT3G16120 70.213 47 14 0 1 47 1 47 3.24e-17 68.6

Find 8 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTGATTGTAGATCAATTGC+TGG 0.453871 6.2:+87530811 MS.gene059623:CDS
CTAAAGATGTTGGAAGGAAA+AGG 0.470654 6.2:+87530703 None:intergenic
GCTTGAATTTGCATCTTCAA+AGG 0.513495 6.2:-87530748 None:intergenic
AAGCAACTAAAGATGTTGGA+AGG 0.603964 6.2:+87530697 None:intergenic
AATTGCTGGTAATATCAAGA+AGG 0.615321 6.2:+87530825 MS.gene059623:CDS
GTTGGAAGGAAAAGGTGTGG+TGG 0.639264 6.2:+87530711 MS.gene059623:CDS
AGCTTGAGAAGCAAATGACA+TGG 0.664039 6.2:-87530770 None:intergenic
GATGTTGGAAGGAAAAGGTG+TGG 0.753253 6.2:+87530708 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAATAAAAATAAAAATTTTG+GGG + chr6.2:87531468-87531487 MS.gene059623:intron 10.0%
!!! GTCAATAAAAATAAAAATTT+TGG + chr6.2:87531466-87531485 MS.gene059623:intron 10.0%
!! CTAAACAAATTATTTGTATT+TGG - chr6.2:87531081-87531100 None:intergenic 15.0%
!! GTAGCTAAAAAAATATTATT+GGG + chr6.2:87531414-87531433 MS.gene059623:intron 15.0%
!! TAATTATTTGCAAATGAATT+TGG + chr6.2:87531386-87531405 MS.gene059623:intron 15.0%
!! TAGCTAAAAAAATATTATTG+GGG + chr6.2:87531415-87531434 MS.gene059623:intron 15.0%
!! TGAAAATATTAGAATGAATT+TGG - chr6.2:87530930-87530949 None:intergenic 15.0%
!!! CAAATACAAATAATTTGTTT+AGG + chr6.2:87531079-87531098 MS.gene059623:intron 15.0%
!!! TTTATTTTTATTGACTCATT+AGG - chr6.2:87531461-87531480 None:intergenic 15.0%
!! AATGTACAATTAGTATAAAC+AGG - chr6.2:87531014-87531033 None:intergenic 20.0%
!! GGTAGCTAAAAAAATATTAT+TGG + chr6.2:87531413-87531432 MS.gene059623:intron 20.0%
!!! GAAAATCACTCAATTTTTTT+GGG - chr6.2:87530891-87530910 None:intergenic 20.0%
! AAATTGTGTTGTGAGTAAAT+AGG - chr6.2:87531598-87531617 None:intergenic 25.0%
! ACTAATTGTACATTTCTTTG+TGG + chr6.2:87531020-87531039 MS.gene059623:intron 25.0%
! TGAATTTGGATTTATGAGAT+TGG - chr6.2:87530916-87530935 None:intergenic 25.0%
! TTTCTATTCAATAAAGCAAG+AGG + chr6.2:87531714-87531733 MS.gene059623:intron 25.0%
!!! GGAAAATCACTCAATTTTTT+TGG - chr6.2:87530892-87530911 None:intergenic 25.0%
!!! TTTTTTCAACGTAGACAAAT+AGG + chr6.2:87531208-87531227 MS.gene059623:intron 25.0%
AATTGCTGGTAATATCAAGA+AGG + chr6.2:87530825-87530844 MS.gene059623:CDS 30.0%
ATTTGGATTTATGAGATTGG+TGG - chr6.2:87530913-87530932 None:intergenic 30.0%
GAATATTACGAAGATTCTTG+AGG - chr6.2:87531545-87531564 None:intergenic 30.0%
TTTGCAAATGAATTTGGTTG+AGG + chr6.2:87531392-87531411 MS.gene059623:intron 30.0%
! AAGCTAGAGAAATTTTTACG+AGG + chr6.2:87531052-87531071 MS.gene059623:intron 30.0%
! ACAATCCTTTGTTTCTCATA+TGG + chr6.2:87531623-87531642 MS.gene059623:intron 30.0%
! AGCTAGAGAAATTTTTACGA+GGG + chr6.2:87531053-87531072 MS.gene059623:intron 30.0%
! CAATCCTTTGTTTCTCATAT+GGG + chr6.2:87531624-87531643 MS.gene059623:intron 30.0%
ATAACGAATAGAATGACCAG+AGG - chr6.2:87531657-87531676 None:intergenic 35.0%
CCATGGATACAAAAGTTTGT+TGG - chr6.2:87530987-87531006 None:intergenic 35.0%
GCTTGAATTTGCATCTTCAA+AGG - chr6.2:87530751-87530770 None:intergenic 35.0%
GTAACCCATATGAGAAACAA+AGG - chr6.2:87531631-87531650 None:intergenic 35.0%
TAGTATAAACAGGAGATCCA+TGG - chr6.2:87531004-87531023 None:intergenic 35.0%
TGTGATTGTAGATCAATTGC+TGG + chr6.2:87530811-87530830 MS.gene059623:CDS 35.0%
! CCAACAAACTTTTGTATCCA+TGG + chr6.2:87530984-87531003 MS.gene059623:intron 35.0%
! CTAGAGAAATTTTTACGAGG+GGG + chr6.2:87531055-87531074 MS.gene059623:intron 35.0%
! GCTAGAGAAATTTTTACGAG+GGG + chr6.2:87531054-87531073 MS.gene059623:intron 35.0%
AGCTTGAGAAGCAAATGACA+TGG - chr6.2:87530773-87530792 None:intergenic 40.0%
GTACATTTCTTTGTGGACAG+CGG + chr6.2:87531027-87531046 MS.gene059623:intron 40.0%
! TCATATGGGTTACAAACCTC+TGG + chr6.2:87531638-87531657 MS.gene059623:intron 40.0%
AAGCTACCCCATCCTTTCAA+AGG + chr6.2:87531497-87531516 MS.gene059623:intron 45.0%
AGCTACCCCATCCTTTCAAA+GGG + chr6.2:87531498-87531517 MS.gene059623:intron 45.0%
TGTTGGAATCTCAGCGAGTT+CGG - chr6.2:87530970-87530989 None:intergenic 45.0%
TTGAAAGGATGGGGTAGCTT+TGG - chr6.2:87531497-87531516 None:intergenic 45.0%
! CGATTCCCTTTGAAAGGATG+GGG - chr6.2:87531506-87531525 None:intergenic 45.0%
! GCGATTCCCTTTGAAAGGAT+GGG - chr6.2:87531507-87531526 None:intergenic 45.0%
! TCTTGAGGTGTCCACAAACA+GGG - chr6.2:87531530-87531549 None:intergenic 45.0%
! TTCTTGAGGTGTCCACAAAC+AGG - chr6.2:87531531-87531550 None:intergenic 45.0%
!!! TCAATAAAAATAAAAATTTT+GGG + chr6.2:87531467-87531486 MS.gene059623:intron 5.0%
! CTTGAGGTGTCCACAAACAG+GGG - chr6.2:87531529-87531548 None:intergenic 50.0%
! GGCGATTCCCTTTGAAAGGA+TGG - chr6.2:87531508-87531527 None:intergenic 50.0%
! GTTGGAAGGAAAAGGTGTGG+TGG + chr6.2:87530711-87530730 MS.gene059623:CDS 50.0%
AAGGGAATCGCCCCTGTTTG+TGG + chr6.2:87531516-87531535 MS.gene059623:intron 55.0%
CAGGGGCGATTCCCTTTGAA+AGG - chr6.2:87531512-87531531 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 87530709 87531747 87530709 ID=MS.gene059623
chr6.2 mRNA 87530709 87531747 87530709 ID=MS.gene059623.t1;Parent=MS.gene059623
chr6.2 exon 87530709 87530846 87530709 ID=MS.gene059623.t1.exon1;Parent=MS.gene059623.t1
chr6.2 CDS 87530709 87530846 87530709 ID=cds.MS.gene059623.t1;Parent=MS.gene059623.t1
chr6.2 exon 87531730 87531747 87531730 ID=MS.gene059623.t1.exon2;Parent=MS.gene059623.t1
chr6.2 CDS 87531730 87531747 87531730 ID=cds.MS.gene059623.t1;Parent=MS.gene059623.t1
Gene Sequence

>MS.gene059623

ATGTTGGAAGGAAAAGGTGTGGTGGAAGAAACAGATATGCCTTTGAAGATGCAAATTCAAGCCATGTCATTTGCTTCTCAAGCTCTTGATCTCTATGATGTTTGTGATTGTAGATCAATTGCTGGTAATATCAAGAAGGTACATTACTTTTAACACTTGTGAAAATTTTACTCTATATACCCAAAAAAATTGAGTGATTTTCCACCAATCTCATAAATCCAAATTCATTCTAATATTTTCAAGAAACAAAACTCTTATCCGAACTCGCTGAGATTCCAACAAACTTTTGTATCCATGGATCTCCTGTTTATACTAATTGTACATTTCTTTGTGGACAGCGGCGAAGCTAGAGAAATTTTTACGAGGGGGCCAAATACAAATAATTTGTTTAGGTAAAAAAAAACTTATATATTTTAAAATATTATATATTAAATTTAAAAGTTAAGTATGTTTAATCTCTAACTTTTTTTTTCAACGTATCTTTCTAAAAGAATTTTTTTTTTTTCAACGTAGACAAATAGGTTATTTGCATGAAATTATCGTCTATTATGTTTGACTATTGATAGTTTTTATTGCTAAAAATGCTTTCTTTATAGTTGTTGTAGAGAACGAAATGTCAAAATAAGACAAATAAGTTTATTAATCAAGTAATAATTTTTTAATCTTTTAATTTATGCTAATTATTTGCAAATGAATTTGGTTGAGGTAGCTAAAAAAATATTATTGGGGTAGCTAGCTATATTAATATACCTAATGAGTCAATAAAAATAAAAATTTTGGGGTAGCCAAAGCTACCCCATCCTTTCAAAGGGAATCGCCCCTGTTTGTGGACACCTCAAGAATCTTCGTAATATTCGTGCTAATCTTCTTACGTGCTTGATGAAATCCTATTTACTCACAACACAATTTATATCACAATCCTTTGTTTCTCATATGGGTTACAAACCTCTGGTCATTCTATTCGTTATTTATGCTATACAAGCTTAGCATGCATAATATTGATATTTTCTATTCAATAAAGCAAGAGGTGTTTAACTAA
Protein sequence

>MS.gene059623.t1

MLEGKGVVEETDMPLKMQIQAMSFASQALDLYDVCDCRSIAGNIKKQEVFN