AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene025858

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025858.t1 MTR_7g118230 76.705 176 7 2 60 235 33 174 1.33e-79 243
MS.gene025858.t1 MTR_1g045510 36.310 168 96 2 70 237 113 269 1.28e-24 99.8
MS.gene025858.t1 MTR_1g056520 34.783 184 95 4 55 231 101 266 2.98e-23 96.3
MS.gene025858.t1 MTR_7g106440 31.073 177 119 2 57 231 96 271 1.46e-20 89.4
MS.gene025858.t1 MTR_3g027140 31.677 161 107 2 71 231 61 218 2.35e-20 87.0
MS.gene025858.t1 MTR_1g097440 34.783 161 90 4 62 222 113 258 2.35e-16 78.6
MS.gene025858.t1 MTR_1g064230 29.796 245 138 7 9 230 21 254 8.34e-15 72.8
MS.gene025858.t1 MTR_4g104470 29.193 161 106 3 71 231 123 275 1.03e-14 72.8
MS.gene025858.t1 MTR_4g104470 42.697 89 49 1 60 148 208 294 3.76e-14 70.9
MS.gene025858.t1 MTR_3g075500 31.492 181 108 5 59 236 104 271 1.09e-14 72.0
MS.gene025858.t1 MTR_3g075500 30.061 163 105 3 71 231 110 265 1.70e-14 72.0
MS.gene025858.t1 MTR_3g075500 38.889 90 51 2 55 143 193 279 2.40e-12 65.9
MS.gene025858.t1 MTR_7g118120 24.277 173 106 3 52 220 83 234 8.97e-12 64.7
MS.gene025858.t1 MTR_6g040190 31.788 151 87 5 72 222 115 249 1.01e-11 64.7
MS.gene025858.t1 MTR_2g097960 26.543 162 107 5 72 231 17 168 4.40e-11 62.8
MS.gene025858.t1 MTR_4g085540 27.879 165 96 5 62 222 117 262 4.82e-11 62.8
MS.gene025858.t1 MTR_6g040070 30.464 151 92 3 72 222 17 154 6.65e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025858.t1 AT1G01080 54.696 181 74 3 64 239 102 279 1.74e-61 195
MS.gene025858.t1 AT1G01080 54.802 177 72 3 64 235 102 275 1.72e-59 190
MS.gene025858.t1 AT1G01080 54.494 178 72 4 64 235 102 276 7.94e-58 186
MS.gene025858.t1 AT3G52150 30.288 208 126 5 37 230 33 235 3.33e-21 89.7
MS.gene025858.t1 AT3G52150 30.288 208 126 5 37 230 33 235 3.33e-21 89.7
MS.gene025858.t1 AT1G60000 30.040 253 136 9 1 230 1 235 2.21e-20 87.8
MS.gene025858.t1 AT3G52380 31.138 167 112 3 67 231 113 278 1.63e-19 86.7
MS.gene025858.t1 AT5G50250 31.214 173 105 4 59 231 108 266 3.09e-17 79.7
MS.gene025858.t1 AT5G50250 39.560 91 53 1 58 148 197 285 2.71e-13 68.6
MS.gene025858.t1 AT2G37220 27.807 187 102 3 61 225 82 257 1.34e-15 75.1
MS.gene025858.t1 AT4G24770 32.919 161 100 3 71 231 151 303 2.11e-14 72.0
MS.gene025858.t1 AT4G24770 42.308 78 45 0 71 148 245 322 3.38e-13 68.6
MS.gene025858.t1 AT4G24770 32.919 161 100 3 71 231 151 303 2.11e-14 72.0
MS.gene025858.t1 AT4G24770 42.308 78 45 0 71 148 245 322 3.38e-13 68.6
MS.gene025858.t1 AT1G22760 28.436 211 132 5 34 238 103 300 2.09e-13 70.1
MS.gene025858.t1 AT1G71770 28.708 209 130 5 36 238 115 310 5.07e-13 68.9
MS.gene025858.t1 AT1G71770 28.708 209 130 5 36 238 115 310 5.07e-13 68.9
MS.gene025858.t1 AT2G35410 30.769 208 134 6 27 231 54 254 1.96e-12 66.2
MS.gene025858.t1 AT3G16380 29.480 173 108 4 72 243 23 182 9.22e-12 65.1
MS.gene025858.t1 AT2G23350 27.922 154 89 4 72 220 136 272 5.41e-11 62.8
MS.gene025858.t1 AT1G49760 27.072 181 111 3 70 244 45 210 7.58e-11 62.4
MS.gene025858.t1 AT1G49760 27.072 181 111 3 70 244 45 210 7.58e-11 62.4

Find 59 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGACATCTCTTTGGTAAATT+TGG 0.099306 7.1:-366183 MS.gene025858:CDS
AAGAGATGTCTCACGTCTTC+AGG 0.315903 7.1:+366195 None:intergenic
TGTTGAGTATCACAGCTTCT+AGG 0.370545 7.1:+366666 None:intergenic
TCTCACCAGTCTCTGCATTT+CGG 0.377067 7.1:+366520 None:intergenic
CAGAGACTGGTGAGAGTAAA+GGG 0.393341 7.1:-366512 MS.gene025858:CDS
CTCCAAGTAGTGGCTGCTTA+TGG 0.394918 7.1:+366838 None:intergenic
TACCATAAGCAGCCACTACT+TGG 0.428423 7.1:-366840 MS.gene025858:CDS
TGCAGACGTAAACTTGGGTT+GGG 0.442375 7.1:+366694 None:intergenic
GGTGTTGCAAGATTTCAATC+AGG 0.443133 7.1:-366142 MS.gene025858:CDS
TAACGAAGAGGAAGAGAAAG+AGG 0.445652 7.1:+366866 None:intergenic
TTCCCAACATACACCTTATG+AGG 0.456223 7.1:+366237 None:intergenic
GAAGGTTGCAGACGTAAACT+TGG 0.462333 7.1:+366688 None:intergenic
TGTTGGTGGGCGCGAAATGC+GGG 0.472414 7.1:-366340 MS.gene025858:CDS
CTTTGGTAAATTTGGAAATG+TGG 0.479793 7.1:-366175 MS.gene025858:CDS
GCAGAGACTGGTGAGAGTAA+AGG 0.480321 7.1:-366513 MS.gene025858:CDS
GTCCTCATAAGGTGTATGTT+GGG 0.485859 7.1:-366239 MS.gene025858:CDS
TTGCAGACGTAAACTTGGGT+TGG 0.485972 7.1:+366693 None:intergenic
GCTGCAAGAACAAGACTAGT+AGG 0.498268 7.1:+365984 None:intergenic
ATACTATGAAGGTCCTCATA+AGG 0.498833 7.1:-366250 MS.gene025858:CDS
GAAGACGTGAGACATCTCTT+TGG 0.500754 7.1:-366192 MS.gene025858:CDS
AATGCAATTGCTGCATTGGA+TGG 0.502487 7.1:-366450 MS.gene025858:CDS
GGGAGTGCTTATGTCACAAT+GGG 0.508546 7.1:-366492 MS.gene025858:CDS
TCGTTTGAATTGAAGGATGT+TGG 0.510713 7.1:-366357 MS.gene025858:intron
ACAACCACGTAAGTTGAAGC+TGG 0.512125 7.1:-366721 MS.gene025858:CDS
CGCGAGGAGAAAGAAGGATA+AGG 0.512495 7.1:+366777 None:intergenic
GGTCCTCATAAGGTGTATGT+TGG 0.523656 7.1:-366240 MS.gene025858:CDS
GAAACACAGAGTAGCAGAGT+TGG 0.527590 7.1:+366890 None:intergenic
GTATATAGTTCTTCTTCTCA+CGG 0.533646 7.1:+366269 None:intergenic
AGAAGAACTATATACTATGA+AGG 0.536527 7.1:-366261 MS.gene025858:CDS
ATGTTGGTGGGCGCGAAATG+CGG 0.539679 7.1:-366341 MS.gene025858:CDS
TATATAGTTCTTCTTCTCAC+GGG 0.541659 7.1:+366270 None:intergenic
CAACCACGTAAGTTGAAGCT+GGG 0.548485 7.1:-366720 MS.gene025858:CDS
AAGCAGCCACTACTTGGAGT+TGG 0.552480 7.1:-366834 MS.gene025858:CDS
GAGGAGTGAAGAGATGAAGT+AGG 0.557135 7.1:+366643 None:intergenic
CTGTGACGCGAGGAGAAAGA+AGG 0.561006 7.1:+366771 None:intergenic
GTGTTGCAAGATTTCAATCA+GGG 0.561480 7.1:-366141 MS.gene025858:CDS
TTTGAATTGAAGGATGTTGG+TGG 0.563904 7.1:-366354 MS.gene025858:intron
GTTTGCCGAAATGCAGAGAC+TGG 0.571702 7.1:-366525 MS.gene025858:CDS
TTGAATTGAAGGATGTTGGT+GGG 0.579799 7.1:-366353 MS.gene025858:intron
GGTTTCATTGAGGGACAAAG+AGG 0.584074 7.1:+366062 None:intergenic
GAGTATCCAACTCCAAGTAG+TGG 0.587862 7.1:+366828 None:intergenic
GAGTATCACAGCTTCTAGGA+AGG 0.590293 7.1:+366670 None:intergenic
CTTCATCTCTTCACTCCTCA+CGG 0.594839 7.1:-366639 MS.gene025858:CDS
TTCCCCAGCTTCAACTTACG+TGG 0.601446 7.1:+366717 None:intergenic
AGGGAGTGCTTATGTCACAA+TGG 0.612091 7.1:-366493 MS.gene025858:CDS
AAGGTTGCAGACGTAAACTT+GGG 0.613456 7.1:+366689 None:intergenic
TTGAGAGAGATAAGAGACAA+AGG 0.615725 7.1:+366098 None:intergenic
AATGGACGCGCTGTGACGCG+AGG 0.621619 7.1:+366761 None:intergenic
TGGAAATGTGGCTAGTGTGA+GGG 0.626364 7.1:-366163 MS.gene025858:CDS
ATAGTTCTTCTTCTCACGGG+AGG 0.629773 7.1:+366273 None:intergenic
AATTGCTGCATTGGATGGAT+CGG 0.641488 7.1:-366445 MS.gene025858:intron
TTGGAAATGTGGCTAGTGTG+AGG 0.645229 7.1:-366164 MS.gene025858:CDS
ACGTACCTCGGTAGATAGAA+CGG 0.653839 7.1:+366614 None:intergenic
AACCACGTAAGTTGAAGCTG+GGG 0.663989 7.1:-366719 MS.gene025858:CDS
TGTTGCAAGATTTCAATCAG+GGG 0.681995 7.1:-366140 MS.gene025858:CDS
CTTATGGTAGAGTAACGAAG+AGG 0.714741 7.1:+366854 None:intergenic
AAGAGACAAAGGCATAGACA+CGG 0.730141 7.1:+366109 None:intergenic
GTAGATAGAACGGTACCGTG+AGG 0.731002 7.1:+366624 None:intergenic
CGGTACCGTTCTATCTACCG+AGG 0.742490 7.1:-366619 MS.gene025858:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CATTATTACTTGTAATGTAA+TGG - chr7.1:366322-366341 MS.gene025858:CDS 20.0%
! AGAAGAACTATATACTATGA+AGG - chr7.1:366635-366654 MS.gene025858:CDS 25.0%
!! ATATTTTACGGTTTCATTGA+GGG + chr7.1:366846-366865 None:intergenic 25.0%
!!! TTGTTTTTCGTTTGAATTGA+AGG - chr7.1:366532-366551 MS.gene025858:intron 25.0%
AGACATCTCTTTGGTAAATT+TGG - chr7.1:366713-366732 MS.gene025858:CDS 30.0%
CTTTGGTAAATTTGGAAATG+TGG - chr7.1:366721-366740 MS.gene025858:CDS 30.0%
GCAGTAGAAAAAGTGAAAAA+AGG + chr7.1:366876-366895 None:intergenic 30.0%
GTAGAAAAAGTGAAAAAAGG+TGG + chr7.1:366873-366892 None:intergenic 30.0%
GTATATAGTTCTTCTTCTCA+CGG + chr7.1:366630-366649 None:intergenic 30.0%
TAAAAATGCAATTGCTGCAT+TGG - chr7.1:366442-366461 MS.gene025858:intron 30.0%
TATATAGTTCTTCTTCTCAC+GGG + chr7.1:366629-366648 None:intergenic 30.0%
! CATATTTTACGGTTTCATTG+AGG + chr7.1:366847-366866 None:intergenic 30.0%
! TTCTTCTTCGTTTTCTACAA+TGG + chr7.1:366156-366175 None:intergenic 30.0%
ATACTATGAAGGTCCTCATA+AGG - chr7.1:366646-366665 MS.gene025858:CDS 35.0%
GAAAAAGTGAAAAAAGGTGG+AGG + chr7.1:366870-366889 None:intergenic 35.0%
GTGTTGCAAGATTTCAATCA+GGG - chr7.1:366755-366774 MS.gene025858:CDS 35.0%
TCGTTTGAATTGAAGGATGT+TGG - chr7.1:366539-366558 MS.gene025858:intron 35.0%
TGTTGCAAGATTTCAATCAG+GGG - chr7.1:366756-366775 MS.gene025858:CDS 35.0%
TTGAATTGAAGGATGTTGGT+GGG - chr7.1:366543-366562 MS.gene025858:intron 35.0%
TTGAGAGAGATAAGAGACAA+AGG + chr7.1:366801-366820 None:intergenic 35.0%
TTTGAATTGAAGGATGTTGG+TGG - chr7.1:366542-366561 MS.gene025858:intron 35.0%
! TTATAATGCTGTGCTGTTGT+AGG - chr7.1:366349-366368 MS.gene025858:intron 35.0%
!! AAAGGTGGAGGCATATTTTA+CGG + chr7.1:366858-366877 None:intergenic 35.0%
AAGGTTGCAGACGTAAACTT+GGG + chr7.1:366210-366229 None:intergenic 40.0%
AATGCAATTGCTGCATTGGA+TGG - chr7.1:366446-366465 MS.gene025858:CDS 40.0%
AATTGCTGCATTGGATGGAT+CGG - chr7.1:366451-366470 MS.gene025858:CDS 40.0%
AGCAACATACTTACGTACCT+CGG + chr7.1:366297-366316 None:intergenic 40.0%
CTTATGGTAGAGTAACGAAG+AGG + chr7.1:366045-366064 None:intergenic 40.0%
GTCCTCATAAGGTGTATGTT+GGG - chr7.1:366657-366676 MS.gene025858:CDS 40.0%
TAACGAAGAGGAAGAGAAAG+AGG + chr7.1:366033-366052 None:intergenic 40.0%
TGTTGAGTATCACAGCTTCT+AGG + chr7.1:366233-366252 None:intergenic 40.0%
TTCCCAACATACACCTTATG+AGG + chr7.1:366662-366681 None:intergenic 40.0%
! AAGAGACAAAGGCATAGACA+CGG + chr7.1:366790-366809 None:intergenic 40.0%
! GGTGTTGCAAGATTTCAATC+AGG - chr7.1:366754-366773 MS.gene025858:CDS 40.0%
AAGAGATGTCTCACGTCTTC+AGG + chr7.1:366704-366723 None:intergenic 45.0%
ACGTACCTCGGTAGATAGAA+CGG + chr7.1:366285-366304 None:intergenic 45.0%
ATAGTTCTTCTTCTCACGGG+AGG + chr7.1:366626-366645 None:intergenic 45.0%
CAGAGACTGGTGAGAGTAAA+GGG - chr7.1:366384-366403 MS.gene025858:intron 45.0%
CTTCATCTCTTCACTCCTCA+CGG - chr7.1:366257-366276 MS.gene025858:CDS 45.0%
GAAACACAGAGTAGCAGAGT+TGG + chr7.1:366009-366028 None:intergenic 45.0%
GAAGACGTGAGACATCTCTT+TGG - chr7.1:366704-366723 MS.gene025858:CDS 45.0%
GAAGGTTGCAGACGTAAACT+TGG + chr7.1:366211-366230 None:intergenic 45.0%
GAGGAGTGAAGAGATGAAGT+AGG + chr7.1:366256-366275 None:intergenic 45.0%
GAGTATCCAACTCCAAGTAG+TGG + chr7.1:366071-366090 None:intergenic 45.0%
GGTCCTCATAAGGTGTATGT+TGG - chr7.1:366656-366675 MS.gene025858:CDS 45.0%
GGTTTCATTGAGGGACAAAG+AGG + chr7.1:366837-366856 None:intergenic 45.0%
TACCATAAGCAGCCACTACT+TGG - chr7.1:366056-366075 MS.gene025858:CDS 45.0%
TCTCACCAGTCTCTGCATTT+CGG + chr7.1:366379-366398 None:intergenic 45.0%
TGCAGACGTAAACTTGGGTT+GGG + chr7.1:366205-366224 None:intergenic 45.0%
TGGAAATGTGGCTAGTGTGA+GGG - chr7.1:366733-366752 MS.gene025858:CDS 45.0%
TTGCAGACGTAAACTTGGGT+TGG + chr7.1:366206-366225 None:intergenic 45.0%
TTGGAAATGTGGCTAGTGTG+AGG - chr7.1:366732-366751 MS.gene025858:CDS 45.0%
! AACCACGTAAGTTGAAGCTG+GGG - chr7.1:366177-366196 MS.gene025858:CDS 45.0%
! ACAACCACGTAAGTTGAAGC+TGG - chr7.1:366175-366194 MS.gene025858:CDS 45.0%
! CAACCACGTAAGTTGAAGCT+GGG - chr7.1:366176-366195 MS.gene025858:CDS 45.0%
! GAGTATCACAGCTTCTAGGA+AGG + chr7.1:366229-366248 None:intergenic 45.0%
!! AGGGAGTGCTTATGTCACAA+TGG - chr7.1:366403-366422 MS.gene025858:intron 45.0%
!! GGGAGTGCTTATGTCACAAT+GGG - chr7.1:366404-366423 MS.gene025858:intron 45.0%
AAGCAGCCACTACTTGGAGT+TGG - chr7.1:366062-366081 MS.gene025858:CDS 50.0%
CGCGAGGAGAAAGAAGGATA+AGG + chr7.1:366122-366141 None:intergenic 50.0%
CTCCAAGTAGTGGCTGCTTA+TGG + chr7.1:366061-366080 None:intergenic 50.0%
GCAGAGACTGGTGAGAGTAA+AGG - chr7.1:366383-366402 MS.gene025858:intron 50.0%
GTAGATAGAACGGTACCGTG+AGG + chr7.1:366275-366294 None:intergenic 50.0%
GTTTGCCGAAATGCAGAGAC+TGG - chr7.1:366371-366390 MS.gene025858:intron 50.0%
TTCCCCAGCTTCAACTTACG+TGG + chr7.1:366182-366201 None:intergenic 50.0%
CGGTACCGTTCTATCTACCG+AGG - chr7.1:366277-366296 MS.gene025858:CDS 55.0%
CTGTGACGCGAGGAGAAAGA+AGG + chr7.1:366128-366147 None:intergenic 55.0%
! ATGTTGGTGGGCGCGAAATG+CGG - chr7.1:366555-366574 MS.gene025858:intron 55.0%
! TGTTGGTGGGCGCGAAATGC+GGG - chr7.1:366556-366575 MS.gene025858:intron 60.0%
AATGGACGCGCTGTGACGCG+AGG + chr7.1:366138-366157 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr7.1 gene 365999 366919 365999 ID=MS.gene025858
chr7.1 mRNA 365999 366919 365999 ID=MS.gene025858.t1;Parent=MS.gene025858
chr7.1 exon 366620 366919 366620 ID=MS.gene025858.t1.exon1;Parent=MS.gene025858.t1
chr7.1 CDS 366620 366919 366620 ID=cds.MS.gene025858.t1;Parent=MS.gene025858.t1
chr7.1 exon 366446 366547 366446 ID=MS.gene025858.t1.exon2;Parent=MS.gene025858.t1
chr7.1 CDS 366446 366547 366446 ID=cds.MS.gene025858.t1;Parent=MS.gene025858.t1
chr7.1 exon 365999 366364 365999 ID=MS.gene025858.t1.exon3;Parent=MS.gene025858.t1
chr7.1 CDS 365999 366364 365999 ID=cds.MS.gene025858.t1;Parent=MS.gene025858.t1
Gene Sequence

>MS.gene025858

ATGGCTGCCAACTCTGCTACTCTGTGTTTCTCCTCTTTCTCTTCCTCTTCGTTACTCTACCATAAGCAGCCACTACTTGGAGTTGGATACTCAAAACGATTCGTTTCGTTTTCTGCGCTGCCTTATCCTTCTTTCTCCTCGCGTCACAGCGCGTCCATTGTAGAAAACGAAGAAGAACAACCACGTAAGTTGAAGCTGGGGAACCCAACCCAAGTTTACGTCTGCAACCTTCCTAGAAGCTGTGATACTCAACACCTACTTCATCTCTTCACTCCTCACGGTACCGTTCTATCTACCGAGGTACGTAAGTATGTTGCTTTCTTCATTATTACTTGTAATGTAATGGAATCTTATAATGCTGTGCTGTTGTAGGTTTGCCGAAATGCAGAGACTGGTGAGAGTAAAGGGAGTGCTTATGTCACAATGGGATCTTATAATGCTGCTAAAAATGCAATTGCTGCATTGGATGGATCGGTTAGTCACTATCATATCTAATAAATGCACTTGCTGCAATGCATCTGAATAATGAAACTTTGTTTTTCGTTTGAATTGAAGGATGTTGGTGGGCGCGAAATGCGGGTTAAATTTTCTGTTGAGATGAATAATTTAGAGACATTGAACTCACCTCCCGTGAGAAGAAGAACTATATACTATGAAGGTCCTCATAAGGTGTATGTTGGGAATCTCGCTAAGTCTGCTACACCTGAAGACGTGAGACATCTCTTTGGTAAATTTGGAAATGTGGCTAGTGTGAGGGTGTTGCAAGATTTCAATCAGGGGAAAAAAAGCCGTGTCTATGCCTTTGTCTCTTATCTCTCTCAAAGAGAACGTGACGCCTCTTTGTCCCTCAATGAAACCGTAAAATATGCCTCCACCTTTTTTCACTTTTTCTACTGCTTATTTCTATCTCATGCCTACTAG
Protein sequence

>MS.gene025858.t1

MAANSATLCFSSFSSSSLLYHKQPLLGVGYSKRFVSFSALPYPSFSSRHSASIVENEEEQPRKLKLGNPTQVYVCNLPRSCDTQHLLHLFTPHGTVLSTEVCRNAETGESKGSAYVTMGSYNAAKNAIAALDGSDVGGREMRVKFSVEMNNLETLNSPPVRRRTIYYEGPHKVYVGNLAKSATPEDVRHLFGKFGNVASVRVLQDFNQGKKSRVYAFVSYLSQRERDASLSLNETVKYASTFFHFFYCLFLSHAY