AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene059669

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059669.t1 MTR_5g014400 96.667 180 5 1 1 180 73 251 2.42e-127 358
MS.gene059669.t1 MTR_2g076060 87.805 41 5 0 5 45 47 87 3.43e-22 89.7
MS.gene059669.t1 MTR_4g021270 37.805 164 69 6 5 140 56 214 5.88e-20 85.5
MS.gene059669.t1 MTR_3g068095 86.842 38 5 0 5 42 52 89 6.24e-19 81.6
MS.gene059669.t1 MTR_5g080660 74.419 43 11 0 3 45 42 84 9.36e-19 80.9
MS.gene059669.t1 MTR_1g070265 80.000 40 8 0 3 42 30 69 1.82e-18 79.0
MS.gene059669.t1 MTR_1g070250 31.977 172 97 5 8 177 38 191 1.19e-14 68.9
MS.gene059669.t1 MTR_7g063220 76.471 34 8 0 8 41 24 57 5.53e-14 65.9
MS.gene059669.t1 MTR_4g064873 32.749 171 85 4 7 177 20 160 6.48e-14 66.6
MS.gene059669.t1 MTR_1g075430 31.551 187 88 9 8 174 18 184 1.80e-12 63.2
MS.gene059669.t1 MTR_1g044225 43.548 62 26 1 8 60 26 87 8.62e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059669.t1 AT4G17810 41.885 191 71 7 2 177 38 203 4.52e-31 112
MS.gene059669.t1 AT4G17810 39.674 184 55 9 2 177 38 173 2.07e-23 91.7
MS.gene059669.t1 AT5G06070 37.306 193 81 8 5 177 50 222 2.27e-23 92.8
MS.gene059669.t1 AT2G37740 68.421 57 14 1 2 54 31 87 1.77e-20 86.7
MS.gene059669.t1 AT3G23130 79.070 43 9 0 1 43 38 80 9.95e-20 82.8
MS.gene059669.t1 AT2G42410 35.979 189 82 6 5 174 44 212 1.22e-19 82.8
MS.gene059669.t1 AT2G42410 35.979 189 82 6 5 174 44 212 1.22e-19 82.8
MS.gene059669.t1 AT2G42410 67.925 53 17 0 5 57 70 122 2.00e-19 82.8
MS.gene059669.t1 AT3G09290 31.792 173 70 7 8 174 33 163 3.45e-13 64.7
MS.gene059669.t1 AT3G53820 63.889 36 13 0 7 42 18 53 3.43e-11 58.5

Find 39 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAAAAGCATTATTATTATT+AGG 0.154031 5.1:-7185477 None:intergenic
TATTATTAGGGTTTGGTAAA+TGG 0.178618 5.1:-7185464 None:intergenic
ATTTGCATCATCAAATTATT+TGG 0.195764 5.1:-7185576 None:intergenic
CAAAAGCATTATTATTATTA+GGG 0.268434 5.1:-7185476 None:intergenic
TTAACGGTGGTTGGCTTTGA+TGG 0.294750 5.1:-7185362 None:intergenic
CTTGATCTTGAGCTCCGTTT+AGG 0.296503 5.1:+7185744 MS.gene059669:CDS
TACAATAGTTCTAGTCCTAA+TGG 0.356996 5.1:+7185504 MS.gene059669:CDS
TTGATCTTGAGCTCCGTTTA+GGG 0.364351 5.1:+7185745 MS.gene059669:CDS
GAGATTGAGAGAAAAGTAGA+AGG 0.386084 5.1:-7185534 None:intergenic
GTAGAAGGAGATTCTCCATT+AGG 0.392764 5.1:-7185519 None:intergenic
TTCATGACCGTTATCATCAA+TGG 0.401936 5.1:-7185712 None:intergenic
GCATTATTATTATTAGGGTT+TGG 0.403821 5.1:-7185471 None:intergenic
CAAGAGCTTGTTGCTAATGC+TGG 0.417258 5.1:+7185426 MS.gene059669:CDS
GTGTTGGCTTGTTCCCTAAA+CGG 0.435644 5.1:-7185758 None:intergenic
TCCACTTGAAAATTAAAAGA+TGG 0.441538 5.1:-7185612 None:intergenic
ATTAGGACTAGAACTATTGT+AGG 0.449818 5.1:-7185502 None:intergenic
TTCCGGTCAGCTCAAGCTCT+TGG 0.471669 5.1:+7185300 MS.gene059669:CDS
GAGATGAATTTAACGGTGGT+TGG 0.484111 5.1:-7185371 None:intergenic
TGCATCATCAAATTATTTGG+AGG 0.491401 5.1:-7185573 None:intergenic
GGTTTGGTAAATGGTAAAGA+AGG 0.506848 5.1:-7185455 None:intergenic
CGGTCAGCTCAAGCTCTTGG+TGG 0.515963 5.1:+7185303 MS.gene059669:CDS
GATGGAGACGAGCACGGTCG+CGG 0.516231 5.1:-7185344 None:intergenic
CACCAAGAGCTTGAGCTGAC+CGG 0.533757 5.1:-7185302 None:intergenic
TGTGGAGGAATATTTATGAA+TGG 0.545539 5.1:-7185405 None:intergenic
GAAGGATGAGATGAATTTAA+CGG 0.547030 5.1:-7185378 None:intergenic
AGGTGCAAGTAGCATGTTGA+TGG 0.551205 5.1:-7185689 None:intergenic
TGCACCTCCATTGATGATAA+CGG 0.570866 5.1:+7185705 MS.gene059669:CDS
GCATTAGCAACAAGCTCTTG+TGG 0.586992 5.1:-7185423 None:intergenic
GGCTTTGATGGAGACGAGCA+CGG 0.589738 5.1:-7185350 None:intergenic
ATATTTATGAATGGTGATGA+AGG 0.596989 5.1:-7185396 None:intergenic
GTGCAGGTATAAGACCTTGG+TGG 0.619194 5.1:-7185261 None:intergenic
AAAGTGCAGGTATAAGACCT+TGG 0.621514 5.1:-7185264 None:intergenic
TTCAAGTGGATAATTCAGCT+AGG 0.628424 5.1:+7185625 MS.gene059669:CDS
ATGACCGTTATCATCAATGG+AGG 0.643461 5.1:-7185709 None:intergenic
TGAACACAACATGGCCACCA+AGG 0.646071 5.1:+7185247 MS.gene059669:CDS
GGAGACGAGCACGGTCGCGG+CGG 0.650175 5.1:-7185341 None:intergenic
TTAGCAACAAGCTCTTGTGG+AGG 0.690594 5.1:-7185420 None:intergenic
GGAATATTATGAACACAACA+TGG 0.697427 5.1:+7185238 None:intergenic
GGATGAGATGAATTTAACGG+TGG 0.714956 5.1:-7185375 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAAAAGCATTATTATTATTA+GGG - chr5.1:7185479-7185498 None:intergenic 15.0%
!! ATTTGCATCATCAAATTATT+TGG - chr5.1:7185579-7185598 None:intergenic 20.0%
!!! GCAAAAGCATTATTATTATT+AGG - chr5.1:7185480-7185499 None:intergenic 20.0%
! GCATTATTATTATTAGGGTT+TGG - chr5.1:7185474-7185493 None:intergenic 25.0%
! TCCACTTGAAAATTAAAAGA+TGG - chr5.1:7185615-7185634 None:intergenic 25.0%
!! ATATTTATGAATGGTGATGA+AGG - chr5.1:7185399-7185418 None:intergenic 25.0%
!! TATTATTAGGGTTTGGTAAA+TGG - chr5.1:7185467-7185486 None:intergenic 25.0%
!!! TCCATCTTTTAATTTTCAAG+TGG + chr5.1:7185611-7185630 MS.gene059669:CDS 25.0%
ATTAGGACTAGAACTATTGT+AGG - chr5.1:7185505-7185524 None:intergenic 30.0%
GAAGGATGAGATGAATTTAA+CGG - chr5.1:7185381-7185400 None:intergenic 30.0%
TGCATCATCAAATTATTTGG+AGG - chr5.1:7185576-7185595 None:intergenic 30.0%
TGTGGAGGAATATTTATGAA+TGG - chr5.1:7185408-7185427 None:intergenic 30.0%
!! TACAATAGTTCTAGTCCTAA+TGG + chr5.1:7185504-7185523 MS.gene059669:CDS 30.0%
!! TTCTTCTTTTTCTAGCAAAG+TGG + chr5.1:7185665-7185684 MS.gene059669:CDS 30.0%
GAGATTGAGAGAAAAGTAGA+AGG - chr5.1:7185537-7185556 None:intergenic 35.0%
TTCAAGTGGATAATTCAGCT+AGG + chr5.1:7185625-7185644 MS.gene059669:CDS 35.0%
TTCATGACCGTTATCATCAA+TGG - chr5.1:7185715-7185734 None:intergenic 35.0%
! GGTTTGGTAAATGGTAAAGA+AGG - chr5.1:7185458-7185477 None:intergenic 35.0%
AAAGTGCAGGTATAAGACCT+TGG - chr5.1:7185267-7185286 None:intergenic 40.0%
ATGACCGTTATCATCAATGG+AGG - chr5.1:7185712-7185731 None:intergenic 40.0%
GAGATGAATTTAACGGTGGT+TGG - chr5.1:7185374-7185393 None:intergenic 40.0%
GGATGAGATGAATTTAACGG+TGG - chr5.1:7185378-7185397 None:intergenic 40.0%
GTAGAAGGAGATTCTCCATT+AGG - chr5.1:7185522-7185541 None:intergenic 40.0%
TTGATCTTGAGCTCCGTTTA+GGG + chr5.1:7185745-7185764 MS.gene059669:CDS 40.0%
! CTTTTTGCAGAAGAGAGTTC+CGG + chr5.1:7185283-7185302 MS.gene059669:CDS 40.0%
! TGCACCTCCATTGATGATAA+CGG + chr5.1:7185705-7185724 MS.gene059669:CDS 40.0%
AGGTGCAAGTAGCATGTTGA+TGG - chr5.1:7185692-7185711 None:intergenic 45.0%
CTTGATCTTGAGCTCCGTTT+AGG + chr5.1:7185744-7185763 MS.gene059669:CDS 45.0%
GCATTAGCAACAAGCTCTTG+TGG - chr5.1:7185426-7185445 None:intergenic 45.0%
TTAGCAACAAGCTCTTGTGG+AGG - chr5.1:7185423-7185442 None:intergenic 45.0%
! CTCTCTTCTGCAAAAAGTGC+AGG - chr5.1:7185280-7185299 None:intergenic 45.0%
!! CAAGAGCTTGTTGCTAATGC+TGG + chr5.1:7185426-7185445 MS.gene059669:CDS 45.0%
!! GTGTTGGCTTGTTCCCTAAA+CGG - chr5.1:7185761-7185780 None:intergenic 45.0%
!! TTAACGGTGGTTGGCTTTGA+TGG - chr5.1:7185365-7185384 None:intergenic 45.0%
GTGCAGGTATAAGACCTTGG+TGG - chr5.1:7185264-7185283 None:intergenic 50.0%
TGAACACAACATGGCCACCA+AGG + chr5.1:7185247-7185266 MS.gene059669:CDS 50.0%
CACCAAGAGCTTGAGCTGAC+CGG - chr5.1:7185305-7185324 None:intergenic 55.0%
TTCCGGTCAGCTCAAGCTCT+TGG + chr5.1:7185300-7185319 MS.gene059669:CDS 55.0%
! GGCTTTGATGGAGACGAGCA+CGG - chr5.1:7185353-7185372 None:intergenic 55.0%
CGGTCAGCTCAAGCTCTTGG+TGG + chr5.1:7185303-7185322 MS.gene059669:CDS 60.0%
GATGGAGACGAGCACGGTCG+CGG - chr5.1:7185347-7185366 None:intergenic 65.0%
GGAGACGAGCACGGTCGCGG+CGG - chr5.1:7185344-7185363 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 7185246 7185788 7185246 ID=MS.gene059669
chr5.1 mRNA 7185246 7185788 7185246 ID=MS.gene059669.t1;Parent=MS.gene059669
chr5.1 exon 7185246 7185788 7185246 ID=MS.gene059669.t1.exon1;Parent=MS.gene059669.t1
chr5.1 CDS 7185246 7185788 7185246 ID=cds.MS.gene059669.t1;Parent=MS.gene059669.t1
Gene Sequence

>MS.gene059669

ATGAACACAACATGGCCACCAAGGTCTTATACCTGCACTTTTTGCAGAAGAGAGTTCCGGTCAGCTCAAGCTCTTGGTGGTCACATGAATGTTCACCGCCGCGACCGTGCTCGTCTCCATCAAAGCCAACCACCGTTAAATTCATCTCATCCTTCATCACCATTCATAAATATTCCTCCACAAGAGCTTGTTGCTAATGCTGGATTGTGCCTTCTTTACCATTTACCAAACCCTAATAATAATAATGCTTTTGCTTCCTACAATAGTTCTAGTCCTAATGGAGAATCTCCTTCTACTTTTCTCTCAATCTCATCATCAACATCTTATCCTCCAAATAATTTGATGATGCAAATGCAAACTTGTTCTCCATCTTTTAATTTTCAAGTGGATAATTCAGCTAGGTTGATCAATAATAGCATTTCTTCTTTTTCTAGCAAAGTGGACCATCAACATGCTACTTGCACCTCCATTGATGATAACGGTCATGAAATTGAAGAGCTTGATCTTGAGCTCCGTTTAGGGAACAAGCCAACACCAACTTGA
Protein sequence

>MS.gene059669.t1

MNTTWPPRSYTCTFCRREFRSAQALGGHMNVHRRDRARLHQSQPPLNSSHPSSPFINIPPQELVANAGLCLLYHLPNPNNNNAFASYNSSSPNGESPSTFLSISSSTSYPPNNLMMQMQTCSPSFNFQVDNSARLINNSISSFSSKVDHQHATCTSIDDNGHEIEELDLELRLGNKPTPT