AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054295

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054295.t1 MTR_8g019520 79.747 79 16 0 100 178 178 256 1.06e-31 115
MS.gene054295.t1 MTR_8g019520 79.747 79 16 0 100 178 179 257 1.12e-31 115
MS.gene054295.t1 MTR_2g099500 75.862 58 14 0 120 177 193 250 5.51e-27 102
MS.gene054295.t1 MTR_1g015185 76.364 55 12 1 124 178 210 263 1.79e-24 96.3
MS.gene054295.t1 MTR_2g040990 68.333 60 16 2 121 178 195 253 2.74e-22 90.5
MS.gene054295.t1 MTR_4g134510 69.231 52 16 0 123 174 201 252 1.27e-21 88.6
MS.gene054295.t1 MTR_4g015830 69.091 55 16 1 124 178 187 240 6.70e-21 86.3
MS.gene054295.t1 MTR_7g068590 65.455 55 18 1 124 178 189 242 1.38e-19 83.2
MS.gene054295.t1 MTR_0024s0330 61.538 65 22 1 1 65 96 157 1.23e-16 77.0
MS.gene054295.t1 MTR_6g017265 56.250 64 25 1 2 65 106 166 1.61e-13 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054295.t1 AT5G20510 70.000 60 17 1 119 178 161 219 3.51e-25 97.1
MS.gene054295.t1 AT5G20510 70.000 60 17 1 119 178 202 260 6.45e-25 97.4
MS.gene054295.t1 AT3G42790 72.881 59 15 1 119 177 192 249 1.09e-24 96.7
MS.gene054295.t1 AT2G02470 74.545 55 13 1 124 178 203 256 6.75e-24 94.7
MS.gene054295.t1 AT2G02470 74.545 55 13 1 124 178 194 247 8.67e-24 94.4
MS.gene054295.t1 AT5G26210 75.000 56 13 1 122 177 200 254 2.47e-23 93.2
MS.gene054295.t1 AT1G14510 68.519 54 17 0 124 177 198 251 4.66e-22 89.7
MS.gene054295.t1 AT5G05610 65.385 52 18 0 119 170 183 234 1.10e-19 83.2
MS.gene054295.t1 AT5G05610 65.385 52 18 0 119 170 183 234 1.10e-19 83.2
MS.gene054295.t1 AT3G11200 61.538 52 20 0 119 170 188 239 2.39e-18 79.7
MS.gene054295.t1 AT3G11200 61.538 52 20 0 119 170 175 226 3.54e-18 79.0
MS.gene054295.t1 AT5G38690 55.102 49 22 0 1 49 82 130 9.50e-12 62.8
MS.gene054295.t1 AT5G38690 55.102 49 22 0 1 49 82 130 9.50e-12 62.8

Find 43 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGCATATTCTTCCTTTAT+AGG 0.158707 6.1:+24885149 None:intergenic
CTTAATACTTGTTGGATATA+TGG 0.216059 6.1:-24884569 MS.gene054295:CDS
TCTTCCACATCCTCGTCTTT+AGG 0.289074 6.1:+24884495 None:intergenic
TGCAAATGCCTCTGCACTTC+GGG 0.304977 6.1:+24885425 None:intergenic
CATATATCCAACAAGTATTA+AGG 0.316202 6.1:+24884570 None:intergenic
ATGACATCCTTAATACTTGT+TGG 0.337001 6.1:-24884577 MS.gene054295:CDS
TACTAATGTTGGGCCTATAA+AGG 0.359306 6.1:-24885162 MS.gene054295:CDS
CAGAAAATCCAGAATTCATC+AGG 0.388348 6.1:+24884405 None:intergenic
TATAAAGGAAGAATATGCTT+TGG 0.417141 6.1:-24885147 MS.gene054295:CDS
ATAAAGGAAGAATATGCTTT+GGG 0.425102 6.1:-24885146 MS.gene054295:CDS
ATGGGTAATAATACTAATGT+TGG 0.425773 6.1:-24885173 MS.gene054295:CDS
GTTCGTATAGCGAAGGCATC+TGG 0.430043 6.1:-24885254 MS.gene054295:CDS
TCGATATGCTTAGCCCTAGC+AGG 0.441225 6.1:+24884336 None:intergenic
CTAAAGCATCAGCCGCCTAC+AGG 0.441391 6.1:-24885284 MS.gene054295:CDS
GGTGCATGCGGTGAGCAATA+TGG 0.455947 6.1:-24884429 MS.gene054295:CDS
CTCTTGTTGTTATTGCATGA+TGG 0.456815 6.1:+24884300 None:intergenic
AATATGGCCCTGATGAATTC+TGG 0.457151 6.1:-24884413 MS.gene054295:CDS
CTCAGAAATGCTTAGCAAGA+TGG 0.474202 6.1:-24885219 MS.gene054295:CDS
TGGGTAATAATACTAATGTT+GGG 0.488773 6.1:-24885172 MS.gene054295:CDS
GTGTGAATATCACCCCTGCT+AGG 0.500091 6.1:-24884350 MS.gene054295:CDS
TTGCAAATGCCTCTGCACTT+CGG 0.508058 6.1:+24885424 None:intergenic
TAAAGCATCAGCCGCCTACA+GGG 0.517220 6.1:-24885283 MS.gene054295:CDS
GTTACCTAAAGACGAGGATG+TGG 0.537974 6.1:-24884499 MS.gene054295:CDS
TCTGTGACATTTGTGAGAGG+TGG 0.541786 6.1:-24884386 MS.gene054295:CDS
GAGGAAGATGAAGATGAATA+CGG 0.542593 6.1:-24884465 MS.gene054295:CDS
TTTGTGAGAGGTGGTTCCAT+GGG 0.542875 6.1:-24884377 MS.gene054295:CDS
TGTGAATATCACCCCTGCTA+GGG 0.567860 6.1:-24884349 MS.gene054295:CDS
CGATATGCTTAGCCCTAGCA+GGG 0.574696 6.1:+24884337 None:intergenic
TGATATTCACACATTTCCCA+TGG 0.578749 6.1:+24884361 None:intergenic
ATTTGTGAGAGGTGGTTCCA+TGG 0.579292 6.1:-24884378 MS.gene054295:CDS
AACAAGAGAGCTCGCCCTTG+AGG 0.603261 6.1:-24884285 None:intergenic
GGCACTTGTTCGTATAGCGA+AGG 0.607034 6.1:-24885261 MS.gene054295:CDS
GGAAGAATATGCTTTGGGAA+AGG 0.614050 6.1:-24885141 MS.gene054295:intron
GGATGTGGAAGAACATTGTG+AGG 0.641770 6.1:-24884484 MS.gene054295:CDS
AAAGCATCAGCCGCCTACAG+GGG 0.652248 6.1:-24885282 MS.gene054295:CDS
TGGATGTGCCCGAAGTGCAG+AGG 0.655876 6.1:-24885433 MS.gene054295:CDS
CGAACAAGTGCCCCTGTAGG+CGG 0.661590 6.1:+24885272 None:intergenic
ATACGAACAAGTGCCCCTGT+AGG 0.685462 6.1:+24885269 None:intergenic
AGAAAATCCAGAATTCATCA+GGG 0.689840 6.1:+24884406 None:intergenic
GAGAACTCATGTGGTGCATG+CGG 0.697071 6.1:-24884441 MS.gene054295:CDS
TTTGGAGTTACCTAAAGACG+AGG 0.697923 6.1:-24884505 MS.gene054295:CDS
GAATACGGAGAGAACTCATG+TGG 0.703470 6.1:-24884450 MS.gene054295:CDS
GATATGCTTAGCCCTAGCAG+GGG 0.762022 6.1:+24884338 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAAACATGTTTTATGATTT+TGG - chr6.1:24884344-24884363 MS.gene054295:CDS 15.0%
!!! TAATTGATAATAATGCTATA+AGG - chr6.1:24884966-24884985 MS.gene054295:intron 15.0%
!!! TTTTGAATTATCTCTTAAAT+AGG - chr6.1:24885188-24885207 MS.gene054295:CDS 15.0%
!! TTCAACTCATACAATAAATT+GGG - chr6.1:24884871-24884890 MS.gene054295:intron 20.0%
!!! TAGATTTTAACACATTGATT+GGG - chr6.1:24885101-24885120 MS.gene054295:intron 20.0%
! AAAGCATATTCTTCCTTTAT+AGG + chr6.1:24884571-24884590 None:intergenic 25.0%
! ATAAAGGAAGAATATGCTTT+GGG - chr6.1:24884571-24884590 MS.gene054295:CDS 25.0%
! ATCATTATCACCAATAACAA+TGG + chr6.1:24884903-24884922 None:intergenic 25.0%
! ATGGGTAATAATACTAATGT+TGG - chr6.1:24884544-24884563 MS.gene054295:intron 25.0%
! ATTATCTCTTAAATAGGCTT+TGG - chr6.1:24885194-24885213 MS.gene054295:CDS 25.0%
! CATATATCCAACAAGTATTA+AGG + chr6.1:24885150-24885169 None:intergenic 25.0%
! CTTCAACTCATACAATAAAT+TGG - chr6.1:24884870-24884889 MS.gene054295:intron 25.0%
! GAAAAATTGGAACTTTCTAT+GGG - chr6.1:24884526-24884545 MS.gene054295:intron 25.0%
! TATAAAGGAAGAATATGCTT+TGG - chr6.1:24884570-24884589 MS.gene054295:CDS 25.0%
! TGAAAAATTGGAACTTTCTA+TGG - chr6.1:24884525-24884544 MS.gene054295:intron 25.0%
! TGGGTAATAATACTAATGTT+GGG - chr6.1:24884545-24884564 MS.gene054295:intron 25.0%
!! CTTAATACTTGTTGGATATA+TGG - chr6.1:24885148-24885167 MS.gene054295:CDS 25.0%
!! GTTATTGGTGATAATGATAT+TGG - chr6.1:24884905-24884924 MS.gene054295:intron 25.0%
!! TCTTTATTTGATGCTGAATA+AGG - chr6.1:24884642-24884661 MS.gene054295:intron 25.0%
!!! ATGTTTTATGATTTTGGTGT+TGG - chr6.1:24884350-24884369 MS.gene054295:CDS 25.0%
!!! GTAGATTTTAACACATTGAT+TGG - chr6.1:24885100-24885119 MS.gene054295:intron 25.0%
ACCAAACATTGAAAATGTAC+TGG - chr6.1:24885033-24885052 MS.gene054295:intron 30.0%
ACTCATACAATAAATTGGGA+TGG - chr6.1:24884875-24884894 MS.gene054295:intron 30.0%
AGAAAATCCAGAATTCATCA+GGG + chr6.1:24885314-24885333 None:intergenic 30.0%
ATGACATCCTTAATACTTGT+TGG - chr6.1:24885140-24885159 MS.gene054295:intron 30.0%
GTGACAGCTACATAAAAATA+GGG + chr6.1:24884613-24884632 None:intergenic 30.0%
TGTGACAGCTACATAAAAAT+AGG + chr6.1:24884614-24884633 None:intergenic 30.0%
TTAACGAAGATTAACGATGT+AGG - chr6.1:24884407-24884426 MS.gene054295:CDS 30.0%
! AAGTTGATCTATCTCCATAT+GGG + chr6.1:24884942-24884961 None:intergenic 30.0%
! ATTGTATGAGTTGAAGACAA+AGG + chr6.1:24884866-24884885 None:intergenic 30.0%
! TCCAGTACATTTTCAATGTT+TGG + chr6.1:24885037-24885056 None:intergenic 30.0%
!! CATATTTGTTATTATGCTGC+AGG - chr6.1:24884748-24884767 MS.gene054295:intron 30.0%
!! TTTTAACACATTGATTGGGA+AGG - chr6.1:24885105-24885124 MS.gene054295:intron 30.0%
CAAGATGGAAGCTGAAAAAT+TGG - chr6.1:24884513-24884532 MS.gene054295:intron 35.0%
CAGAAAATCCAGAATTCATC+AGG + chr6.1:24885315-24885334 None:intergenic 35.0%
GAGGAAGATGAAGATGAATA+CGG - chr6.1:24885252-24885271 MS.gene054295:CDS 35.0%
TACTAATGTTGGGCCTATAA+AGG - chr6.1:24884555-24884574 MS.gene054295:intron 35.0%
TGATATTCACACATTTCCCA+TGG + chr6.1:24885359-24885378 None:intergenic 35.0%
! ATTTTCAATGTTTGGTCCAG+AGG + chr6.1:24885029-24885048 None:intergenic 35.0%
! GAAGTTGATCTATCTCCATA+TGG + chr6.1:24884943-24884962 None:intergenic 35.0%
! TTTTCAATGTTTGGTCCAGA+GGG + chr6.1:24885028-24885047 None:intergenic 35.0%
! TTTTCTGTGACATTTGTGAG+AGG - chr6.1:24885328-24885347 MS.gene054295:intron 35.0%
!! ATTTGTTATTATGCTGCAGG+AGG - chr6.1:24884751-24884770 MS.gene054295:intron 35.0%
!! CTCTTGTTGTTATTGCATGA+TGG + chr6.1:24885420-24885439 None:intergenic 35.0%
AATATGGCCCTGATGAATTC+TGG - chr6.1:24885304-24885323 MS.gene054295:intron 40.0%
CTCAGAAATGCTTAGCAAGA+TGG - chr6.1:24884498-24884517 MS.gene054295:CDS 40.0%
GAAGAAATTTCTCATCCCTC+TGG - chr6.1:24885010-24885029 MS.gene054295:intron 40.0%
TAGTGTGTGCATGTAAGTTG+TGG - chr6.1:24884319-24884338 MS.gene054295:CDS 40.0%
TGGTAGACTGAATTCCCATA+TGG - chr6.1:24884925-24884944 MS.gene054295:intron 40.0%
! TCCTCAATTAGTTCTCTCTC+TGG + chr6.1:24884992-24885011 None:intergenic 40.0%
! TGAGTTGAAGACAAAGGACT+AGG + chr6.1:24884860-24884879 None:intergenic 40.0%
! TTTGGAGTTACCTAAAGACG+AGG - chr6.1:24885212-24885231 MS.gene054295:CDS 40.0%
!! AGAATATGCTTTGGGAAAGG+TGG - chr6.1:24884579-24884598 MS.gene054295:CDS 40.0%
!! GGAAGAATATGCTTTGGGAA+AGG - chr6.1:24884576-24884595 MS.gene054295:CDS 40.0%
AACATTTCCAGCCCAATCCT+CGG + chr6.1:24884825-24884844 None:intergenic 45.0%
ATATTGCCCAACTCCTTGTG+TGG - chr6.1:24884790-24884809 MS.gene054295:intron 45.0%
ATTTGTGAGAGGTGGTTCCA+TGG - chr6.1:24885339-24885358 MS.gene054295:intron 45.0%
GAATACGGAGAGAACTCATG+TGG - chr6.1:24885267-24885286 MS.gene054295:CDS 45.0%
GCCAGAGAGAGAACTAATTG+AGG - chr6.1:24884988-24885007 MS.gene054295:intron 45.0%
GGATGTGGAAGAACATTGTG+AGG - chr6.1:24885233-24885252 MS.gene054295:CDS 45.0%
GTTACCTAAAGACGAGGATG+TGG - chr6.1:24885218-24885237 MS.gene054295:CDS 45.0%
TCTGTGACATTTGTGAGAGG+TGG - chr6.1:24885331-24885350 MS.gene054295:intron 45.0%
TCTTCCACATCCTCGTCTTT+AGG + chr6.1:24885225-24885244 None:intergenic 45.0%
TGGGATGGCACCATTGTTAT+TGG - chr6.1:24884890-24884909 MS.gene054295:intron 45.0%
TGTGAATATCACCCCTGCTA+GGG - chr6.1:24885368-24885387 MS.gene054295:intron 45.0%
TTGCAAATGCCTCTGCACTT+CGG + chr6.1:24884296-24884315 None:intergenic 45.0%
TTTGTGAGAGGTGGTTCCAT+GGG - chr6.1:24885340-24885359 MS.gene054295:intron 45.0%
ATACGAACAAGTGCCCCTGT+AGG + chr6.1:24884451-24884470 None:intergenic 50.0%
CCAACTCCTTGTGTGGCAAT+GGG - chr6.1:24884797-24884816 MS.gene054295:intron 50.0%
CCATTGCCACACAAGGAGTT+GGG + chr6.1:24884799-24884818 None:intergenic 50.0%
CGATATGCTTAGCCCTAGCA+GGG + chr6.1:24885383-24885402 None:intergenic 50.0%
GAGAACTCATGTGGTGCATG+CGG - chr6.1:24885276-24885295 MS.gene054295:CDS 50.0%
GATATGCTTAGCCCTAGCAG+GGG + chr6.1:24885382-24885401 None:intergenic 50.0%
GGCACTTGTTCGTATAGCGA+AGG - chr6.1:24884456-24884475 MS.gene054295:CDS 50.0%
GTGTGAATATCACCCCTGCT+AGG - chr6.1:24885367-24885386 MS.gene054295:intron 50.0%
TCGATATGCTTAGCCCTAGC+AGG + chr6.1:24885384-24885403 None:intergenic 50.0%
TGCAAATGCCTCTGCACTTC+GGG + chr6.1:24884295-24884314 None:intergenic 50.0%
! TAAAGCATCAGCCGCCTACA+GGG - chr6.1:24884434-24884453 MS.gene054295:CDS 50.0%
!! GTTCGTATAGCGAAGGCATC+TGG - chr6.1:24884463-24884482 MS.gene054295:CDS 50.0%
CCCAACTCCTTGTGTGGCAA+TGG - chr6.1:24884796-24884815 MS.gene054295:intron 55.0%
CCCATTGCCACACAAGGAGT+TGG + chr6.1:24884800-24884819 None:intergenic 55.0%
GGTGCATGCGGTGAGCAATA+TGG - chr6.1:24885288-24885307 MS.gene054295:CDS 55.0%
TCGGTACCCATTGCCACACA+AGG + chr6.1:24884806-24884825 None:intergenic 55.0%
! AAAGCATCAGCCGCCTACAG+GGG - chr6.1:24884435-24884454 MS.gene054295:CDS 55.0%
! CTAAAGCATCAGCCGCCTAC+AGG - chr6.1:24884433-24884452 MS.gene054295:CDS 55.0%
! TTGTGTGGCAATGGGTACCG+AGG - chr6.1:24884805-24884824 MS.gene054295:intron 55.0%
!! GGCAATGGGTACCGAGGATT+GGG - chr6.1:24884811-24884830 MS.gene054295:intron 55.0%
!! TGGCAATGGGTACCGAGGAT+TGG - chr6.1:24884810-24884829 MS.gene054295:intron 55.0%
CGAACAAGTGCCCCTGTAGG+CGG + chr6.1:24884448-24884467 None:intergenic 60.0%
!! ATGGGTACCGAGGATTGGGC+TGG - chr6.1:24884815-24884834 MS.gene054295:intron 60.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 24884287 24885452 24884287 ID=MS.gene054295
chr6.1 mRNA 24884287 24885452 24884287 ID=MS.gene054295.t1;Parent=MS.gene054295
chr6.1 exon 24885409 24885452 24885409 ID=MS.gene054295.t1.exon1;Parent=MS.gene054295.t1
chr6.1 CDS 24885409 24885452 24885409 ID=cds.MS.gene054295.t1;Parent=MS.gene054295.t1
chr6.1 exon 24885142 24885310 24885142 ID=MS.gene054295.t1.exon2;Parent=MS.gene054295.t1
chr6.1 CDS 24885142 24885310 24885142 ID=cds.MS.gene054295.t1;Parent=MS.gene054295.t1
chr6.1 exon 24884562 24884642 24884562 ID=MS.gene054295.t1.exon3;Parent=MS.gene054295.t1
chr6.1 CDS 24884562 24884642 24884562 ID=cds.MS.gene054295.t1;Parent=MS.gene054295.t1
chr6.1 exon 24884287 24884529 24884287 ID=MS.gene054295.t1.exon4;Parent=MS.gene054295.t1
chr6.1 CDS 24884287 24884529 24884287 ID=cds.MS.gene054295.t1;Parent=MS.gene054295.t1
Gene Sequence

>MS.gene054295

ATGTGCCCGAAGTGCAGAGGCATTTGCAACTGTAGTGTGTGCATGTAAGTTGTGGTTTAAAACATGTTTTATGATTTTGGTGTTGGAGTTTTCATTTTGTAACATTTTGTGTATTAGATCTTAACGAAGATTAACGATGTAGGAGACTAAAGCATCAGCCGCCTACAGGGGCACTTGTTCGTATAGCGAAGGCATCTGGTTTTACGTGTGTCTCAGAAATGCTTAGCAAGATGGAAGCTGAAAAATTGGAACTTTCTATGGGTAATAATACTAATGTTGGGCCTATAAAGGAAGAATATGCTTTGGGAAAGGTGGTTTTCTTTCCCTATTTTTATGTAGCTGTCACAATAAGTTTTCTTTATTTGATGCTGAATAAGGCTCTTTTTATTTATTCAATTTCAAATAATGATAAAAAATGTAAGAGTGTGCTGATTATCATTGTATTTTAAAGATTTGAATTTCATATTTGTTATTATGCTGCAGGAGGTTTTAGTAGAAGAGAAATATTGCCCAACTCCTTGTGTGGCAATGGGTACCGAGGATTGGGCTGGAAATGTTTTATTTTCTGATCCTAGTCCTTTGTCTTCAACTCATACAATAAATTGGGATGGCACCATTGTTATTGGTGATAATGATATTGGTAGACTGAATTCCCATATGGAGATAGATCAACTTCAAATAATTGATAATAATGCTATAAGGCCAGAGAGAGAACTAATTGAGGAAGAAATTTCTCATCCCTCTGGACCAAACATTGAAAATGTACTGGACGTTGAATTTCAACGAGAAGATGCTGCGAGTGAAATGCAGTTTGTAGATTTTAACACATTGATTGGGAAGGTATGCATTTTCGATGACATCCTTAATACTTGTTGGATATATGGTAGTTATGTGTTTATAATTTTGAATTATCTCTTAAATAGGCTTTGGAGTTACCTAAAGACGAGGATGTGGAAGAACATTGTGAGGAAGATGAAGATGAATACGGAGAGAACTCATGTGGTGCATGCGGTGAGCAATATGGCCCTGATGAATTCTGGATTTTCTGTGACATTTGTGAGAGGTGGTTCCATGGGAAATGTGTGAATATCACCCCTGCTAGGGCTAAGCATATCGAGATATACAAGTGTCCATCATGCAATAACAACAAGAGAGCTCGCCCTTGA
Protein sequence

>MS.gene054295.t1

MCPKCRGICNCSVCMRLKHQPPTGALVRIAKASGFTCVSEMLSKMEAEKLELSMGNNTNVGPIKEEYALGKFVDFNTLIGKVCIFDDILNTCWIYGSYALELPKDEDVEEHCEEDEDEYGENSCGACGEQYGPDEFWIFCDICERWFHGKCVNITPARAKHIEIYKCPSCNNNKRARP