AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64740

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64740.t1 MTR_5g021610 98.969 194 2 0 1 194 14 207 1.30e-145 403
MS.gene64740.t1 MTR_8g076160 76.410 195 43 3 1 194 1 193 4.18e-108 308
MS.gene64740.t1 MTR_2g005880 53.846 182 80 1 12 193 3 180 1.57e-66 202
MS.gene64740.t1 MTR_4g114080 57.343 143 57 1 9 151 2 140 6.85e-57 177
MS.gene64740.t1 MTR_4g011020 54.362 149 60 2 9 155 6 148 2.06e-55 174
MS.gene64740.t1 MTR_2g103490 53.103 145 63 2 9 152 6 146 3.62e-51 162
MS.gene64740.t1 MTR_2g103460 51.724 145 65 2 9 152 6 146 3.15e-49 157
MS.gene64740.t1 MTR_0003s0630 47.333 150 77 2 4 152 26 174 5.59e-48 155
MS.gene64740.t1 MTR_1g115170 46.617 133 66 2 29 160 3 131 1.52e-39 132
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64740.t1 AT1G15380 57.746 142 56 1 9 150 6 143 1.42e-58 181
MS.gene64740.t1 AT1G15380 57.746 142 56 1 9 150 6 143 1.42e-58 181
MS.gene64740.t1 AT1G80160 55.102 147 62 1 9 155 6 148 3.90e-58 180
MS.gene64740.t1 AT1G80160 56.250 144 59 1 12 155 50 189 9.72e-58 181
MS.gene64740.t1 AT2G28420 51.389 144 66 2 13 155 17 157 3.52e-52 166
MS.gene64740.t1 AT1G80160 51.000 100 45 1 56 155 27 122 5.87e-33 115

Find 34 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATCTTCTTTCAAATTTAC+AGG 0.226834 5.2:-12747249 MS.gene64740:CDS
TGGTTATCCTTTGGGTTAAT+AGG 0.237987 5.2:+12747016 None:intergenic
CTCTTAAAGCTATGGCTTCT+AGG 0.268260 5.2:+12746473 None:intergenic
GGTAGAAGATGAAGGAATTA+AGG 0.296959 5.2:-12746600 MS.gene64740:CDS
ATGAGATATGGTTATCCTTT+GGG 0.339132 5.2:+12747008 None:intergenic
TAAGAAGAGATTAGAAGAAA+AGG 0.341886 5.2:-12746645 MS.gene64740:CDS
GAAGCAGTGCATGAAGAAAT+AGG 0.352827 5.2:+12746503 None:intergenic
GAATCCTCCACACTTGGAAT+TGG 0.363613 5.2:+12746442 None:intergenic
AATGAGATATGGTTATCCTT+TGG 0.372091 5.2:+12747007 None:intergenic
CATGAAGAAATAGGAATGAT+TGG 0.374847 5.2:+12746512 None:intergenic
AAGAAGAGATTAGAAGAAAA+GGG 0.385631 5.2:-12746644 MS.gene64740:CDS
GAAAGAAGATGGTCGTTTGA+TGG 0.396618 5.2:+12747260 None:intergenic
AATACATTTGATTCAGAATC+CGG 0.396961 5.2:-12747077 MS.gene64740:CDS
AGCTCAATCATGTAGCCATC+AGG 0.416541 5.2:+12746554 None:intergenic
GGATAACCATATCTCATTCC+AGG 0.423753 5.2:-12747002 MS.gene64740:intron
AAAGAAGATGGTCGTTTGAT+GGG 0.476824 5.2:+12747261 None:intergenic
CCTGTAAATTTGAAAGAAGA+TGG 0.492613 5.2:+12747249 None:intergenic
ATGAAGAAATAGGAATGATT+GGG 0.499317 5.2:+12746513 None:intergenic
CTGCATGAATCCTCCACACT+TGG 0.500461 5.2:+12746436 None:intergenic
AAGTAGATCTCTTAAAGCTA+TGG 0.522280 5.2:+12746465 None:intergenic
ATTCATGCAGAATGTTATGA+TGG 0.532345 5.2:-12746423 MS.gene64740:CDS
GTATCGAATTCATCAATGTC+CGG 0.533358 5.2:+12747058 None:intergenic
TCATGTAGCCATCAGGGTCA+TGG 0.545015 5.2:+12746561 None:intergenic
CTTTCAAATTTACAGGAGCA+TGG 0.546255 5.2:-12747242 MS.gene64740:intron
AATGAGATATGTTACAGCAT+TGG 0.548154 5.2:-12746621 MS.gene64740:CDS
ATACTTATATGAATGAATCA+AGG 0.557156 5.2:-12747039 MS.gene64740:CDS
ACAGCATTGGTAGAAGATGA+AGG 0.580373 5.2:-12746608 MS.gene64740:CDS
GTGTTCTTCCATGACCCTGA+TGG 0.589307 5.2:-12746569 MS.gene64740:CDS
ACATGATTCAATGAGAGCAA+TGG 0.593307 5.2:+12747348 None:intergenic
GCTCAATCATGTAGCCATCA+GGG 0.602960 5.2:+12746555 None:intergenic
ATCAAGGCCTATTAACCCAA+AGG 0.603538 5.2:-12747023 MS.gene64740:CDS
TCTACTTCCAATTCCAAGTG+TGG 0.614729 5.2:-12746449 MS.gene64740:CDS
ACTTCCAATTCCAAGTGTGG+AGG 0.621587 5.2:-12746446 MS.gene64740:CDS
TATGATGGAAAGCTTGAGCA+TGG 0.636263 5.2:-12746408 MS.gene64740:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAATTTATATACTAAAAG+TGG - chr5.2:12746858-12746877 MS.gene64740:intron 10.0%
!!! TTTTTTTTTGTTTATATTCT+TGG - chr5.2:12746562-12746581 MS.gene64740:CDS 10.0%
!! CCAAAAATTTATATACAATA+TGG - chr5.2:12747071-12747090 MS.gene64740:CDS 15.0%
!! GCACATAATAATTATAATAA+AGG + chr5.2:12746979-12746998 None:intergenic 15.0%
!! TATTATAATTATTATGTGCA+TGG - chr5.2:12746980-12746999 MS.gene64740:intron 15.0%
!!! AATATAGTCATTTTTTGAAA+TGG - chr5.2:12746817-12746836 MS.gene64740:intron 15.0%
!!! CCATATTGTATATAAATTTT+TGG + chr5.2:12747074-12747093 None:intergenic 15.0%
!!! TATAAATCTTTATTTTTACC+TGG + chr5.2:12746788-12746807 None:intergenic 15.0%
!! AAAATATTAGTGTAGTTACA+TGG - chr5.2:12746627-12746646 MS.gene64740:CDS 20.0%
!! ATACTTATATGAATGAATCA+AGG - chr5.2:12746730-12746749 MS.gene64740:intron 20.0%
!!! AGGTTTTATAATTATGGTAT+TGG - chr5.2:12746669-12746688 MS.gene64740:intron 20.0%
!!! GTTTTAACTTTTTTTTTTGC+AGG - chr5.2:12746649-12746668 MS.gene64740:CDS 20.0%
!!! TTTTGCAGGTTTTATAATTA+TGG - chr5.2:12746663-12746682 MS.gene64740:CDS 20.0%
! AAAGGTCATAATACAAAAAG+TGG + chr5.2:12746961-12746980 None:intergenic 25.0%
! AAGAAGAGATTAGAAGAAAA+GGG - chr5.2:12747125-12747144 MS.gene64740:intron 25.0%
! AATACATTTGATTCAGAATC+CGG - chr5.2:12746692-12746711 MS.gene64740:intron 25.0%
! ATGAAGAAATAGGAATGATT+GGG + chr5.2:12747259-12747278 None:intergenic 25.0%
! TAAGAAGAGATTAGAAGAAA+AGG - chr5.2:12747124-12747143 MS.gene64740:intron 25.0%
!! CAATTTTATGAGGATGTTTT+GGG - chr5.2:12746478-12746497 MS.gene64740:CDS 25.0%
!!! GTCATTTTTTGAAATGGTTA+TGG - chr5.2:12746823-12746842 MS.gene64740:intron 25.0%
AAGTAGATCTCTTAAAGCTA+TGG + chr5.2:12747307-12747326 None:intergenic 30.0%
AATGAGATATGGTTATCCTT+TGG + chr5.2:12746765-12746784 None:intergenic 30.0%
AATGAGATATGTTACAGCAT+TGG - chr5.2:12747148-12747167 MS.gene64740:intron 30.0%
ATGAGATATGGTTATCCTTT+GGG + chr5.2:12746764-12746783 None:intergenic 30.0%
ATTCATGCAGAATGTTATGA+TGG - chr5.2:12747346-12747365 MS.gene64740:CDS 30.0%
CATGAAGAAATAGGAATGAT+TGG + chr5.2:12747260-12747279 None:intergenic 30.0%
CCATCTTCTTTCAAATTTAC+AGG - chr5.2:12746520-12746539 MS.gene64740:CDS 30.0%
CCTGTAAATTTGAAAGAAGA+TGG + chr5.2:12746523-12746542 None:intergenic 30.0%
TGGAAATCTATGCATATGTA+GGG - chr5.2:12746878-12746897 MS.gene64740:intron 30.0%
! GCAATTTTATGAGGATGTTT+TGG - chr5.2:12746477-12746496 MS.gene64740:CDS 30.0%
! TTTTTACCTGGAATGAGATA+TGG + chr5.2:12746776-12746795 None:intergenic 30.0%
!!! ATATGGTTTTTTGCAGTGTA+CGG - chr5.2:12747088-12747107 MS.gene64740:CDS 30.0%
AAAGAAGATGGTCGTTTGAT+GGG + chr5.2:12746511-12746530 None:intergenic 35.0%
ACATGATTCAATGAGAGCAA+TGG + chr5.2:12746424-12746443 None:intergenic 35.0%
AGCTAAATTTGTCATCCATG+TGG + chr5.2:12747026-12747045 None:intergenic 35.0%
CTTTCAAATTTACAGGAGCA+TGG - chr5.2:12746527-12746546 MS.gene64740:CDS 35.0%
GGTAGAAGATGAAGGAATTA+AGG - chr5.2:12747169-12747188 MS.gene64740:intron 35.0%
GTATCGAATTCATCAATGTC+CGG + chr5.2:12746714-12746733 None:intergenic 35.0%
GTCGTAAGTAAATAACCACA+TGG - chr5.2:12747008-12747027 MS.gene64740:CDS 35.0%
GTGGAAATCTATGCATATGT+AGG - chr5.2:12746877-12746896 MS.gene64740:intron 35.0%
! GGAGTCTATGCAATTTTATG+AGG - chr5.2:12746468-12746487 MS.gene64740:CDS 35.0%
! TCTTTTGTGTAGATCAGTGT+TGG - chr5.2:12746447-12746466 MS.gene64740:CDS 35.0%
! TGGTTATCCTTTGGGTTAAT+AGG + chr5.2:12746756-12746775 None:intergenic 35.0%
!! TTTTTGGTAAGCATAGCTAC+AGG + chr5.2:12747058-12747077 None:intergenic 35.0%
ATCAAGGCCTATTAACCCAA+AGG - chr5.2:12746746-12746765 MS.gene64740:intron 40.0%
CTCTTAAAGCTATGGCTTCT+AGG + chr5.2:12747299-12747318 None:intergenic 40.0%
GAAAGAAGATGGTCGTTTGA+TGG + chr5.2:12746512-12746531 None:intergenic 40.0%
GAAGCAGTGCATGAAGAAAT+AGG + chr5.2:12747269-12747288 None:intergenic 40.0%
GGATAACCATATCTCATTCC+AGG - chr5.2:12746767-12746786 MS.gene64740:intron 40.0%
TCTACTTCCAATTCCAAGTG+TGG - chr5.2:12747320-12747339 MS.gene64740:CDS 40.0%
! TATGATGGAAAGCTTGAGCA+TGG - chr5.2:12747361-12747380 MS.gene64740:CDS 40.0%
!! ACAGCATTGGTAGAAGATGA+AGG - chr5.2:12747161-12747180 MS.gene64740:intron 40.0%
ACTTCCAATTCCAAGTGTGG+AGG - chr5.2:12747323-12747342 MS.gene64740:CDS 45.0%
AGCTCAATCATGTAGCCATC+AGG + chr5.2:12747218-12747237 None:intergenic 45.0%
GAATCCTCCACACTTGGAAT+TGG + chr5.2:12747330-12747349 None:intergenic 45.0%
GCTCAATCATGTAGCCATCA+GGG + chr5.2:12747217-12747236 None:intergenic 45.0%
CTGCATGAATCCTCCACACT+TGG + chr5.2:12747336-12747355 None:intergenic 50.0%
GTGTTCTTCCATGACCCTGA+TGG - chr5.2:12747200-12747219 MS.gene64740:intron 50.0%
TCATGTAGCCATCAGGGTCA+TGG + chr5.2:12747211-12747230 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 12746385 12747406 12746385 ID=MS.gene64740
chr5.2 mRNA 12746385 12747406 12746385 ID=MS.gene64740.t1;Parent=MS.gene64740
chr5.2 exon 12747243 12747406 12747243 ID=MS.gene64740.t1.exon1;Parent=MS.gene64740.t1
chr5.2 CDS 12747243 12747406 12747243 ID=cds.MS.gene64740.t1;Parent=MS.gene64740.t1
chr5.2 exon 12747003 12747120 12747003 ID=MS.gene64740.t1.exon2;Parent=MS.gene64740.t1
chr5.2 CDS 12747003 12747120 12747003 ID=cds.MS.gene64740.t1;Parent=MS.gene64740.t1
chr5.2 exon 12746385 12746687 12746385 ID=MS.gene64740.t1.exon3;Parent=MS.gene64740.t1
chr5.2 CDS 12746385 12746687 12746385 ID=cds.MS.gene64740.t1;Parent=MS.gene64740.t1
Gene Sequence

>MS.gene64740

ATGGAGATTGAAGAAGTTTGTGAAGCACAAGCACTTCCATTGCTCTCATTGAATCATGTGTCTCTTTTGTGTAGATCAGTGTTGGAGTCTATGCAATTTTATGAGGATGTTTTGGGTTTTGTTCCCATCAAACGACCATCTTCTTTCAAATTTACAGGAGCATGGTTAGCTTTTTTTTTTTTTTTTGTTTATATTCTTGGTTACTAATTAATTTCTCTACTACATCAACTATCTTGCTACACAAAATATTAGTGTAGTTACATGGTTTTAACTTTTTTTTTTGCAGGTTTTATAATTATGGTATTGGAATACATTTGATTCAGAATCCGGACATTGATGAATTCGATACTTATATGAATGAATCAAGGCCTATTAACCCAAAGGATAACCATATCTCATTCCAGGTAAAAATAAAGATTTATAATGCGACTAAATATAGTCATTTTTTGAAATGGTTATGGACGATAAAAGAAATAAATTTATATACTAAAAGTGGAAATCTATGCATATGTAGGGCTAAAAACATATTTAAATCTTTATTTATCTAATCTAATATATCACAAGATTTTATAGCCACTTTTTGTATTATGACCTTTATTATAATTATTATGTGCATGGAGTTTGTCGTAAGTAAATAACCACATGGATGACAAATTTAGCTACTGTTAATCCTGTAGCTATGCTTACCAAAAATTTATATACAATATGGTTTTTTGCAGTGTACGGACGTTGAACTTGTTAAGAAGAGATTAGAAGAAAAGGGAATGAGATATGTTACAGCATTGGTAGAAGATGAAGGAATTAAGGTAGATCAAGTGTTCTTCCATGACCCTGATGGCTACATGATTGAGCTATGCAACTGTGAGAATATCCCAATCATTCCTATTTCTTCATGCACTGCTTCTTTCAAGCCTAGAAGCCATAGCTTTAAGAGATCTACTTCCAATTCCAAGTGTGGAGGATTCATGCAGAATGTTATGATGGAAAGCTTGAGCATGGATATGATGAACTTTGCGTTTTAA
Protein sequence

>MS.gene64740.t1

MEIEEVCEAQALPLLSLNHVSLLCRSVLESMQFYEDVLGFVPIKRPSSFKFTGAWFYNYGIGIHLIQNPDIDEFDTYMNESRPINPKDNHISFQCTDVELVKKRLEEKGMRYVTALVEDEGIKVDQVFFHDPDGYMIELCNCENIPIIPISSCTASFKPRSHSFKRSTSNSKCGGFMQNVMMESLSMDMMNFAF