AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene04973


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene04973.t1 MTR_3g061510 93.496 123 8 0 46 168 200 322 1.43e-69 214
MS.gene04973.t1 MTR_3g061510 93.496 123 8 0 46 168 220 342 4.03e-69 213
MS.gene04973.t1 MTR_3g461520 96.000 50 2 0 1 50 1 50 2.80e-27 107
MS.gene04973.t1 MTR_3g461520 96.000 50 2 0 1 50 1 50 2.80e-27 107
MS.gene04973.t1 MTR_3g461520 96.000 50 2 0 1 50 1 50 2.88e-27 107
MS.gene04973.t1 MTR_3g461500 94.000 50 3 0 1 50 1 50 1.64e-26 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene04973.t1 AT3G20910 48.031 127 37 6 46 168 195 296 1.65e-19 83.6
MS.gene04973.t1 AT3G13330 62.000 50 19 0 1 50 1 50 1.06e-15 74.3
MS.gene04973.t1 AT5G12840 57.812 64 26 1 51 114 205 267 8.96e-14 67.4
MS.gene04973.t1 AT5G12840 57.812 64 26 1 51 114 205 267 8.96e-14 67.4
MS.gene04973.t1 AT5G12840 57.812 64 26 1 51 114 206 268 9.33e-14 67.4
MS.gene04973.t1 AT5G12840 57.812 64 26 1 51 114 206 268 9.33e-14 67.4
MS.gene04973.t1 AT5G12840 57.812 64 26 1 51 114 206 268 9.33e-14 67.4

Find 57 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGGAAGAAGGGGACTGTTC+AGG 0.315135 3.3:-58973921 MS.gene04973:CDS
GCATACCATTGTTGTTAGTA+TGG 0.321193 3.3:+58973970 None:intergenic
TATGCAATCTTCAAGGTATC+AGG 0.338770 3.3:-58973952 MS.gene04973:CDS
GCAAGAGGAACAAACGAAAA+TGG 0.355771 3.3:-58974005 MS.gene04973:CDS
TCGCATGTTGGGAGAATTCC+AGG 0.360834 3.3:+58974034 None:intergenic
AGAGTAGAATAAACGGATTC+GGG 0.373601 3.3:+58975125 None:intergenic
GAGAGTAGAATAAACGGATT+CGG 0.379774 3.3:+58975124 None:intergenic
CTTGCATCTTGTCGCATGTT+GGG 0.394811 3.3:+58974023 None:intergenic
TTCGGGATCGTCACGGTTGA+AGG 0.401714 3.3:+58975142 None:intergenic
TCGCAATCAATTAGTTCATC+TGG 0.408092 3.3:-58974089 MS.gene04973:CDS
GAAAACTGATGGTGAGGCCT+CGG 0.419006 3.3:-58974144 MS.gene04973:CDS
GAGGCCTCGGGAAAGGATAA+TGG 0.429841 3.3:-58974131 MS.gene04973:CDS
TCTTGCATCTTGTCGCATGT+TGG 0.437702 3.3:+58974022 None:intergenic
TGTCTAGATTCATGAAGATA+TGG 0.448950 3.3:+58974215 None:intergenic
CTTCAGACTCTGCGGAAACC+TGG 0.454407 3.3:-58974052 MS.gene04973:CDS
TGGAAGAAGGGGACTGTTCA+GGG 0.467131 3.3:-58973920 MS.gene04973:CDS
TTGAGAAGGGCAAGAGGCAC+CGG 0.467176 3.3:-58974182 MS.gene04973:CDS
ATTGATTGCGACGACAAGAC+TGG 0.480972 3.3:+58974101 None:intergenic
CCTCTACGATGCCTCGTTCG+AGG 0.487485 3.3:+58973878 None:intergenic
CCGGCGGTTTGAGACGCCAC+TGG 0.491542 3.3:+58975209 None:intergenic
GTATTTGAGAGTAGAATAAA+CGG 0.498856 3.3:+58975118 None:intergenic
TCGGGAAAGGATAATGGCTC+TGG 0.498937 3.3:-58974125 MS.gene04973:CDS
CAGGGTGAAAGAGTGGAAGA+AGG 0.503255 3.3:-58973933 MS.gene04973:CDS
GTTTGAGACGCCACTGGTGG+CGG 0.506912 3.3:+58975215 None:intergenic
TTTCTTTGCAAATCGTCCTC+CGG 0.509061 3.3:+58974163 None:intergenic
AAAACTGATGGTGAGGCCTC+GGG 0.514204 3.3:-58974143 MS.gene04973:CDS
ACGGTTGAAGGAAGAGTTAA+CGG 0.520754 3.3:+58975154 None:intergenic
ACCATTGTTGTTAGTATGGT+AGG 0.523686 3.3:+58973974 None:intergenic
AGGGTGAAAGAGTGGAAGAA+GGG 0.525419 3.3:-58973932 MS.gene04973:CDS
ACAATGGTATGCAATCTTCA+AGG 0.528717 3.3:-58973959 MS.gene04973:CDS
TGATGGTGAGGCCTCGGGAA+AGG 0.531610 3.3:-58974138 MS.gene04973:CDS
TGCATGGTTGCCGCCACCAG+TGG 0.536142 3.3:-58975225 MS.gene04973:CDS
AGCGAATGAATCTCTTTCGC+CGG 0.538984 3.3:+58975190 None:intergenic
AAATGCATCTCTACAATGCA+TGG 0.547105 3.3:-58975241 MS.gene04973:CDS
GACATCAGCATGCTTTGAGA+AGG 0.559068 3.3:-58974196 MS.gene04973:CDS
CAGGTTTCCGCAGAGTCTGA+AGG 0.567519 3.3:+58974053 None:intergenic
AAGGTATCAGGGTGAAAGAG+TGG 0.579884 3.3:-58973940 MS.gene04973:CDS
TGCAAAGAAAACTGATGGTG+AGG 0.591393 3.3:-58974150 MS.gene04973:CDS
GAATGAATCTCTTTCGCCGG+CGG 0.591645 3.3:+58975193 None:intergenic
ATGCAATCTTCAAGGTATCA+GGG 0.599536 3.3:-58973951 MS.gene04973:CDS
AAACGGATTCGGGATCGTCA+CGG 0.603559 3.3:+58975135 None:intergenic
GGAACAAACGAAAATGGTGG+TGG 0.605222 3.3:-58973999 MS.gene04973:CDS
CATGCTTTGAGAAGGGCAAG+AGG 0.607747 3.3:-58974188 MS.gene04973:CDS
CCAGTGGCGTCTCAAACCGC+CGG 0.618665 3.3:-58975209 MS.gene04973:CDS
ACATCAGCATGCTTTGAGAA+GGG 0.618856 3.3:-58974195 MS.gene04973:CDS
GACTGTTCAGGGCAGCTACG+TGG 0.623934 3.3:-58973909 MS.gene04973:CDS
CGATTTGCAAAGAAAACTGA+TGG 0.624607 3.3:-58974155 MS.gene04973:CDS
GCGGTTTGAGACGCCACTGG+TGG 0.630936 3.3:+58975212 None:intergenic
AGAAGGGCAAGAGGCACCGG+AGG 0.637214 3.3:-58974179 MS.gene04973:CDS
GGGTGAAAGAGTGGAAGAAG+GGG 0.642943 3.3:-58973931 MS.gene04973:CDS
AGAGCCATTATCCTTTCCCG+AGG 0.653284 3.3:+58974127 None:intergenic
TCCTACCATACTAACAACAA+TGG 0.657295 3.3:-58973975 MS.gene04973:CDS
TGGAAGCATCTCCTCGAACG+AGG 0.669556 3.3:-58973889 MS.gene04973:CDS
CCTCGAACGAGGCATCGTAG+AGG 0.699167 3.3:-58973878 None:intergenic
AGAGGAACAAACGAAAATGG+TGG 0.699790 3.3:-58974002 MS.gene04973:CDS
AACATGCGACAAGATGCAAG+AGG 0.701252 3.3:-58974020 MS.gene04973:CDS
GTTGAAGGAAGAGTTAACGG+TGG 0.773498 3.3:+58975157 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGCTTATTTTTAATTAATTT+AGG - chr3.3:58974186-58974205 MS.gene04973:CDS 10.0%
!! AAAATTGAAGAGTTGAAAAA+TGG + chr3.3:58974052-58974071 None:intergenic 20.0%
!! CTTAATTATGAGAGAAATAA+TGG - chr3.3:58974628-58974647 MS.gene04973:intron 20.0%
! GTATTTGAGAGTAGAATAAA+CGG + chr3.3:58974005-58974024 None:intergenic 25.0%
!!! GATTTTTTCACTGTTTTGTA+AGG - chr3.3:58974364-58974383 MS.gene04973:intron 25.0%
!!! GGTAGTAGTTATTATTTTAG+TGG - chr3.3:58974207-58974226 MS.gene04973:CDS 25.0%
ACAGTCAGCTTAATTATGTT+TGG - chr3.3:58974600-58974619 MS.gene04973:intron 30.0%
AGTTGAAAAATGGAACTAAC+AGG + chr3.3:58974042-58974061 None:intergenic 30.0%
CAGTCAGCTTAATTATGTTT+GGG - chr3.3:58974601-58974620 MS.gene04973:intron 30.0%
TACGAAATGTTGTCAATTAG+CGG + chr3.3:58974488-58974507 None:intergenic 30.0%
TATGCTCCTTCAATATAAAG+CGG + chr3.3:58974675-58974694 None:intergenic 30.0%
TGTCTAGATTCATGAAGATA+TGG + chr3.3:58974908-58974927 None:intergenic 30.0%
TTGTTATATAGCAGCTATAG+CGG + chr3.3:58974581-58974600 None:intergenic 30.0%
AATATCGAATCACGAAACTC+TGG - chr3.3:58974511-58974530 MS.gene04973:intron 35.0%
ACAATGGTATGCAATCTTCA+AGG - chr3.3:58975161-58975180 MS.gene04973:CDS 35.0%
ACTATACCACTATAGAGTAG+CGG + chr3.3:58974557-58974576 None:intergenic 35.0%
ATTGCCTGAGTGTGAAAAAT+AGG - chr3.3:58974404-58974423 MS.gene04973:intron 35.0%
CGATTTGCAAAGAAAACTGA+TGG - chr3.3:58974965-58974984 MS.gene04973:intron 35.0%
GGACTCATGCAAGTAAAAAA+TGG + chr3.3:58974833-58974852 None:intergenic 35.0%
GTCTCACTTGAAACATATTC+TGG + chr3.3:58974854-58974873 None:intergenic 35.0%
TCCTACCATACTAACAACAA+TGG - chr3.3:58975145-58975164 MS.gene04973:CDS 35.0%
TCGCAATCAATTAGTTCATC+TGG - chr3.3:58975031-58975050 MS.gene04973:intron 35.0%
! ACCATTGTTGTTAGTATGGT+AGG + chr3.3:58975149-58975168 None:intergenic 35.0%
! AGAGTAGAATAAACGGATTC+GGG + chr3.3:58973998-58974017 None:intergenic 35.0%
! ATGCAATCTTCAAGGTATCA+GGG - chr3.3:58975169-58975188 MS.gene04973:CDS 35.0%
! GAGAGTAGAATAAACGGATT+CGG + chr3.3:58973999-58974018 None:intergenic 35.0%
! GCATACCATTGTTGTTAGTA+TGG + chr3.3:58975153-58975172 None:intergenic 35.0%
! TATGCAATCTTCAAGGTATC+AGG - chr3.3:58975168-58975187 MS.gene04973:CDS 35.0%
! TTTGTTGTGATCGAATTCGA+AGG - chr3.3:58974266-58974285 MS.gene04973:intron 35.0%
!! CTGAAACGTTATTGACTTCA+TGG - chr3.3:58974321-58974340 MS.gene04973:intron 35.0%
ACGGTTGAAGGAAGAGTTAA+CGG + chr3.3:58973969-58973988 None:intergenic 40.0%
AGAGGAACAAACGAAAATGG+TGG - chr3.3:58975118-58975137 MS.gene04973:CDS 40.0%
CCATACATATGTGTCAGTGT+CGG + chr3.3:58974711-58974730 None:intergenic 40.0%
GCAAGAGGAACAAACGAAAA+TGG - chr3.3:58975115-58975134 MS.gene04973:CDS 40.0%
TGAATTCCGCTACTCTATAG+TGG - chr3.3:58974548-58974567 MS.gene04973:intron 40.0%
TGGAACTAACAGGTCAAGAA+CGG + chr3.3:58974032-58974051 None:intergenic 40.0%
TGTGATCGAATTCGAAGGTT+TGG - chr3.3:58974271-58974290 MS.gene04973:intron 40.0%
TTGTCAATTAGCGGCTATTG+TGG + chr3.3:58974479-58974498 None:intergenic 40.0%
TTTCTTTGCAAATCGTCCTC+CGG + chr3.3:58974960-58974979 None:intergenic 40.0%
! TGCAAAGAAAACTGATGGTG+AGG - chr3.3:58974970-58974989 MS.gene04973:intron 40.0%
!! ACATCAGCATGCTTTGAGAA+GGG - chr3.3:58974925-58974944 MS.gene04973:intron 40.0%
!! GTCTCCTATTTTTCACACTC+AGG + chr3.3:58974411-58974430 None:intergenic 40.0%
AACATGCGACAAGATGCAAG+AGG - chr3.3:58975100-58975119 MS.gene04973:intron 45.0%
AGCGAATGAATCTCTTTCGC+CGG + chr3.3:58973933-58973952 None:intergenic 45.0%
AGGGTGAAAGAGTGGAAGAA+GGG - chr3.3:58975188-58975207 MS.gene04973:CDS 45.0%
ATCGAATCACGAAACTCTGG+TGG - chr3.3:58974514-58974533 MS.gene04973:intron 45.0%
ATTGATTGCGACGACAAGAC+TGG + chr3.3:58975022-58975041 None:intergenic 45.0%
CCGACACTGACACATATGTA+TGG - chr3.3:58974708-58974727 MS.gene04973:intron 45.0%
CTTGCATCTTGTCGCATGTT+GGG + chr3.3:58975100-58975119 None:intergenic 45.0%
GGAACAAACGAAAATGGTGG+TGG - chr3.3:58975121-58975140 MS.gene04973:CDS 45.0%
GTTGAAGGAAGAGTTAACGG+TGG + chr3.3:58973966-58973985 None:intergenic 45.0%
TCTTGCATCTTGTCGCATGT+TGG + chr3.3:58975101-58975120 None:intergenic 45.0%
! AAGGTATCAGGGTGAAAGAG+TGG - chr3.3:58975180-58975199 MS.gene04973:CDS 45.0%
! ACTTTTGCCTTCAGACTCTG+CGG - chr3.3:58975060-58975079 MS.gene04973:intron 45.0%
! GTAGTTGTCACTTGCGGATA+GGG - chr3.3:58974434-58974453 MS.gene04973:intron 45.0%
!! GACATCAGCATGCTTTGAGA+AGG - chr3.3:58974924-58974943 MS.gene04973:intron 45.0%
!! GCAGTGCCGCTTTATATTGA+AGG - chr3.3:58974666-58974685 MS.gene04973:intron 45.0%
!! TCGAATTCGAAGGTTTGGTG+AGG - chr3.3:58974276-58974295 MS.gene04973:intron 45.0%
AGAGCCATTATCCTTTCCCG+AGG + chr3.3:58974996-58975015 None:intergenic 50.0%
CAGGGTGAAAGAGTGGAAGA+AGG - chr3.3:58975187-58975206 MS.gene04973:CDS 50.0%
GAATGAATCTCTTTCGCCGG+CGG + chr3.3:58973930-58973949 None:intergenic 50.0%
GGGTGAAAGAGTGGAAGAAG+GGG - chr3.3:58975189-58975208 MS.gene04973:CDS 50.0%
TCGCATGTTGGGAGAATTCC+AGG + chr3.3:58975089-58975108 None:intergenic 50.0%
TGGAAGAAGGGGACTGTTCA+GGG - chr3.3:58975200-58975219 MS.gene04973:CDS 50.0%
! AAAACTGATGGTGAGGCCTC+GGG - chr3.3:58974977-58974996 MS.gene04973:intron 50.0%
! AAACGGATTCGGGATCGTCA+CGG + chr3.3:58973988-58974007 None:intergenic 50.0%
! CGTAGTTGTCACTTGCGGAT+AGG - chr3.3:58974433-58974452 MS.gene04973:intron 50.0%
! GAAAACTGATGGTGAGGCCT+CGG - chr3.3:58974976-58974995 MS.gene04973:intron 50.0%
! GACTGCGTAGTTGTCACTTG+CGG - chr3.3:58974428-58974447 MS.gene04973:intron 50.0%
! TCGGGAAAGGATAATGGCTC+TGG - chr3.3:58974995-58975014 MS.gene04973:intron 50.0%
!! CATGCTTTGAGAAGGGCAAG+AGG - chr3.3:58974932-58974951 MS.gene04973:intron 50.0%
CAGGTTTCCGCAGAGTCTGA+AGG + chr3.3:58975070-58975089 None:intergenic 55.0%
CTTCAGACTCTGCGGAAACC+TGG - chr3.3:58975068-58975087 MS.gene04973:intron 55.0%
GAGGCCTCGGGAAAGGATAA+TGG - chr3.3:58974989-58975008 MS.gene04973:intron 55.0%
GTGGAAGAAGGGGACTGTTC+AGG - chr3.3:58975199-58975218 MS.gene04973:CDS 55.0%
TTCGGGATCGTCACGGTTGA+AGG + chr3.3:58973981-58974000 None:intergenic 55.0%
! TTGAGAAGGGCAAGAGGCAC+CGG - chr3.3:58974938-58974957 MS.gene04973:intron 55.0%
!! TGGAAGCATCTCCTCGAACG+AGG - chr3.3:58975231-58975250 MS.gene04973:CDS 55.0%
GACTGTTCAGGGCAGCTACG+TGG - chr3.3:58975211-58975230 MS.gene04973:CDS 60.0%
! GTTTGAGACGCCACTGGTGG+CGG + chr3.3:58973908-58973927 None:intergenic 60.0%
! TGATGGTGAGGCCTCGGGAA+AGG - chr3.3:58974982-58975001 MS.gene04973:intron 60.0%
CCAGTGGCGTCTCAAACCGC+CGG - chr3.3:58973911-58973930 MS.gene04973:CDS 65.0%
TGCATGGTTGCCGCCACCAG+TGG - chr3.3:58973895-58973914 MS.gene04973:CDS 65.0%
! GCGGTTTGAGACGCCACTGG+TGG + chr3.3:58973911-58973930 None:intergenic 65.0%
!! AGAAGGGCAAGAGGCACCGG+AGG - chr3.3:58974941-58974960 MS.gene04973:intron 65.0%
! CCGGCGGTTTGAGACGCCAC+TGG + chr3.3:58973914-58973933 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 58973881 58975261 58973881 ID=MS.gene04973
chr3.3 mRNA 58973881 58975261 58973881 ID=MS.gene04973.t1;Parent=MS.gene04973
chr3.3 exon 58975112 58975261 58975112 ID=MS.gene04973.t1.exon1;Parent=MS.gene04973.t1
chr3.3 CDS 58975112 58975261 58975112 ID=cds.MS.gene04973.t1;Parent=MS.gene04973.t1
chr3.3 exon 58973881 58974237 58973881 ID=MS.gene04973.t1.exon2;Parent=MS.gene04973.t1
chr3.3 CDS 58973881 58974237 58973881 ID=cds.MS.gene04973.t1;Parent=MS.gene04973.t1
Gene Sequence

>MS.gene04973

ATGCATCTCTACAATGCATGGTTGCCGCCACCAGTGGCGTCTCAAACCGCCGGCGAAAGAGATTCATTCGCTCGCATCATCGCCACCGTTAACTCTTCCTTCAACCGTGACGATCCCGAATCCGTTTATTCTACTCTCAAATACATCTCCGTTCTTGACCTGTTAGTTCCATTTTTCAACTCTTCAATTTTCAATTTCGATTTTCTCTCTCTTCATACGTTGTTGATTTTCGTTTTCTTTAATTTCTTTTGTGTTATATTTTGATTTTATCGTGTTTTCGTTTCAATTGATTTGTTTTTTGTTTTTGCTTATTTTTAATTAATTTAGGTAGTAGTTATTATTTTAGTGGTAATTGTTCGAAGATTTTGTGTTTACACTAAGAAAATTTGTTGTGATCGAATTCGAAGGTTTGGTGAGGTTTTGAAGATTGAAGTTAGTTACTGAAACGTTATTGACTTCATGGTTTTAAGTCTTTTAGACTGTGATTTTTTCACTGTTTTGTAAGGAATTTGTAATTATTCTGATTGCCTGAGTGTGAAAAATAGGAGACTGCGTAGTTGTCACTTGCGGATAGGGAAGCAGTACTGCGATAGCGCCACAATAGCCGCTAATTGACAACATTTCGTACTAAATATCGAATCACGAAACTCTGGTGGAGTGATTTGTCTGAATTCCGCTACTCTATAGTGGTATAGTGCCGCTATAGCTGCTATATAACAACAGTCAGCTTAATTATGTTTGGGTCAGCTTAATTATGAGAGAAATAATGGCTTCTGTTCTATGTAGCAGTGCCGCTTTATATTGAAGGAGCATACACTGTACAATGTCCGACACTGACACATATGTATGGTTATGATCAATCACGTCGATTTTAAATTATCATCAGTGTGTATGTAGTCACATTCATGTAAAATGAGAAAAGCAAATAGAGCTAAGTTGCTGATTTTCACCATTTTTTACTTGCATGAGTCCAGAATATGTTTCAAGTGAGACAGAACTTGATGCTAACATCTATTATTTTCAGCCATATCTTCATGAATCTAGACATCAGCATGCTTTGAGAAGGGCAAGAGGCACCGGAGGACGATTTGCAAAGAAAACTGATGGTGAGGCCTCGGGAAAGGATAATGGCTCTGGTCCAGTCTTGTCGTCGCAATCAATTAGTTCATCTGGTTCAGAACTTTTGCCTTCAGACTCTGCGGAAACCTGGAATTCTCCCAACATGCGACAAGATGCAAGAGGAACAAACGAAAATGGTGGTGGCTCCTACCATACTAACAACAATGGTATGCAATCTTCAAGGTATCAGGGTGAAAGAGTGGAAGAAGGGGACTGTTCAGGGCAGCTACGTGGAAGCATCTCCTCGAACGAGGCATCGTAG

Protein sequence

>MS.gene04973.t1

MHLYNAWLPPPVASQTAGERDSFARIIATVNSSFNRDDPESVYSTLKYISPYLHESRHQHALRRARGTGGRFAKKTDGEASGKDNGSGPVLSSQSISSSGSELLPSDSAETWNSPNMRQDARGTNENGGGSYHTNNNGMQSSRYQGERVEEGDCSGQLRGSISSNEAS