AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene006406

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene006406.t1 MTR_1g102890 97.326 187 5 0 1 187 1 187 4.42e-136 378
MS.gene006406.t1 MTR_1g102890 94.631 149 8 0 1 149 1 149 1.98e-103 294
MS.gene006406.t1 MTR_1g102870 65.730 178 61 0 2 179 12 189 4.99e-91 265
MS.gene006406.t1 MTR_1g102870 67.586 145 47 0 2 146 12 156 5.86e-75 222
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene006406.t1 AT5G43850 78.610 187 40 0 1 187 1 187 1.89e-110 313
MS.gene006406.t1 AT2G26400 65.000 180 63 0 2 181 27 206 9.62e-90 262
MS.gene006406.t1 AT2G26400 65.000 180 63 0 2 181 12 191 1.24e-89 261
MS.gene006406.t1 AT4G14710 63.842 177 64 0 2 178 14 190 1.34e-89 261
MS.gene006406.t1 AT4G14710 63.842 177 64 0 2 178 12 188 1.62e-89 261
MS.gene006406.t1 AT4G14710 63.842 177 64 0 2 178 12 188 1.62e-89 261
MS.gene006406.t1 AT4G14716 64.535 172 61 0 2 173 12 183 4.76e-88 256
MS.gene006406.t1 AT4G14710 63.483 178 64 1 2 178 12 189 9.14e-88 256
MS.gene006406.t1 AT2G26400 67.262 168 55 0 2 169 27 194 2.91e-87 256
MS.gene006406.t1 AT2G26400 67.262 168 55 0 2 169 12 179 3.26e-87 255
MS.gene006406.t1 AT4G14710 64.881 168 59 0 2 169 12 179 1.22e-86 253
MS.gene006406.t1 AT4G14710 64.327 171 61 0 8 178 1 171 2.87e-86 252
MS.gene006406.t1 AT4G14716 65.060 166 58 0 8 173 1 166 1.07e-84 248

Find 48 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTAGAAAGGAATACATTA+AGG 0.274694 1.3:-70692988 MS.gene006406:CDS
TGATCATTCTCATAGTCATT+AGG 0.279982 1.3:+70694219 None:intergenic
ATGATTAATAACCTGCTAAT+TGG 0.292079 1.3:+70694341 None:intergenic
GATCATTCTCATAGTCATTA+GGG 0.297534 1.3:+70694220 None:intergenic
GCAGTTAATGAGGTTGTTTA+TGG 0.306900 1.3:-70693057 MS.gene006406:intron
CCCCAATGAATTTGTTTCCT+TGG 0.318267 1.3:-70694365 MS.gene006406:CDS
CAGAATTGGGAGTCTTATAC+TGG 0.335864 1.3:-70694251 MS.gene006406:CDS
GTCCAAGGAAACAAATTCAT+TGG 0.347689 1.3:+70694363 None:intergenic
TGAAGAGATTCGTTACTGTT+TGG 0.363134 1.3:-70693391 MS.gene006406:CDS
CTTCGATGTTCGAGACAAAA+AGG 0.370547 1.3:-70693355 MS.gene006406:CDS
TGTGCCACTTGCAGCTCATT+AGG 0.372112 1.3:-70692946 None:intergenic
AGGATCGCTGGATTCGCATT+TGG 0.387790 1.3:-70693335 MS.gene006406:CDS
TCCAAGGAAACAAATTCATT+GGG 0.393021 1.3:+70694364 None:intergenic
TACCATGTAATTGTATCCTC+TGG 0.413679 1.3:+70694173 None:intergenic
TTAATGTATTCCTTTCTAGC+AGG 0.416178 1.3:+70692990 None:intergenic
CTGGATTCGCATTTGGATCA+AGG 0.420712 1.3:-70693328 MS.gene006406:CDS
CAGTTAATGAGGTTGTTTAT+GGG 0.429331 1.3:-70693056 MS.gene006406:CDS
GCTAGAAAGGAATACATTAA+GGG 0.444455 1.3:-70692987 MS.gene006406:CDS
GGAAGATAACCCTGCTAGAA+AGG 0.448092 1.3:-70693000 MS.gene006406:CDS
ATTGTGATAGGCATGGTTCA+TGG 0.474686 1.3:-70694428 MS.gene006406:intron
GTTTCCTTGGACCAATTAGC+AGG 0.487915 1.3:-70694352 MS.gene006406:intron
CTACACTGAGCACATTCATC+AGG 0.491343 1.3:-70693415 MS.gene006406:CDS
CGTTACTGTTTGGAGGGAAG+TGG 0.493451 1.3:-70693381 MS.gene006406:CDS
AAGGGCTTGACTGAGAAAAC+TGG 0.495479 1.3:-70692969 MS.gene006406:CDS
TAGCCATGGTGAGGAAGTCT+TGG 0.507430 1.3:+70694388 None:intergenic
AGAGATTCGTTACTGTTTGG+AGG 0.508489 1.3:-70693388 MS.gene006406:CDS
TAATGTATTCCTTTCTAGCA+GGG 0.526328 1.3:+70692991 None:intergenic
ATTCGCATTTGGATCAAGGC+TGG 0.542481 1.3:-70693324 MS.gene006406:CDS
AACCGATGGTAGATTCCTGC+AGG 0.545163 1.3:+70693285 None:intergenic
GGATTTACTTGATTTATGCC+CGG 0.551505 1.3:-70693475 MS.gene006406:CDS
CAAATTCATTGGGGTAGCCA+TGG 0.553222 1.3:+70694374 None:intergenic
GAGATTCGTTACTGTTTGGA+GGG 0.561571 1.3:-70693387 MS.gene006406:CDS
GAGGTTGTTTATGGGTGAGC+CGG 0.570174 1.3:-70693048 MS.gene006406:CDS
ATTGTTACTCATGGCGATTG+AGG 0.572796 1.3:-70694517 None:intergenic
CTAGCAGGGTTATCTTCCTG+TGG 0.575444 1.3:+70693005 None:intergenic
TACCTGCAGGAATCTACCAT+CGG 0.576810 1.3:-70693287 MS.gene006406:CDS
CGATTATATGCTGTCCACAC+CGG 0.591841 1.3:+70693029 None:intergenic
CGACACAAATAACTATGTGA+AGG 0.598188 1.3:-70693256 MS.gene006406:intron
ATAACCTGCTAATTGGTCCA+AGG 0.599536 1.3:+70694348 None:intergenic
TTGTGTCGAGAGTGAACCGA+TGG 0.605251 1.3:+70693271 None:intergenic
TGTTTATGGGTGAGCCGGTG+TGG 0.615047 1.3:-70693043 MS.gene006406:CDS
AGCCAGAGGATACAATTACA+TGG 0.637470 1.3:-70694175 MS.gene006406:intron
GACAGCATATAATCGACCAC+AGG 0.646228 1.3:-70693021 MS.gene006406:CDS
GGGTCCTAATGAGCTGCAAG+TGG 0.648299 1.3:+70692942 None:intergenic
TCATTGGGGTAGCCATGGTG+AGG 0.672207 1.3:+70694379 None:intergenic
GATCCAAGACTTCCTCACCA+TGG 0.679886 1.3:-70694391 MS.gene006406:CDS
AAGAACATTAGAGAAGCCAG+AGG 0.683987 1.3:-70694189 MS.gene006406:CDS
CCAAGGAAACAAATTCATTG+GGG 0.686962 1.3:+70694365 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATCTAATATATTGTAAA+CGG - chr1.3:70693489-70693508 MS.gene006406:intron 10.0%
!! TAATAATTAAAAATTGTGAT+AGG - chr1.3:70693014-70693033 MS.gene006406:CDS 10.0%
!! TATATTAAGATTAATTCATA+AGG + chr1.3:70692981-70693000 None:intergenic 10.0%
!! AATTAGTTGAAAATAACTTA+CGG - chr1.3:70693703-70693722 MS.gene006406:intron 15.0%
!! TAAAAAAAACATGTTAAAAC+AGG - chr1.3:70693451-70693470 MS.gene006406:CDS 15.0%
!!! AATTTTAATTTTTGCAGAAT+TGG - chr1.3:70693189-70693208 MS.gene006406:intron 15.0%
!!! ATTTTAATTTTTGCAGAATT+GGG - chr1.3:70693190-70693209 MS.gene006406:intron 15.0%
!! TTACATCAACAAAAATTTGA+AGG + chr1.3:70693515-70693534 None:intergenic 20.0%
!! TTTGTTGATGTAAATTTCTT+AGG - chr1.3:70693522-70693541 MS.gene006406:intron 20.0%
!!! ATTTTGATTGTACTAATTGA+AGG - chr1.3:70693875-70693894 MS.gene006406:intron 20.0%
!!! TAACATGTTTTTTTTACATG+TGG + chr1.3:70693422-70693441 None:intergenic 20.0%
!!! TCATAATTTTCAACTTTTTC+CGG + chr1.3:70694001-70694020 None:intergenic 20.0%
!!! TTTTGATTGTACTAATTGAA+GGG - chr1.3:70693876-70693895 MS.gene006406:intron 20.0%
! ATAGCTTATGAAAACAACTT+TGG + chr1.3:70693734-70693753 None:intergenic 25.0%
! ATGATTAATAACCTGCTAAT+TGG + chr1.3:70693116-70693135 None:intergenic 25.0%
! ATTAAAAATTGTGATAGGCA+TGG - chr1.3:70693019-70693038 MS.gene006406:CDS 25.0%
! ATTTCATCTTTCAAATGTTC+TGG - chr1.3:70693901-70693920 MS.gene006406:intron 25.0%
! GTACTATTTGAATATGTTGT+AGG - chr1.3:70693958-70693977 MS.gene006406:intron 25.0%
! TTGAAATTGATCAAGATTCA+AGG - chr1.3:70694315-70694334 MS.gene006406:intron 25.0%
! TTTCATCTTTCAAATGTTCT+GGG - chr1.3:70693902-70693921 MS.gene006406:intron 25.0%
!! AAGTTATCTTTGAGAGTTTA+TGG - chr1.3:70693679-70693698 MS.gene006406:intron 25.0%
!! TTTCTAGTGATACAATTACA+CGG - chr1.3:70693364-70693383 MS.gene006406:CDS 25.0%
!!! CATAATTTTCAACTTTTTCC+GGG + chr1.3:70694000-70694019 None:intergenic 25.0%
ATAAGTTGTTTACCTAACAG+TGG + chr1.3:70693576-70693595 None:intergenic 30.0%
CAAGATTCAAGGTAATATGT+TGG - chr1.3:70694326-70694345 MS.gene006406:intron 30.0%
CAGTTAATGAGGTTGTTTAT+GGG - chr1.3:70694398-70694417 MS.gene006406:CDS 30.0%
CCTATCAATATTCTTGATCA+AGG - chr1.3:70694229-70694248 MS.gene006406:CDS 30.0%
CCTTGATCAAGAATATTGAT+AGG + chr1.3:70694232-70694251 None:intergenic 30.0%
GAGCTCAAATAAGTCAATTT+AGG - chr1.3:70693789-70693808 MS.gene006406:intron 30.0%
GATCATTCTCATAGTCATTA+GGG + chr1.3:70693237-70693256 None:intergenic 30.0%
GCTAGAAAGGAATACATTAA+GGG - chr1.3:70694467-70694486 MS.gene006406:intron 30.0%
GTACAATCAAAATGTTCAAC+AGG + chr1.3:70693868-70693887 None:intergenic 30.0%
TCCAAGGAAACAAATTCATT+GGG + chr1.3:70693093-70693112 None:intergenic 30.0%
TGATCATTCTCATAGTCATT+AGG + chr1.3:70693238-70693257 None:intergenic 30.0%
TGCTAGAAAGGAATACATTA+AGG - chr1.3:70694466-70694485 MS.gene006406:intron 30.0%
TTATTGTGACACAAGTTTGA+GGG - chr1.3:70693164-70693183 MS.gene006406:intron 30.0%
TTTATTGTGACACAAGTTTG+AGG - chr1.3:70693163-70693182 MS.gene006406:intron 30.0%
! TAATGTATTCCTTTCTAGCA+GGG + chr1.3:70694466-70694485 None:intergenic 30.0%
! TTAATGTATTCCTTTCTAGC+AGG + chr1.3:70694467-70694486 None:intergenic 30.0%
!! TTGATCAAGGCTTCATTTTT+GGG - chr1.3:70694242-70694261 MS.gene006406:CDS 30.0%
!!! GAAAGTGGATTTTTTCTTGT+GGG - chr1.3:70693394-70693413 MS.gene006406:CDS 30.0%
!!! TGAAAGTGGATTTTTTCTTG+TGG - chr1.3:70693393-70693412 MS.gene006406:CDS 30.0%
ACTTATTTGAGCTCATCTAC+CGG + chr1.3:70693783-70693802 None:intergenic 35.0%
CCAAGGAAACAAATTCATTG+GGG + chr1.3:70693092-70693111 None:intergenic 35.0%
CGACACAAATAACTATGTGA+AGG - chr1.3:70694198-70694217 MS.gene006406:CDS 35.0%
GCAGTTAATGAGGTTGTTTA+TGG - chr1.3:70694397-70694416 MS.gene006406:CDS 35.0%
GGATTTACTTGATTTATGCC+CGG - chr1.3:70693979-70693998 MS.gene006406:intron 35.0%
GTCCAAGGAAACAAATTCAT+TGG + chr1.3:70693094-70693113 None:intergenic 35.0%
TACCATGTAATTGTATCCTC+TGG + chr1.3:70693284-70693303 None:intergenic 35.0%
TGAAGAGATTCGTTACTGTT+TGG - chr1.3:70694063-70694082 MS.gene006406:intron 35.0%
TTACACGGTAAGATTGAAAG+TGG - chr1.3:70693379-70693398 MS.gene006406:CDS 35.0%
TTGTTCGATGCATATGTATG+TGG - chr1.3:70694368-70694387 MS.gene006406:CDS 35.0%
! CTTGATCAAGGCTTCATTTT+TGG - chr1.3:70694241-70694260 MS.gene006406:CDS 35.0%
! GATCTTATCATTTTACCTGC+AGG - chr1.3:70694154-70694173 MS.gene006406:intron 35.0%
AAGAACATTAGAGAAGCCAG+AGG - chr1.3:70693265-70693284 MS.gene006406:CDS 40.0%
AGAGATTCGTTACTGTTTGG+AGG - chr1.3:70694066-70694085 MS.gene006406:intron 40.0%
AGCCAGAGGATACAATTACA+TGG - chr1.3:70693279-70693298 MS.gene006406:CDS 40.0%
AGTCTCGCAAATACTTATGC+CGG - chr1.3:70693761-70693780 MS.gene006406:intron 40.0%
ATAACCTGCTAATTGGTCCA+AGG + chr1.3:70693109-70693128 None:intergenic 40.0%
ATTGTGATAGGCATGGTTCA+TGG - chr1.3:70693026-70693045 MS.gene006406:CDS 40.0%
CTTCGATGTTCGAGACAAAA+AGG - chr1.3:70694099-70694118 MS.gene006406:intron 40.0%
GAGATTCGTTACTGTTTGGA+GGG - chr1.3:70694067-70694086 MS.gene006406:intron 40.0%
! CAGAATTGGGAGTCTTATAC+TGG - chr1.3:70693203-70693222 MS.gene006406:intron 40.0%
! CCCCAATGAATTTGTTTCCT+TGG - chr1.3:70693089-70693108 MS.gene006406:intron 40.0%
!!! AAGGCTTCATTTTTGGGATG+TGG - chr1.3:70694248-70694267 MS.gene006406:CDS 40.0%
!!! GTGGTTTTGTGCAGTTAATG+AGG - chr1.3:70694387-70694406 MS.gene006406:CDS 40.0%
AAGGGCTTGACTGAGAAAAC+TGG - chr1.3:70694485-70694504 MS.gene006406:intron 45.0%
ATTCGCATTTGGATCAAGGC+TGG - chr1.3:70694130-70694149 MS.gene006406:intron 45.0%
CAAATTCATTGGGGTAGCCA+TGG + chr1.3:70693083-70693102 None:intergenic 45.0%
CGATTATATGCTGTCCACAC+CGG + chr1.3:70694428-70694447 None:intergenic 45.0%
CTACACTGAGCACATTCATC+AGG - chr1.3:70694039-70694058 MS.gene006406:intron 45.0%
CTGGATTCGCATTTGGATCA+AGG - chr1.3:70694126-70694145 MS.gene006406:intron 45.0%
GACAGCATATAATCGACCAC+AGG - chr1.3:70694433-70694452 MS.gene006406:intron 45.0%
GGAAGATAACCCTGCTAGAA+AGG - chr1.3:70694454-70694473 MS.gene006406:intron 45.0%
GTTTCCTTGGACCAATTAGC+AGG - chr1.3:70693102-70693121 MS.gene006406:intron 45.0%
TACCTGCAGGAATCTACCAT+CGG - chr1.3:70694167-70694186 MS.gene006406:intron 45.0%
TTCGAGACAAAAAGGATCGC+TGG - chr1.3:70694107-70694126 MS.gene006406:intron 45.0%
AACCGATGGTAGATTCCTGC+AGG + chr1.3:70694172-70694191 None:intergenic 50.0%
AGGATCGCTGGATTCGCATT+TGG - chr1.3:70694119-70694138 MS.gene006406:intron 50.0%
CGTTACTGTTTGGAGGGAAG+TGG - chr1.3:70694073-70694092 MS.gene006406:intron 50.0%
CTAGCAGGGTTATCTTCCTG+TGG + chr1.3:70694452-70694471 None:intergenic 50.0%
GAGGTTGTTTATGGGTGAGC+CGG - chr1.3:70694406-70694425 MS.gene006406:CDS 50.0%
GATCCAAGACTTCCTCACCA+TGG - chr1.3:70693063-70693082 MS.gene006406:intron 50.0%
TAGCCATGGTGAGGAAGTCT+TGG + chr1.3:70693069-70693088 None:intergenic 50.0%
TTAGCAGCAACGCCACTGTT+AGG - chr1.3:70693561-70693580 MS.gene006406:intron 50.0%
TTGTGTCGAGAGTGAACCGA+TGG + chr1.3:70694186-70694205 None:intergenic 50.0%
TCATTGGGGTAGCCATGGTG+AGG + chr1.3:70693078-70693097 None:intergenic 55.0%
TGTTTATGGGTGAGCCGGTG+TGG - chr1.3:70694411-70694430 MS.gene006406:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 70692947 70694529 70692947 ID=MS.gene006406
chr1.3 mRNA 70692947 70694529 70692947 ID=MS.gene006406.t1;Parent=MS.gene006406
chr1.3 exon 70694518 70694529 70694518 ID=MS.gene006406.t1.exon1;Parent=MS.gene006406.t1
chr1.3 CDS 70694518 70694529 70694518 ID=cds.MS.gene006406.t1;Parent=MS.gene006406.t1
chr1.3 exon 70694353 70694440 70694353 ID=MS.gene006406.t1.exon2;Parent=MS.gene006406.t1
chr1.3 CDS 70694353 70694440 70694353 ID=cds.MS.gene006406.t1;Parent=MS.gene006406.t1
chr1.3 exon 70694176 70694270 70694176 ID=MS.gene006406.t1.exon3;Parent=MS.gene006406.t1
chr1.3 CDS 70694176 70694270 70694176 ID=cds.MS.gene006406.t1;Parent=MS.gene006406.t1
chr1.3 exon 70693257 70693496 70693257 ID=MS.gene006406.t1.exon4;Parent=MS.gene006406.t1
chr1.3 CDS 70693257 70693496 70693257 ID=cds.MS.gene006406.t1;Parent=MS.gene006406.t1
chr1.3 exon 70692947 70693075 70692947 ID=MS.gene006406.t1.exon5;Parent=MS.gene006406.t1
chr1.3 CDS 70692947 70693075 70692947 ID=cds.MS.gene006406.t1;Parent=MS.gene006406.t1
Gene Sequence

>MS.gene006406

ATGGCGATTGAGGTGAGTTCTTATTCTTCTTCCTTATGAATTAATCTTAATATAAGATTTGTGATGTTAATAATTAAAAATTGTGATAGGCATGGTTCATGGACAATAGCAATGAAGATCCAAGACTTCCTCACCATGGCTACCCCAATGAATTTGTTTCCTTGGACCAATTAGCAGGTTATTAATCATATCTCTTTATGTAATATATAGTTTTAATTTATTGTGACACAAGTTTGAGGGAAAATTTTAATTTTTGCAGAATTGGGAGTCTTATACTGGAAGCTGAACCCTAATGACTATGAGAATGATCAAGAATTGAAGAACATTAGAGAAGCCAGAGGATACAATTACATGGTAATAATATTGTTGTGTTTTTTATTTTTATTTTTTTATTAAATGCAATTATTCATATTCAGTTTTCTAGTGATACAATTACACGGTAAGATTGAAAGTGGATTTTTTCTTGTGGGTTTAACATGTAAAAAAAACATGTTACTCCACATGTAAAAAAAACATGTTAAAACAGGAACATATGACTTACTATTATCTAATATATTGTAAACGGCCTTCAAATTTTTGTTGATGTAAATTTCTTAGGACATGCTGCACAGAGCTTAGCAGCAACGCCACTGTTAGGTAAACAACTTATTAAGTGTTTGTCGATAAACTATTTTTATAACAAAAGATAAAATTAAGTCAATTATTTATATATAAGTTGTAAGTTGTATTCATAAGTTATCTTTGAGAGTTTATGGAAATTAGTTGAAAATAACTTACGGAGATGCCAAAGTTGTTTTCATAAGCTATATTGAACAGTCTCGCAAATACTTATGCCGGTAGATGAGCTCAAATAAGTCAATTTAGGAACACTTGCACTAGAGTTGTTAGAGATATGACGATTTCAAGATTAATTTTTGACCTGTTGAACATTTTGATTGTACTAATTGAAGGGAAATTTCATCTTTCAAATGTTCTGGGTGTTGATAACATCTTCGTATCTTGAATATTTCTGTACTATTTGAATATGTTGTAGGATTTACTTGATTTATGCCCGGAAAAAGTTGAAAATTATGAAGAGAAGTTGAAGAACTTCTACACTGAGCACATTCATCAGGATGAAGAGATTCGTTACTGTTTGGAGGGAAGTGGCTACTTCGATGTTCGAGACAAAAAGGATCGCTGGATTCGCATTTGGATCAAGGCTGGTGATCTTATCATTTTACCTGCAGGAATCTACCATCGGTTCACTCTCGACACAAATAACTATGTGAAGGTAATCACACCTATCAATATTCTTGATCAAGGCTTCATTTTTGGGATGTGGAATGTAGAAAGTAATGCAGTTTTAACTTTAAGCATGTTTAAAACTTGAAATTGATCAAGATTCAAGGTAATATGTTGGATGATTAGAATTAATTGTTTTGTTCGATGCATATGTATGTGGTTTTGTGCAGTTAATGAGGTTGTTTATGGGTGAGCCGGTGTGGACAGCATATAATCGACCACAGGAAGATAACCCTGCTAGAAAGGAATACATTAAGGGCTTGACTGAGAAAACTGGTGTGCCACTTGCAGCTCATTAG
Protein sequence

>MS.gene006406.t1

MAIEAWFMDNSNEDPRLPHHGYPNEFVSLDQLAELGVLYWKLNPNDYENDQELKNIREARGYNYMDLLDLCPEKVENYEEKLKNFYTEHIHQDEEIRYCLEGSGYFDVRDKKDRWIRIWIKAGDLIILPAGIYHRFTLDTNNYVKLMRLFMGEPVWTAYNRPQEDNPARKEYIKGLTEKTGVPLAAH