AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene21830

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21830.t1 MTR_5g006470 91.489 188 16 0 1 188 1 188 2.01e-127 356
MS.gene21830.t1 MTR_5g006450 76.842 190 42 1 1 188 1 190 2.80e-101 290
MS.gene21830.t1 MTR_5g006460 75.897 195 38 6 1 188 1 193 8.91e-96 276
MS.gene21830.t1 MTR_5g006520 74.211 190 47 1 1 188 1719 1908 5.58e-92 293
MS.gene21830.t1 MTR_5g006510 72.626 179 44 3 13 188 15 191 1.28e-88 258
MS.gene21830.t1 MTR_1g103110 63.158 190 68 1 1 188 1 190 3.99e-84 246
MS.gene21830.t1 MTR_1g103150 61.579 190 71 1 1 188 1 190 2.71e-83 244
MS.gene21830.t1 MTR_7g114410 43.787 169 94 1 17 185 4 171 1.70e-44 145
MS.gene21830.t1 MTR_7g024780 41.765 170 97 2 16 185 3 170 2.52e-40 135
MS.gene21830.t1 MTR_7g114410 42.857 154 87 1 17 170 4 156 3.22e-39 132
MS.gene21830.t1 MTR_3g463610 41.279 172 97 2 17 185 3 173 7.49e-39 132
MS.gene21830.t1 MTR_7g024760 40.964 166 95 2 20 185 7 169 2.03e-38 130
MS.gene21830.t1 MTR_7g024765 40.964 166 95 2 20 185 7 169 3.18e-37 127
MS.gene21830.t1 MTR_1g103320 46.835 79 42 0 51 129 11 89 6.88e-19 78.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21830.t1 AT2G32020 55.090 167 70 3 20 185 18 180 1.53e-57 179
MS.gene21830.t1 AT2G32030 53.012 166 73 3 21 185 24 185 1.74e-55 174
MS.gene21830.t1 AT3G22560 37.791 172 104 2 16 185 2 172 2.58e-34 119

Find 36 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGAGTTCTTAGGAAGTATT+TGG 0.241791 5.2:-1238990 MS.gene21830:CDS
ATAATCTAAGCTCTATATAT+TGG 0.258828 5.2:-1239159 MS.gene21830:CDS
TCCTAAGAACTCCCTCCTTT+TGG 0.260104 5.2:+1238999 None:intergenic
ATCAAGGTCAGAAAGATTAA+AGG 0.290557 5.2:+1239393 None:intergenic
TAATCTAAGCTCTATATATT+GGG 0.291812 5.2:-1239158 MS.gene21830:CDS
TGCTGTGAAGCAAATTATTA+AGG 0.344585 5.2:-1239116 MS.gene21830:CDS
AAAATGAAACTTATTAAAGT+TGG 0.351635 5.2:+1238912 None:intergenic
TCTCCAAGTATGAAAATTCA+TGG 0.373432 5.2:+1239086 None:intergenic
TCCAAAAGGAGGGAGTTCTT+AGG 0.394554 5.2:-1239000 MS.gene21830:CDS
TAAAGGGTCGGAGTGTGATT+TGG 0.396804 5.2:+1239410 None:intergenic
TGCATTGATGATCGTGCTAT+TGG 0.407515 5.2:-1239241 MS.gene21830:CDS
AGGAAACATTCTGCAGAACT+TGG 0.440863 5.2:-1239184 MS.gene21830:CDS
TTCTGACCTTGATGATGTAA+TGG 0.440976 5.2:-1239383 MS.gene21830:CDS
CCATCGTCTCTGCTGGTGTA+TGG 0.442715 5.2:+1239316 None:intergenic
GGTTGCCAAGTTCTGCTCTT+GGG 0.451345 5.2:-1239341 MS.gene21830:CDS
GTTGATGCCATCGTCTCTGC+TGG 0.472064 5.2:+1239309 None:intergenic
TCAAGGTCAGAAAGATTAAA+GGG 0.477441 5.2:+1239394 None:intergenic
CTTGTCGATGTTGAAAATGT+TGG 0.484592 5.2:-1239052 MS.gene21830:CDS
GCTCTATATATTGGGGCAAA+GGG 0.493310 5.2:-1239150 MS.gene21830:CDS
AGGTTGCCAAGTTCTGCTCT+TGG 0.493839 5.2:-1239342 MS.gene21830:CDS
AGCTCTATATATTGGGGCAA+AGG 0.501996 5.2:-1239151 MS.gene21830:CDS
TTGTCGATGTTGAAAATGTT+GGG 0.503194 5.2:-1239051 MS.gene21830:CDS
CATAGAGTGTTGGAGAAAGC+TGG 0.509643 5.2:-1239025 MS.gene21830:CDS
AGGAAGTATTTGGTCATGAA+AGG 0.520639 5.2:-1238980 MS.gene21830:CDS
GGAGAAAGCTGGTTTCCAAA+AGG 0.547990 5.2:-1239014 MS.gene21830:CDS
GAAAGCTGGTTTCCAAAAGG+AGG 0.562242 5.2:-1239011 MS.gene21830:CDS
TGGTTCCCAAGAGCAGAACT+TGG 0.574822 5.2:+1239336 None:intergenic
TGTTGGGTCACATAGAGTGT+TGG 0.584536 5.2:-1239035 MS.gene21830:CDS
AATCTAAGCTCTATATATTG+GGG 0.593409 5.2:-1239157 MS.gene21830:CDS
GCCACACCATTACATCATCA+AGG 0.594693 5.2:+1239377 None:intergenic
GGTCAGAAAGATTAAAGGGT+CGG 0.596865 5.2:+1239398 None:intergenic
TCACACCTGAAGATAAAAGC+AGG 0.598275 5.2:-1239204 MS.gene21830:CDS
GGTGTGGCATACTGATGTAA+AGG 0.604925 5.2:-1239362 MS.gene21830:CDS
CCATACACCAGCAGAGACGA+TGG 0.622747 5.2:-1239316 MS.gene21830:CDS
AAAGCTGGTTTCCAAAAGGA+GGG 0.657724 5.2:-1239010 MS.gene21830:CDS
ACCTTGATGATGTAATGGTG+TGG 0.686805 5.2:-1239378 MS.gene21830:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATCTAAGCTCTATATAT+TGG - chr5.2:1239235-1239254 MS.gene21830:CDS 20.0%
!! TAATCTAAGCTCTATATATT+GGG - chr5.2:1239236-1239255 MS.gene21830:CDS 20.0%
! AATCTAAGCTCTATATATTG+GGG - chr5.2:1239237-1239256 MS.gene21830:CDS 25.0%
!! ATTCCATGAATTTTCATACT+TGG - chr5.2:1239305-1239324 MS.gene21830:CDS 25.0%
ATCAAGGTCAGAAAGATTAA+AGG + chr5.2:1239004-1239023 None:intergenic 30.0%
TCAAGGTCAGAAAGATTAAA+GGG + chr5.2:1239003-1239022 None:intergenic 30.0%
TCTCCAAGTATGAAAATTCA+TGG + chr5.2:1239311-1239330 None:intergenic 30.0%
TGCTGTGAAGCAAATTATTA+AGG - chr5.2:1239278-1239297 MS.gene21830:CDS 30.0%
TTGTCGATGTTGAAAATGTT+GGG - chr5.2:1239343-1239362 MS.gene21830:CDS 30.0%
! ATGAATTTTCATACTTGGAG+AGG - chr5.2:1239310-1239329 MS.gene21830:CDS 30.0%
CTTGTCGATGTTGAAAATGT+TGG - chr5.2:1239342-1239361 MS.gene21830:CDS 35.0%
!! AGGAAGTATTTGGTCATGAA+AGG - chr5.2:1239414-1239433 MS.gene21830:CDS 35.0%
!! TGTTTCCTGCTTTTATCTTC+AGG + chr5.2:1239198-1239217 None:intergenic 35.0%
!! TTCTGACCTTGATGATGTAA+TGG - chr5.2:1239011-1239030 MS.gene21830:CDS 35.0%
AGCTCTATATATTGGGGCAA+AGG - chr5.2:1239243-1239262 MS.gene21830:CDS 40.0%
AGGAAACATTCTGCAGAACT+TGG - chr5.2:1239210-1239229 MS.gene21830:CDS 40.0%
GCTCTATATATTGGGGCAAA+GGG - chr5.2:1239244-1239263 MS.gene21830:CDS 40.0%
GGTCAGAAAGATTAAAGGGT+CGG + chr5.2:1238999-1239018 None:intergenic 40.0%
TCACACCTGAAGATAAAAGC+AGG - chr5.2:1239190-1239209 MS.gene21830:CDS 40.0%
! AAAGCTGGTTTCCAAAAGGA+GGG - chr5.2:1239384-1239403 MS.gene21830:CDS 40.0%
! TGCATTGATGATCGTGCTAT+TGG - chr5.2:1239153-1239172 MS.gene21830:CDS 40.0%
!! ACCTTGATGATGTAATGGTG+TGG - chr5.2:1239016-1239035 MS.gene21830:CDS 40.0%
!! GGGAGTTCTTAGGAAGTATT+TGG - chr5.2:1239404-1239423 MS.gene21830:CDS 40.0%
GCCACACCATTACATCATCA+AGG + chr5.2:1239020-1239039 None:intergenic 45.0%
GGTGTGGCATACTGATGTAA+AGG - chr5.2:1239032-1239051 MS.gene21830:CDS 45.0%
TAAAGGGTCGGAGTGTGATT+TGG + chr5.2:1238987-1239006 None:intergenic 45.0%
TCCAAAAGGAGGGAGTTCTT+AGG - chr5.2:1239394-1239413 MS.gene21830:CDS 45.0%
TGTTGGGTCACATAGAGTGT+TGG - chr5.2:1239359-1239378 MS.gene21830:CDS 45.0%
! GAAAGCTGGTTTCCAAAAGG+AGG - chr5.2:1239383-1239402 MS.gene21830:CDS 45.0%
! GGAGAAAGCTGGTTTCCAAA+AGG - chr5.2:1239380-1239399 MS.gene21830:CDS 45.0%
! TCCTAAGAACTCCCTCCTTT+TGG + chr5.2:1239398-1239417 None:intergenic 45.0%
!! CATAGAGTGTTGGAGAAAGC+TGG - chr5.2:1239369-1239388 MS.gene21830:CDS 45.0%
AGGTTGCCAAGTTCTGCTCT+TGG - chr5.2:1239052-1239071 MS.gene21830:CDS 50.0%
GGTTGCCAAGTTCTGCTCTT+GGG - chr5.2:1239053-1239072 MS.gene21830:CDS 50.0%
TGGTTCCCAAGAGCAGAACT+TGG + chr5.2:1239061-1239080 None:intergenic 50.0%
CCATACACCAGCAGAGACGA+TGG - chr5.2:1239078-1239097 MS.gene21830:CDS 55.0%
CCATCGTCTCTGCTGGTGTA+TGG + chr5.2:1239081-1239100 None:intergenic 55.0%
GTTGATGCCATCGTCTCTGC+TGG + chr5.2:1239088-1239107 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 1238925 1239491 1238925 ID=MS.gene21830
chr5.2 mRNA 1238925 1239491 1238925 ID=MS.gene21830.t1;Parent=MS.gene21830
chr5.2 exon 1238925 1239491 1238925 ID=MS.gene21830.t1.exon1;Parent=MS.gene21830.t1
chr5.2 CDS 1238925 1239491 1238925 ID=cds.MS.gene21830.t1;Parent=MS.gene21830.t1
Gene Sequence

>MS.gene21830

ATGGAGGAAACTTTTATTTCTTCAAAATCATGTGTCAAAGAAGAGATCATTGATTTGAACCAAATCACACTCCGACCCTTTAATCTTTCTGACCTTGATGATGTAATGGTGTGGCATACTGATGTAAAGGTTGCCAAGTTCTGCTCTTGGGAACCATACACCAGCAGAGACGATGGCATCAACTTCATTGAAAATATAGAAAGCAAGTTTCTTTGTTGCAAAGCAATATGCATTGATGATCGTGCTATTGGTTGTATTCTTTTGTTCACACCTGAAGATAAAAGCAGGAAACATTCTGCAGAACTTGGCTATAATCTAAGCTCTATATATTGGGGCAAAGGGATTGTCACGTGTGCTGTGAAGCAAATTATTAAGGTTGCATTCCATGAATTTTCATACTTGGAGAGGCTTGAAGCACTTGTCGATGTTGAAAATGTTGGGTCACATAGAGTGTTGGAGAAAGCTGGTTTCCAAAAGGAGGGAGTTCTTAGGAAGTATTTGGTCATGAAAGGAAAAAGCAGAGATATGATCATGTTTAGTGTTCTTTCTACTGATCTCCAACTTTAA
Protein sequence

>MS.gene21830.t1

MEETFISSKSCVKEEIIDLNQITLRPFNLSDLDDVMVWHTDVKVAKFCSWEPYTSRDDGINFIENIESKFLCCKAICIDDRAIGCILLFTPEDKSRKHSAELGYNLSSIYWGKGIVTCAVKQIIKVAFHEFSYLERLEALVDVENVGSHRVLEKAGFQKEGVLRKYLVMKGKSRDMIMFSVLSTDLQL