AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene034438

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene034438.t1 AT5G22250 55.678 273 111 4 14 283 12 277 1.95e-98 290
MS.gene034438.t1 AT3G44260 52.613 287 117 6 4 283 5 279 3.24e-95 282
MS.gene034438.t1 AT2G32070 46.863 271 127 6 14 281 10 266 2.30e-76 234
MS.gene034438.t1 AT1G15920 45.230 283 147 5 1 282 1 276 5.66e-76 233
MS.gene034438.t1 AT1G15920 45.230 283 147 5 1 282 1 276 5.66e-76 233
MS.gene034438.t1 AT5G10960 47.388 268 129 5 14 281 10 265 8.94e-74 228
MS.gene034438.t1 AT1G80780 45.185 270 132 5 14 281 10 265 2.26e-72 224
MS.gene034438.t1 AT1G80780 45.185 270 132 5 14 281 10 265 2.26e-72 224
MS.gene034438.t1 AT1G80780 45.185 270 132 5 14 281 10 265 2.49e-72 224
MS.gene034438.t1 AT1G61470 34.413 247 137 6 18 260 4 229 2.64e-34 125
MS.gene034438.t1 AT1G27820 34.783 253 142 7 12 260 2 235 1.09e-33 125
MS.gene034438.t1 AT1G06450 33.730 252 138 8 15 259 8 237 2.09e-32 122
MS.gene034438.t1 AT3G44240 34.188 234 133 7 29 260 2 216 3.00e-32 119
MS.gene034438.t1 AT1G27890 34.413 247 139 7 18 260 3 230 2.61e-31 118

Find 61 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGGGCAATCTTCCCGATTT+TGG 0.132015 2.3:+12303430 MS.gene034438:CDS
CTCGTATGATTTCGGATATT+TGG 0.195704 2.3:+12303666 MS.gene034438:CDS
AAATATGCTGGAGTGCTCTT+TGG 0.291631 2.3:+12303961 MS.gene034438:CDS
TTTCATAGCTCGTATGATTT+CGG 0.312575 2.3:+12303658 MS.gene034438:CDS
TTAGTTGAAGACGGCTGATT+TGG 0.325349 2.3:-12303157 None:intergenic
CGTCTCTTGACACAATTGTT+TGG 0.329196 2.3:+12303739 MS.gene034438:CDS
TCAATGTTTACAAAATTTCC+TGG 0.365989 2.3:+12303268 MS.gene034438:CDS
CAAACTTGACGGATCACAAT+AGG 0.371885 2.3:-12303181 None:intergenic
CTATTGTGATCCGTCAAGTT+TGG 0.384439 2.3:+12303182 MS.gene034438:CDS
GGAGTTATCTGTTCCAAAAT+CGG 0.385198 2.3:-12303443 None:intergenic
TTTCAACGACCAAGTTGTTT+GGG 0.390947 2.3:+12303630 MS.gene034438:CDS
GCTGAATTAATGTTCTCTTC+CGG 0.392181 2.3:+12303601 MS.gene034438:CDS
CGGTTAATGTAAGGCCGACT+TGG 0.392203 2.3:-12303402 None:intergenic
GAACAGATAACTCCTACATA+TGG 0.393078 2.3:+12303452 MS.gene034438:CDS
CAGAGTAGATTAACTGAGTC+TGG 0.394312 2.3:-12303520 None:intergenic
TTGGTCGTTGAAAAGGATTC+CGG 0.394492 2.3:-12303620 None:intergenic
GTTCAAAGTCGATCCCTTGA+TGG 0.401109 2.3:-12303543 None:intergenic
TAATGAGTTGTACGACAGTC+TGG 0.414224 2.3:+12303801 MS.gene034438:CDS
CCTTGTCGTCGGTTAATGTA+AGG 0.416041 2.3:-12303411 None:intergenic
TGCTGGAGTGCTCTTTGGAT+TGG 0.446608 2.3:+12303966 MS.gene034438:CDS
AAACAACTTGGTCGTTGAAA+AGG 0.451021 2.3:-12303627 None:intergenic
AGGTATAGTGACATCGACTT+TGG 0.458606 2.3:-12303305 None:intergenic
GTTAATCTACTCTGCCATCA+AGG 0.460897 2.3:+12303529 MS.gene034438:CDS
GAAGTTACCATCTCGCTTAG+AGG 0.462416 2.3:+12303708 MS.gene034438:CDS
ATCAACATCAACAAATATGC+TGG 0.464781 2.3:+12303949 MS.gene034438:CDS
CTGGTTAGCTTTCGATAAGA+TGG 0.469314 2.3:+12303900 MS.gene034438:CDS
GGTATAGTGACATCGACTTT+GGG 0.469620 2.3:-12303304 None:intergenic
CATCTTATCGAAAGCTAACC+AGG 0.475919 2.3:-12303899 None:intergenic
CGAGCAATACTCATATTTGA+AGG 0.482644 2.3:+12303354 MS.gene034438:CDS
AATGTAAGGCCGACTTGGAT+AGG 0.495460 2.3:-12303397 None:intergenic
ACGAATCCATGTGGCGGAGG+TGG 0.498503 2.3:-12303330 None:intergenic
GCTCGGATAGTTTGTTGACC+TGG 0.498750 2.3:+12303881 MS.gene034438:CDS
AATTGTCAGACCAAACTTGA+CGG 0.499910 2.3:-12303192 None:intergenic
TCCATGTGGCGGAGGTGGTA+AGG 0.503759 2.3:-12303325 None:intergenic
TTTGAACGCAATCGTTTATG+TGG 0.507147 2.3:+12303559 MS.gene034438:CDS
TACAAGTGAGTCATGCAGTC+GGG 0.514800 2.3:+12303842 MS.gene034438:CDS
GAGTTATCTGTTCCAAAATC+GGG 0.521622 2.3:-12303442 None:intergenic
GAAATTGAACTCCCATATGT+AGG 0.530575 2.3:-12303464 None:intergenic
GAAAAGTCACCCAAACAACT+TGG 0.541604 2.3:-12303639 None:intergenic
GGGAAGATTGCCCTTGTCGT+CGG 0.546043 2.3:-12303422 None:intergenic
TGACATCGACTTTGGGTGCA+TGG 0.548830 2.3:-12303297 None:intergenic
ACCTTACCACCTCCGCCACA+TGG 0.552072 2.3:+12303324 MS.gene034438:CDS
CGTACGAATCCATGTGGCGG+AGG 0.557071 2.3:-12303333 None:intergenic
AACAGATAACTCCTACATAT+GGG 0.559299 2.3:+12303453 MS.gene034438:CDS
GTTGTACGACAGTCTGGAGC+GGG 0.559358 2.3:+12303807 MS.gene034438:CDS
ACAATAGGTTTAGTTGAAGA+CGG 0.574619 2.3:-12303166 None:intergenic
CCTTACATTAACCGACGACA+AGG 0.579664 2.3:+12303411 MS.gene034438:CDS
GTCGGGAATTCTCATCAAGC+CGG 0.579736 2.3:+12303859 MS.gene034438:CDS
GAATTCTCATCAAGCCGGCT+CGG 0.580731 2.3:+12303864 MS.gene034438:CDS
TTAATCTACTCTGCCATCAA+GGG 0.584976 2.3:+12303530 MS.gene034438:CDS
GGTCAACAAACTATCCGAGC+CGG 0.615610 2.3:-12303878 None:intergenic
GAAACTTGCGAAAGATGCTA+CGG 0.634561 2.3:-12303237 None:intergenic
GTACGACAGTCTGGAGCGGG+TGG 0.637722 2.3:+12303810 MS.gene034438:CDS
CTACAAGTGAGTCATGCAGT+CGG 0.640054 2.3:+12303841 MS.gene034438:CDS
TTGGGTGCATGGATGACACC+AGG 0.647634 2.3:-12303286 None:intergenic
AGAAACTCCTCTAAGCGAGA+TGG 0.649937 2.3:-12303715 None:intergenic
GATTTGAAACCTATCCAAGT+CGG 0.655871 2.3:+12303388 MS.gene034438:CDS
CTTACATTAACCGACGACAA+GGG 0.672450 2.3:+12303412 MS.gene034438:CDS
AGTTGTACGACAGTCTGGAG+CGG 0.678062 2.3:+12303806 MS.gene034438:CDS
GCTCGTACGAATCCATGTGG+CGG 0.707562 2.3:-12303336 None:intergenic
ATTGCTCGTACGAATCCATG+TGG 0.744442 2.3:-12303339 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TCAATGTTTACAAAATTTCC+TGG + chr2.3:12303268-12303287 MS.gene034438:CDS 25.0%
AACAGATAACTCCTACATAT+GGG + chr2.3:12303453-12303472 MS.gene034438:CDS 30.0%
ACAATAGGTTTAGTTGAAGA+CGG - chr2.3:12303169-12303188 None:intergenic 30.0%
ATCAACATCAACAAATATGC+TGG + chr2.3:12303949-12303968 MS.gene034438:CDS 30.0%
TTTCATAGCTCGTATGATTT+CGG + chr2.3:12303658-12303677 MS.gene034438:CDS 30.0%
!! ATTTGGTGAAAGCTTTTACT+GGG + chr2.3:12303683-12303702 MS.gene034438:CDS 30.0%
!! TATTTGGTGAAAGCTTTTAC+TGG + chr2.3:12303682-12303701 MS.gene034438:CDS 30.0%
AAACAACTTGGTCGTTGAAA+AGG - chr2.3:12303630-12303649 None:intergenic 35.0%
AATTGTCAGACCAAACTTGA+CGG - chr2.3:12303195-12303214 None:intergenic 35.0%
CGAGCAATACTCATATTTGA+AGG + chr2.3:12303354-12303373 MS.gene034438:CDS 35.0%
CTCGTATGATTTCGGATATT+TGG + chr2.3:12303666-12303685 MS.gene034438:CDS 35.0%
GAAATTGAACTCCCATATGT+AGG - chr2.3:12303467-12303486 None:intergenic 35.0%
GAACAGATAACTCCTACATA+TGG + chr2.3:12303452-12303471 MS.gene034438:CDS 35.0%
GAGTTATCTGTTCCAAAATC+GGG - chr2.3:12303445-12303464 None:intergenic 35.0%
GCTGAATTAATGTTCTCTTC+CGG + chr2.3:12303601-12303620 MS.gene034438:CDS 35.0%
GGAGTTATCTGTTCCAAAAT+CGG - chr2.3:12303446-12303465 None:intergenic 35.0%
TTAATCTACTCTGCCATCAA+GGG + chr2.3:12303530-12303549 MS.gene034438:CDS 35.0%
TTTCAACGACCAAGTTGTTT+GGG + chr2.3:12303630-12303649 MS.gene034438:CDS 35.0%
TTTGAACGCAATCGTTTATG+TGG + chr2.3:12303559-12303578 MS.gene034438:CDS 35.0%
! GATTTGAAACCTATCCAAGT+CGG + chr2.3:12303388-12303407 MS.gene034438:CDS 35.0%
! TTTTCAACGACCAAGTTGTT+TGG + chr2.3:12303629-12303648 MS.gene034438:CDS 35.0%
CAGAGTAGATTAACTGAGTC+TGG - chr2.3:12303523-12303542 None:intergenic 40.0%
CATCTTATCGAAAGCTAACC+AGG - chr2.3:12303902-12303921 None:intergenic 40.0%
CGTCTCTTGACACAATTGTT+TGG + chr2.3:12303739-12303758 MS.gene034438:CDS 40.0%
CTATTGTGATCCGTCAAGTT+TGG + chr2.3:12303182-12303201 MS.gene034438:CDS 40.0%
CTTACATTAACCGACGACAA+GGG + chr2.3:12303412-12303431 MS.gene034438:CDS 40.0%
GAAAAGTCACCCAAACAACT+TGG - chr2.3:12303642-12303661 None:intergenic 40.0%
GAAACTTGCGAAAGATGCTA+CGG - chr2.3:12303240-12303259 None:intergenic 40.0%
GTTAATCTACTCTGCCATCA+AGG + chr2.3:12303529-12303548 MS.gene034438:CDS 40.0%
TAATGAGTTGTACGACAGTC+TGG + chr2.3:12303801-12303820 MS.gene034438:CDS 40.0%
TTAGTTGAAGACGGCTGATT+TGG - chr2.3:12303160-12303179 None:intergenic 40.0%
TTGGTCGTTGAAAAGGATTC+CGG - chr2.3:12303623-12303642 None:intergenic 40.0%
! AAATATGCTGGAGTGCTCTT+TGG + chr2.3:12303961-12303980 MS.gene034438:CDS 40.0%
! CAAACTTGACGGATCACAAT+AGG - chr2.3:12303184-12303203 None:intergenic 40.0%
!! AGGTATAGTGACATCGACTT+TGG - chr2.3:12303308-12303327 None:intergenic 40.0%
!! CTGGTTAGCTTTCGATAAGA+TGG + chr2.3:12303900-12303919 MS.gene034438:CDS 40.0%
!! GGTATAGTGACATCGACTTT+GGG - chr2.3:12303307-12303326 None:intergenic 40.0%
AGAAACTCCTCTAAGCGAGA+TGG - chr2.3:12303718-12303737 None:intergenic 45.0%
ATTGCTCGTACGAATCCATG+TGG - chr2.3:12303342-12303361 None:intergenic 45.0%
CCTTACATTAACCGACGACA+AGG + chr2.3:12303411-12303430 MS.gene034438:CDS 45.0%
CTACAAGTGAGTCATGCAGT+CGG + chr2.3:12303841-12303860 MS.gene034438:CDS 45.0%
GAAGTTACCATCTCGCTTAG+AGG + chr2.3:12303708-12303727 MS.gene034438:CDS 45.0%
GTTCAAAGTCGATCCCTTGA+TGG - chr2.3:12303546-12303565 None:intergenic 45.0%
TACAAGTGAGTCATGCAGTC+GGG + chr2.3:12303842-12303861 MS.gene034438:CDS 45.0%
! AAGGGCAATCTTCCCGATTT+TGG + chr2.3:12303430-12303449 MS.gene034438:CDS 45.0%
! CCTTGTCGTCGGTTAATGTA+AGG - chr2.3:12303414-12303433 None:intergenic 45.0%
! TGGTGAAAGCTTTTACTGGG+AGG + chr2.3:12303686-12303705 MS.gene034438:CDS 45.0%
!! AATGTAAGGCCGACTTGGAT+AGG - chr2.3:12303400-12303419 None:intergenic 45.0%
AGTTGTACGACAGTCTGGAG+CGG + chr2.3:12303806-12303825 MS.gene034438:CDS 50.0%
CGGTTAATGTAAGGCCGACT+TGG - chr2.3:12303405-12303424 None:intergenic 50.0%
GAATTCTCATCAAGCCGGCT+CGG + chr2.3:12303864-12303883 MS.gene034438:CDS 50.0%
GGTCAACAAACTATCCGAGC+CGG - chr2.3:12303881-12303900 None:intergenic 50.0%
GTCGGGAATTCTCATCAAGC+CGG + chr2.3:12303859-12303878 MS.gene034438:CDS 50.0%
! TGCTGGAGTGCTCTTTGGAT+TGG + chr2.3:12303966-12303985 MS.gene034438:CDS 50.0%
!! GCTCGGATAGTTTGTTGACC+TGG + chr2.3:12303881-12303900 MS.gene034438:CDS 50.0%
!! TGACATCGACTTTGGGTGCA+TGG - chr2.3:12303300-12303319 None:intergenic 50.0%
GCTCGTACGAATCCATGTGG+CGG - chr2.3:12303339-12303358 None:intergenic 55.0%
GGGAAGATTGCCCTTGTCGT+CGG - chr2.3:12303425-12303444 None:intergenic 55.0%
TTGGGTGCATGGATGACACC+AGG - chr2.3:12303289-12303308 None:intergenic 55.0%
! GTTGTACGACAGTCTGGAGC+GGG + chr2.3:12303807-12303826 MS.gene034438:CDS 55.0%
ACCTTACCACCTCCGCCACA+TGG + chr2.3:12303324-12303343 MS.gene034438:CDS 60.0%
CGTACGAATCCATGTGGCGG+AGG - chr2.3:12303336-12303355 None:intergenic 60.0%
! ACGAATCCATGTGGCGGAGG+TGG - chr2.3:12303333-12303352 None:intergenic 60.0%
! TCCATGTGGCGGAGGTGGTA+AGG - chr2.3:12303328-12303347 None:intergenic 60.0%
! GTACGACAGTCTGGAGCGGG+TGG + chr2.3:12303810-12303829 MS.gene034438:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 12303145 12304005 12303145 ID=MS.gene034438
chr2.3 mRNA 12303145 12304005 12303145 ID=MS.gene034438.t1;Parent=MS.gene034438
chr2.3 exon 12303145 12304005 12303145 ID=MS.gene034438.t1.exon1;Parent=MS.gene034438.t1
chr2.3 CDS 12303145 12304005 12303145 ID=cds.MS.gene034438.t1;Parent=MS.gene034438.t1
Gene Sequence

>MS.gene034438

ATGAGCAGCAAGCCAAATCAGCCGTCTTCAACTAAACCTATTGTGATCCGTCAAGTTTGGTCTGACAATTTAGATTTAGAATTTGCTTATATCCGTAGCATCTTTCGCAAGTTTCGTTACATATCAATGTTTACAAAATTTCCTGGTGTCATCCATGCACCCAAAGTCGATGTCACTATACCTTACCACCTCCGCCACATGGATTCGTACGAGCAATACTCATATTTGAAGGCTAACGTCGATGATTTGAAACCTATCCAAGTCGGCCTTACATTAACCGACGACAAGGGCAATCTTCCCGATTTTGGAACAGATAACTCCTACATATGGGAGTTCAATTTCAATGATTTTGATGTTGAACATGATCTTCAAAATCCAGACTCAGTTAATCTACTCTGCCATCAAGGGATCGACTTTGAACGCAATCGTTTATGTGGTGTCAGCTCTTCTCAGTTTGCTGAATTAATGTTCTCTTCCGGAATCCTTTTCAACGACCAAGTTGTTTGGGTGACTTTTCATAGCTCGTATGATTTCGGATATTTGGTGAAAGCTTTTACTGGGAGGAAGTTACCATCTCGCTTAGAGGAGTTTCTACGTCTCTTGACACAATTGTTTGGAAAAAATGTATTCGACATCAAGTATATGATCAAGCATTGTAATGAGTTGTACGACAGTCTGGAGCGGGTGGCTAAATCACTACAAGTGAGTCATGCAGTCGGGAATTCTCATCAAGCCGGCTCGGATAGTTTGTTGACCTGGTTAGCTTTCGATAAGATGGTCGACACTCATTTCATCAACAACAAAATCAACATCAACAAATATGCTGGAGTGCTCTTTGGATTGGAATTAACAGCAGCTTAA
Protein sequence

>MS.gene034438.t1

MSSKPNQPSSTKPIVIRQVWSDNLDLEFAYIRSIFRKFRYISMFTKFPGVIHAPKVDVTIPYHLRHMDSYEQYSYLKANVDDLKPIQVGLTLTDDKGNLPDFGTDNSYIWEFNFNDFDVEHDLQNPDSVNLLCHQGIDFERNRLCGVSSSQFAELMFSSGILFNDQVVWVTFHSSYDFGYLVKAFTGRKLPSRLEEFLRLLTQLFGKNVFDIKYMIKHCNELYDSLERVAKSLQVSHAVGNSHQAGSDSLLTWLAFDKMVDTHFINNKININKYAGVLFGLELTAA