AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene85953

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85953.t1 MTR_2g104900 97.166 247 6 1 1 246 1 247 2.38e-179 492
MS.gene85953.t1 MTR_4g006575 51.867 241 78 14 19 246 9 224 2.50e-54 174
MS.gene85953.t1 MTR_4g006600 51.867 241 78 14 19 246 9 224 2.50e-54 174
MS.gene85953.t1 MTR_1g013130 35.943 281 126 12 1 246 1 262 2.67e-35 127
MS.gene85953.t1 MTR_3g106230 44.379 169 75 8 34 186 25 190 1.92e-32 118
MS.gene85953.t1 MTR_5g077370 67.532 77 17 3 80 155 86 155 9.55e-27 103
MS.gene85953.t1 MTR_1g033340 64.935 77 22 2 81 157 97 168 2.11e-26 103
MS.gene85953.t1 MTR_3g065020 61.728 81 23 3 76 155 80 153 6.91e-25 99.0
MS.gene85953.t1 MTR_4g128340 34.911 169 69 5 78 246 42 169 1.76e-17 77.8
MS.gene85953.t1 MTR_1g107055 36.232 138 69 4 24 159 12 132 2.53e-16 75.1
MS.gene85953.t1 MTR_7g086860 47.761 67 28 2 60 119 2 68 3.11e-12 63.2
MS.gene85953.t1 MTR_7g083210 75.758 33 8 0 81 113 39 71 1.08e-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.gene85953.t1 AT5G10970 39.683 252 120 11 13 246 35 272 6.16e-39 136
MS.gene85953.t1 AT1G80730 40.773 233 94 11 32 246 22 228 1.87e-33 121
MS.gene85953.t1 AT5G25160 40.741 216 99 9 48 246 32 235 4.48e-32 117
MS.gene85953.t1 AT1G24625 39.860 143 50 4 28 170 29 135 8.34e-22 90.1
MS.gene85953.t1 AT1G66140 52.525 99 31 3 81 163 83 181 3.22e-21 89.7
MS.gene85953.t1 AT5G57520 57.143 63 24 1 79 138 48 110 5.46e-17 75.9
MS.gene85953.t1 AT5G14010 39.796 98 45 3 81 164 36 133 1.81e-13 66.6
MS.gene85953.t1 AT5G01860 57.778 45 19 0 70 114 54 98 3.90e-12 63.9

Find 35 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAAGGTGCAAAATGAATT+TGG 0.272167 2.1:+1083359 MS.gene85953:CDS
GGCAGCTTCTGCCACTGGTT+TGG 0.325271 2.1:-1083230 None:intergenic
TGAACACAGGTACTCAAGTA+TGG 0.334170 2.1:+1083085 MS.gene85953:CDS
ACCATCATCACTTGGAATTC+AGG 0.350325 2.1:+1083142 MS.gene85953:CDS
GAAAATTTCCCTGATCTTGT+AGG 0.357308 2.1:-1083332 None:intergenic
TTTCCCTGATCTTGTAGGTA+TGG 0.467787 2.1:-1083327 None:intergenic
AACATGGCTCTAATCTTAGA+AGG 0.477004 2.1:-1082719 None:intergenic
ATATAGGCAGCTTCTGCCAC+TGG 0.477130 2.1:-1083235 None:intergenic
ACACAAAAGAGAAAGAACTA+TGG 0.484621 2.1:+1083025 MS.gene85953:CDS
GTAAAAGCACTCAGAGTTTG+AGG 0.499487 2.1:-1083442 None:intergenic
ACATGAAGATTCCTTGATGC+TGG 0.502045 2.1:-1083266 None:intergenic
TCATCACAAGAATCTTTACT+AGG 0.516480 2.1:-1082828 None:intergenic
GATGCTGGTTGTGAATATAT+AGG 0.519086 2.1:-1083251 None:intergenic
TCTTCATCGGAATCTAATCA+TGG 0.531083 2.1:+1082915 MS.gene85953:CDS
CATGTTGAGGCAGAAACTGA+TGG 0.531135 2.1:+1083284 MS.gene85953:CDS
AGTGCCATACCTACAAGATC+AGG 0.538472 2.1:+1083323 MS.gene85953:CDS
TTCGGTTTGTCGCGTTACTG+TGG 0.557649 2.1:+1083206 MS.gene85953:CDS
ACCTGAATTCCAAGTGATGA+TGG 0.560861 2.1:-1083143 None:intergenic
TATAGTTCACAGGCACTTGG+TGG 0.564578 2.1:+1082990 MS.gene85953:CDS
TGTAGGTATGGCACTAGTCA+AGG 0.572932 2.1:-1083315 None:intergenic
TATATTCACAACCAGCATCA+AGG 0.576962 2.1:+1083255 MS.gene85953:CDS
TAGTTGCATGAGAAAATCCT+TGG 0.584802 2.1:-1082951 None:intergenic
CGATGAAGAGTTCATCGACA+TGG 0.588026 2.1:-1082901 None:intergenic
AAAAGATCACCATCATCACT+TGG 0.591415 2.1:+1083134 MS.gene85953:CDS
AAGGTGCAAAATGAATTTGG+AGG 0.593011 2.1:+1083362 MS.gene85953:CDS
ATGGCTTCTCTACCTCTGCA+TGG 0.595459 2.1:+1083104 MS.gene85953:CDS
GAAGAGTTCATCGACATGGA+CGG 0.595991 2.1:-1082897 None:intergenic
ATCAAGGAATCTTCATGTTG+AGG 0.598145 2.1:+1083271 MS.gene85953:CDS
CATGTCGATGAACTCTTCAT+CGG 0.601479 2.1:+1082902 MS.gene85953:CDS
TAAAAGCACTCAGAGTTTGA+GGG 0.622554 2.1:-1083441 None:intergenic
ATGGTAATGAATTAGAGCCA+AGG 0.629515 2.1:+1082934 MS.gene85953:CDS
GTTACTGTGGTCCAAACCAG+TGG 0.634342 2.1:+1083219 MS.gene85953:CDS
TTCAAATTATTAGATAAACA+TGG 0.647436 2.1:-1082735 None:intergenic
AAGTTTGAAGAATAAACAAG+AGG 0.648051 2.1:+1083397 MS.gene85953:CDS
GTGCCATACCTACAAGATCA+GGG 0.648274 2.1:+1083324 MS.gene85953:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCAAATTATTAGATAAACA+TGG - chr2.1:1082738-1082757 None:intergenic 15.0%
! AAGTTTGAAGAATAAACAAG+AGG + chr2.1:1083397-1083416 MS.gene85953:CDS 25.0%
!!! AAGAAAGTTTTATAGTTCAC+AGG + chr2.1:1082980-1082999 MS.gene85953:CDS 25.0%
AAAGAACTATGGCAAAAAGA+GGG + chr2.1:1083036-1083055 MS.gene85953:CDS 30.0%
ACACAAAAGAGAAAGAACTA+TGG + chr2.1:1083025-1083044 MS.gene85953:CDS 30.0%
TCATCACAAGAATCTTTACT+AGG - chr2.1:1082831-1082850 None:intergenic 30.0%
! AATTCATTTTGCACCTTTCT+TGG - chr2.1:1083359-1083378 None:intergenic 30.0%
! AGAAAGGTGCAAAATGAATT+TGG + chr2.1:1083359-1083378 MS.gene85953:CDS 30.0%
! TTTCTCTTTTGTGTGCATTT+TGG - chr2.1:1083019-1083038 None:intergenic 30.0%
AAAAGATCACCATCATCACT+TGG + chr2.1:1083134-1083153 MS.gene85953:CDS 35.0%
AAGGTGCAAAATGAATTTGG+AGG + chr2.1:1083362-1083381 MS.gene85953:CDS 35.0%
ATCAAGGAATCTTCATGTTG+AGG + chr2.1:1083271-1083290 MS.gene85953:CDS 35.0%
GAAAATTTCCCTGATCTTGT+AGG - chr2.1:1083335-1083354 None:intergenic 35.0%
GAAAGAACTATGGCAAAAAG+AGG + chr2.1:1083035-1083054 MS.gene85953:CDS 35.0%
TAGTTGCATGAGAAAATCCT+TGG - chr2.1:1082954-1082973 None:intergenic 35.0%
TATATTCACAACCAGCATCA+AGG + chr2.1:1083255-1083274 MS.gene85953:CDS 35.0%
TCTTCATCGGAATCTAATCA+TGG + chr2.1:1082915-1082934 MS.gene85953:CDS 35.0%
! AGGGAAATTTTCTCCAAGAA+AGG + chr2.1:1083343-1083362 MS.gene85953:CDS 35.0%
! ATGGTAATGAATTAGAGCCA+AGG + chr2.1:1082934-1082953 MS.gene85953:CDS 35.0%
! GATGCTGGTTGTGAATATAT+AGG - chr2.1:1083254-1083273 None:intergenic 35.0%
! TTTTATAGTTCACAGGCACT+TGG + chr2.1:1082987-1083006 MS.gene85953:CDS 35.0%
!! AACATGGCTCTAATCTTAGA+AGG - chr2.1:1082722-1082741 None:intergenic 35.0%
!! CCTTATCAAACACCGTTTTT+CGG + chr2.1:1083188-1083207 MS.gene85953:CDS 35.0%
ACATGAAGATTCCTTGATGC+TGG - chr2.1:1083269-1083288 None:intergenic 40.0%
ACCATCATCACTTGGAATTC+AGG + chr2.1:1083142-1083161 MS.gene85953:CDS 40.0%
ACCTGAATTCCAAGTGATGA+TGG - chr2.1:1083146-1083165 None:intergenic 40.0%
CATGTCGATGAACTCTTCAT+CGG + chr2.1:1082902-1082921 MS.gene85953:CDS 40.0%
CCGAAAAACGGTGTTTGATA+AGG - chr2.1:1083191-1083210 None:intergenic 40.0%
TAACGCGACAAACCGAAAAA+CGG - chr2.1:1083203-1083222 None:intergenic 40.0%
TGAACACAGGTACTCAAGTA+TGG + chr2.1:1083085-1083104 MS.gene85953:CDS 40.0%
TTTCCCTGATCTTGTAGGTA+TGG - chr2.1:1083330-1083349 None:intergenic 40.0%
! AAAAAGAGGGCACAAATCTG+TGG + chr2.1:1083049-1083068 MS.gene85953:CDS 40.0%
! CTTCGCTAGATTTTGAACAC+AGG + chr2.1:1083072-1083091 MS.gene85953:CDS 40.0%
! CTTTTATAAGAGCCATGCAG+AGG - chr2.1:1083119-1083138 None:intergenic 40.0%
AGTGCCATACCTACAAGATC+AGG + chr2.1:1083323-1083342 MS.gene85953:CDS 45.0%
CATGTTGAGGCAGAAACTGA+TGG + chr2.1:1083284-1083303 MS.gene85953:CDS 45.0%
CGATGAAGAGTTCATCGACA+TGG - chr2.1:1082904-1082923 None:intergenic 45.0%
GAAGAGTTCATCGACATGGA+CGG - chr2.1:1082900-1082919 None:intergenic 45.0%
GTGCCATACCTACAAGATCA+GGG + chr2.1:1083324-1083343 MS.gene85953:CDS 45.0%
TATAGTTCACAGGCACTTGG+TGG + chr2.1:1082990-1083009 MS.gene85953:CDS 45.0%
TGTAGGTATGGCACTAGTCA+AGG - chr2.1:1083318-1083337 None:intergenic 45.0%
ATATAGGCAGCTTCTGCCAC+TGG - chr2.1:1083238-1083257 None:intergenic 50.0%
ATGGCTTCTCTACCTCTGCA+TGG + chr2.1:1083104-1083123 MS.gene85953:CDS 50.0%
GTTACTGTGGTCCAAACCAG+TGG + chr2.1:1083219-1083238 MS.gene85953:CDS 50.0%
! TTCGGTTTGTCGCGTTACTG+TGG + chr2.1:1083206-1083225 MS.gene85953:CDS 50.0%
! GGCAGCTTCTGCCACTGGTT+TGG - chr2.1:1083233-1083252 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 1082714 1083454 1082714 ID=MS.gene85953
chr2.1 mRNA 1082714 1083454 1082714 ID=MS.gene85953.t1;Parent=MS.gene85953
chr2.1 exon 1082714 1083454 1082714 ID=MS.gene85953.t1.exon1;Parent=MS.gene85953.t1
chr2.1 CDS 1082714 1083454 1082714 ID=cds.MS.gene85953.t1;Parent=MS.gene85953.t1
Gene Sequence

>MS.gene85953

ATGGACCTTCTAAGATTAGAGCCATGTTTATCTAATAATTTGAACATCTCATTTTCTGAGAAGAGACAAACAGAAAATGAAGAGAAAAAACATCTTGTACTAGATTTAACTCTTCCTAGTAAAGATTCTTGTGATGATGAGTCAAAACAAGAACTCAATCTCATAAACTGTTTCGATACAGAACCGTCCATGTCGATGAACTCTTCATCGGAATCTAATCATGGTAATGAATTAGAGCCAAGGATTTTCTCATGCAACTATTGTCAAAGAAAGTTTTATAGTTCACAGGCACTTGGTGGACACCAAAATGCACACAAAAGAGAAAGAACTATGGCAAAAAGAGGGCACAAATCTGTGGCTTCGCTAGATTTTGAACACAGGTACTCAAGTATGGCTTCTCTACCTCTGCATGGCTCTTATAAAAGATCACCATCATCACTTGGAATTCAGGTGCACTCTTCTATGATTCAAAAACCTTATCAAACACCGTTTTTCGGTTTGTCGCGTTACTGTGGTCCAAACCAGTGGCAGAAGCTGCCTATATATTCACAACCAGCATCAAGGAATCTTCATGTTGAGGCAGAAACTGATGGATCATCATCCTTGACTAGTGCCATACCTACAAGATCAGGGAAATTTTCTCCAAGAAAGGTGCAAAATGAATTTGGAGGTTATAATGCTACAAGTTTGAAGAATAAACAAGAGGAGTTGCAGAAGCTTGACTTGTCCCTCAAACTCTGA
Protein sequence

>MS.gene85953.t1

MDLLRLEPCLSNNLNISFSEKRQTENEEKKHLVLDLTLPSKDSCDDESKQELNLINCFDTEPSMSMNSSSESNHGNELEPRIFSCNYCQRKFYSSQALGGHQNAHKRERTMAKRGHKSVASLDFEHRYSSMASLPLHGSYKRSPSSLGIQVHSSMIQKPYQTPFFGLSRYCGPNQWQKLPIYSQPASRNLHVEAETDGSSSLTSAIPTRSGKFSPRKVQNEFGGYNATSLKNKQEELQKLDLSLKL