AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene03034

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene03034.t1 MTR_1g088850 96.818 220 4 1 1 217 1 220 6.68e-161 443
MS.gene03034.t1 MTR_3g450790 47.619 210 104 4 1 206 1 208 1.32e-65 202
MS.gene03034.t1 MTR_3g450930 44.762 210 110 4 1 206 1 208 8.34e-59 184
MS.gene03034.t1 MTR_5g090920 43.602 211 112 5 1 206 1 209 4.83e-54 172
MS.gene03034.t1 MTR_1g088845 40.385 208 120 2 3 207 4 210 5.18e-54 172
MS.gene03034.t1 MTR_1g088840 38.942 208 123 2 3 207 4 210 4.75e-53 170
MS.gene03034.t1 MTR_1g088825 38.942 208 123 2 3 207 4 210 4.75e-53 170
MS.gene03034.t1 MTR_5g090910 42.723 213 111 6 1 206 1 209 1.10e-51 166
MS.gene03034.t1 MTR_3g064700 41.627 209 117 2 1 205 1 208 3.18e-51 165
MS.gene03034.t1 MTR_1g026140 36.321 212 127 2 3 206 5 216 2.20e-46 153
MS.gene03034.t1 MTR_1g088840 38.272 162 96 2 49 207 3 163 2.75e-37 128
MS.gene03034.t1 MTR_5g090910 41.216 148 77 5 66 206 8 152 1.20e-25 98.2
MS.gene03034.t1 MTR_1g088840 35.714 112 69 1 99 207 3 114 2.44e-21 85.5
MS.gene03034.t1 MTR_4g134770 25.877 228 142 5 1 216 1 213 9.56e-13 66.6
MS.gene03034.t1 MTR_3g058940 26.415 212 142 4 1 207 1 203 2.00e-12 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene03034.t1 AT3G62760 54.378 217 96 1 1 214 1 217 7.41e-91 266
MS.gene03034.t1 AT1G02930 41.346 208 117 2 2 206 3 208 2.48e-56 178
MS.gene03034.t1 AT1G02930 41.346 208 117 2 2 206 3 208 2.48e-56 178
MS.gene03034.t1 AT1G02920 40.865 208 119 2 2 206 3 209 2.77e-54 173
MS.gene03034.t1 AT2G30860 43.256 215 116 4 1 211 1 213 4.08e-52 167
MS.gene03034.t1 AT2G47730 40.976 205 118 1 5 206 54 258 7.54e-52 168
MS.gene03034.t1 AT2G47730 40.976 205 118 1 5 206 54 258 7.54e-52 168
MS.gene03034.t1 AT4G02520 40.000 210 119 3 2 205 3 211 1.76e-51 166
MS.gene03034.t1 AT2G02930 39.048 210 123 2 2 206 3 212 1.28e-50 164
MS.gene03034.t1 AT2G30870 43.062 209 113 4 1 205 1 207 3.68e-50 162
MS.gene03034.t1 AT1G02950 34.951 206 131 1 1 203 23 228 1.00e-46 154
MS.gene03034.t1 AT1G02950 34.951 206 131 1 1 203 23 228 1.00e-46 154
MS.gene03034.t1 AT1G02950 34.951 206 131 1 1 203 35 240 1.68e-46 154
MS.gene03034.t1 AT1G02950 35.468 203 128 1 4 203 28 230 1.92e-46 154
MS.gene03034.t1 AT1G49860 40.000 200 112 4 14 206 16 214 4.77e-45 150
MS.gene03034.t1 AT3G03190 36.190 210 129 3 1 206 1 209 1.44e-44 148
MS.gene03034.t1 AT1G02940 35.437 206 130 1 4 206 40 245 8.04e-43 145
MS.gene03034.t1 AT1G02940 35.437 206 130 1 4 206 40 245 8.04e-43 145
MS.gene03034.t1 AT1G02940 35.437 206 130 1 4 206 53 258 1.33e-42 145
MS.gene03034.t1 AT1G02940 35.437 206 130 1 4 206 65 270 1.41e-42 145
MS.gene03034.t1 AT5G17220 32.381 210 137 3 1 206 1 209 1.24e-41 140
MS.gene03034.t1 AT2G30860 41.290 155 89 2 1 155 1 153 1.87e-33 118
MS.gene03034.t1 AT1G02950 28.000 175 119 2 32 203 32 202 3.14e-22 90.9

Find 43 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCACTGACTTGTTTGGTTCT+TGG 0.209731 1.3:-62173516 None:intergenic
ATCATGGCACTCAAGATTTA+TGG 0.277244 1.3:+62172726 None:intergenic
CTTTCAATCACTGACTTGTT+TGG 0.302853 1.3:-62173523 None:intergenic
AATAGTGAGTTGAAGATATA+TGG 0.317000 1.3:-62173636 None:intergenic
ACAAAGTATTCATAGATAAT+TGG 0.324344 1.3:-62173478 None:intergenic
TTCAGCTACATATGAGGTTA+TGG 0.327058 1.3:-62173344 None:intergenic
GATGATGATCTCACCCTCTT+TGG 0.366830 1.3:+62172978 MS.gene03034:CDS
CAATGAACGGATTCATGTTA+AGG 0.371100 1.3:+62173687 MS.gene03034:CDS
TTTGGTTCTTGGCCTTGAAA+TGG 0.372478 1.3:-62173505 None:intergenic
AAATTGGACCTGATTTGATT+AGG 0.392685 1.3:+62173377 MS.gene03034:CDS
TACTTTGTGGCTCCATTTCA+AGG 0.400504 1.3:+62173493 MS.gene03034:CDS
CTTACGTTCTTGTTGAGAAA+AGG 0.412482 1.3:-62172858 None:intergenic
AGCACAACAAAGTACCTTGC+AGG 0.416067 1.3:+62173595 MS.gene03034:CDS
GGTGGGAAGATATATCTTCT+AGG 0.418080 1.3:+62173713 MS.gene03034:CDS
TCTTTGTTCATGCAGCCCTT+TGG 0.422040 1.3:+62172936 MS.gene03034:intron
TGACACAAAAGAAGCTTCAT+TGG 0.444080 1.3:+62173405 MS.gene03034:CDS
TAGATAATTGGTGTGACTGC+AGG 0.445936 1.3:-62173466 None:intergenic
GTACTTTGTTGTGCTTAGCT+TGG 0.454755 1.3:-62173587 None:intergenic
AATTATCTATGAATACTTTG+TGG 0.456418 1.3:+62173480 MS.gene03034:CDS
ACGAGTGGTGTTTGTGGACA+TGG 0.465625 1.3:-62172754 None:intergenic
GTTGTGGGAGGTATGACCTT+TGG 0.467331 1.3:+62173751 MS.gene03034:CDS
AGATCATCATCTTCAAGTAC+TGG 0.467902 1.3:-62172966 None:intergenic
TCATTGTGCCTAATCAAATC+AGG 0.483923 1.3:-62173385 None:intergenic
AACGGATTCATGTTAAGGCT+TGG 0.491423 1.3:+62173692 MS.gene03034:CDS
CATGGCACGAGTGGTGTTTG+TGG 0.516433 1.3:-62172760 None:intergenic
GATTCATGTTAAGGCTTGGT+GGG 0.536813 1.3:+62173696 MS.gene03034:CDS
GGATTCATGTTAAGGCTTGG+TGG 0.539482 1.3:+62173695 MS.gene03034:CDS
GCACAACAAAGTACCTTGCA+GGG 0.549960 1.3:+62173596 MS.gene03034:CDS
AGATAATTGGTGTGACTGCA+GGG 0.554379 1.3:-62173465 None:intergenic
AAAAGAAAGCATACCAAAGA+GGG 0.568007 1.3:-62172991 None:intergenic
TCAGAAGCAAACACATTGAC+TGG 0.571377 1.3:-62172822 None:intergenic
ACGTTCTTGTTGAGAAAAGG+AGG 0.590052 1.3:-62172855 None:intergenic
AGTACTGGAATCAAACCAAA+GGG 0.590562 1.3:-62172951 None:intergenic
AAGCTTCATTGGTCAAAATG+TGG 0.591373 1.3:+62173416 MS.gene03034:CDS
GTGCTTCAATGATCAATGAA+CGG 0.607609 1.3:+62173674 MS.gene03034:CDS
CGAGTGGTGTTTGTGGACAT+GGG 0.611791 1.3:-62172753 None:intergenic
ATTGATCATTGAAGCACAAG+GGG 0.612739 1.3:-62173668 None:intergenic
AAGTACTGGAATCAAACCAA+AGG 0.617639 1.3:-62172952 None:intergenic
TCATTGATCATTGAAGCACA+AGG 0.633784 1.3:-62173670 None:intergenic
CATTGATCATTGAAGCACAA+GGG 0.636560 1.3:-62173669 None:intergenic
CACAACAAAGTACCTTGCAG+GGG 0.682868 1.3:+62173597 MS.gene03034:CDS
TAGACATATCATGGCACGAG+TGG 0.683620 1.3:-62172769 None:intergenic
ATTGGTCAAAATGTGGACAG+AGG 0.694356 1.3:+62173423 MS.gene03034:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTCGAATAAACTTAAA+GGG - chr1.3:62173056-62173075 None:intergenic 15.0%
!!! TATTTTTCGAATAAACTTAA+AGG - chr1.3:62173057-62173076 None:intergenic 15.0%
!! AATTATCTATGAATACTTTG+TGG + chr1.3:62173480-62173499 MS.gene03034:CDS 20.0%
!! ATATGTAGCTGAAAAATATA+AGG + chr1.3:62173354-62173373 MS.gene03034:CDS 20.0%
!! GAATTAGTAACAAAAATTAG+AGG - chr1.3:62173189-62173208 None:intergenic 20.0%
!!! ACAAAGTATTCATAGATAAT+TGG - chr1.3:62173481-62173500 None:intergenic 20.0%
! AAAAGGTTACATATCATTAC+AGG - chr1.3:62173287-62173306 None:intergenic 25.0%
! AATCAAGCAAAAATACTACT+AGG + chr1.3:62173104-62173123 MS.gene03034:intron 25.0%
! ATCATTACAGGTTCAAAAAA+TGG - chr1.3:62173275-62173294 None:intergenic 25.0%
! GCTGAAAAATATAAGGAAAT+TGG + chr1.3:62173361-62173380 MS.gene03034:CDS 25.0%
!! AATAGTGAGTTGAAGATATA+TGG - chr1.3:62173639-62173658 None:intergenic 25.0%
!! TTTTTCATGTAGACATATCA+TGG - chr1.3:62172781-62172800 None:intergenic 25.0%
!!! ATATTTTTCAGCTACATATG+AGG - chr1.3:62173353-62173372 None:intergenic 25.0%
!!! TAACCTTTTTTATGTGACTA+TGG + chr1.3:62173298-62173317 MS.gene03034:intron 25.0%
AGTCCATAGTCACATAAAAA+AGG - chr1.3:62173304-62173323 None:intergenic 30.0%
TTTCGAATAAACTTAAAGGG+TGG - chr1.3:62173053-62173072 None:intergenic 30.0%
! AAAAAGAAAGCATACCAAAG+AGG - chr1.3:62172995-62173014 None:intergenic 30.0%
! AAAAGAAAGCATACCAAAGA+GGG - chr1.3:62172994-62173013 None:intergenic 30.0%
! AAATTGGACCTGATTTGATT+AGG + chr1.3:62173377-62173396 MS.gene03034:CDS 30.0%
AAGCTTCATTGGTCAAAATG+TGG + chr1.3:62173416-62173435 MS.gene03034:CDS 35.0%
AGATCATCATCTTCAAGTAC+TGG - chr1.3:62172969-62172988 None:intergenic 35.0%
ATTGATCATTGAAGCACAAG+GGG - chr1.3:62173671-62173690 None:intergenic 35.0%
CATTGATCATTGAAGCACAA+GGG - chr1.3:62173672-62173691 None:intergenic 35.0%
CTTACGTTCTTGTTGAGAAA+AGG - chr1.3:62172861-62172880 None:intergenic 35.0%
GTGCTTCAATGATCAATGAA+CGG + chr1.3:62173674-62173693 MS.gene03034:CDS 35.0%
TCATTGATCATTGAAGCACA+AGG - chr1.3:62173673-62173692 None:intergenic 35.0%
TCATTGTGCCTAATCAAATC+AGG - chr1.3:62173388-62173407 None:intergenic 35.0%
TCTGCTTTCCAAAAAGTTGT+GGG + chr1.3:62173736-62173755 MS.gene03034:CDS 35.0%
TGACACAAAAGAAGCTTCAT+TGG + chr1.3:62173405-62173424 MS.gene03034:CDS 35.0%
TTCAGCTACATATGAGGTTA+TGG - chr1.3:62173347-62173366 None:intergenic 35.0%
! AGTACTGGAATCAAACCAAA+GGG - chr1.3:62172954-62172973 None:intergenic 35.0%
! CAATGAACGGATTCATGTTA+AGG + chr1.3:62173687-62173706 MS.gene03034:CDS 35.0%
! TTTTTGATCACTCTGACCAA+AGG - chr1.3:62173770-62173789 None:intergenic 35.0%
!! AAGTACTGGAATCAAACCAA+AGG - chr1.3:62172955-62172974 None:intergenic 35.0%
!! CTTTCAATCACTGACTTGTT+TGG - chr1.3:62173526-62173545 None:intergenic 35.0%
ACGTTCTTGTTGAGAAAAGG+AGG - chr1.3:62172858-62172877 None:intergenic 40.0%
AGATAATTGGTGTGACTGCA+GGG - chr1.3:62173468-62173487 None:intergenic 40.0%
ATTGGTCAAAATGTGGACAG+AGG + chr1.3:62173423-62173442 MS.gene03034:CDS 40.0%
GACTATAAAAATCCCCTGCA+AGG - chr1.3:62173612-62173631 None:intergenic 40.0%
GCATGATTAGTGGTCTAGAT+TGG - chr1.3:62173220-62173239 None:intergenic 40.0%
GGTGGGAAGATATATCTTCT+AGG + chr1.3:62173713-62173732 MS.gene03034:CDS 40.0%
GTCTGCTTTCCAAAAAGTTG+TGG + chr1.3:62173735-62173754 MS.gene03034:CDS 40.0%
TACTTTGTGGCTCCATTTCA+AGG + chr1.3:62173493-62173512 MS.gene03034:CDS 40.0%
TAGATAATTGGTGTGACTGC+AGG - chr1.3:62173469-62173488 None:intergenic 40.0%
TCAGAAGCAAACACATTGAC+TGG - chr1.3:62172825-62172844 None:intergenic 40.0%
TGACATGCATGCATGATTAG+TGG - chr1.3:62173230-62173249 None:intergenic 40.0%
! AACGGATTCATGTTAAGGCT+TGG + chr1.3:62173692-62173711 MS.gene03034:CDS 40.0%
! GATTCATGTTAAGGCTTGGT+GGG + chr1.3:62173696-62173715 MS.gene03034:CDS 40.0%
! GTACTTTGTTGTGCTTAGCT+TGG - chr1.3:62173590-62173609 None:intergenic 40.0%
! TCATACCTCCCACAACTTTT+TGG - chr1.3:62173747-62173766 None:intergenic 40.0%
!! TCACTGACTTGTTTGGTTCT+TGG - chr1.3:62173519-62173538 None:intergenic 40.0%
!! TTTGGTTCTTGGCCTTGAAA+TGG - chr1.3:62173508-62173527 None:intergenic 40.0%
GATGATGATCTCACCCTCTT+TGG + chr1.3:62172978-62172997 MS.gene03034:CDS 45.0%
GCTTTCCAAAAAGTTGTGGG+AGG + chr1.3:62173739-62173758 MS.gene03034:CDS 45.0%
GGATTCATGTTAAGGCTTGG+TGG + chr1.3:62173695-62173714 MS.gene03034:CDS 45.0%
TAGACATATCATGGCACGAG+TGG - chr1.3:62172772-62172791 None:intergenic 45.0%
TCTTTGTTCATGCAGCCCTT+TGG + chr1.3:62172936-62172955 MS.gene03034:intron 45.0%
! AGCACAACAAAGTACCTTGC+AGG + chr1.3:62173595-62173614 MS.gene03034:CDS 45.0%
! CACAACAAAGTACCTTGCAG+GGG + chr1.3:62173597-62173616 MS.gene03034:CDS 45.0%
! GCACAACAAAGTACCTTGCA+GGG + chr1.3:62173596-62173615 MS.gene03034:CDS 45.0%
ACGAGTGGTGTTTGTGGACA+TGG - chr1.3:62172757-62172776 None:intergenic 50.0%
CGAGTGGTGTTTGTGGACAT+GGG - chr1.3:62172756-62172775 None:intergenic 50.0%
! GTTGTGGGAGGTATGACCTT+TGG + chr1.3:62173751-62173770 MS.gene03034:CDS 50.0%
CATGGCACGAGTGGTGTTTG+TGG - chr1.3:62172763-62172782 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 62172729 62173792 62172729 ID=MS.gene03034
chr1.3 mRNA 62172729 62173792 62172729 ID=MS.gene03034.t1;Parent=MS.gene03034
chr1.3 exon 62172729 62172875 62172729 ID=MS.gene03034.t1.exon1;Parent=MS.gene03034.t1
chr1.3 CDS 62172729 62172875 62172729 ID=cds.MS.gene03034.t1;Parent=MS.gene03034.t1
chr1.3 exon 62172951 62172999 62172951 ID=MS.gene03034.t1.exon2;Parent=MS.gene03034.t1
chr1.3 CDS 62172951 62172999 62172951 ID=cds.MS.gene03034.t1;Parent=MS.gene03034.t1
chr1.3 exon 62173335 62173792 62173335 ID=MS.gene03034.t1.exon3;Parent=MS.gene03034.t1
chr1.3 CDS 62173335 62173792 62173335 ID=cds.MS.gene03034.t1;Parent=MS.gene03034.t1
Gene Sequence

>MS.gene03034

ATGGCACTCAAGATTTATGGTCTGCCCATGTCCACAAACACCACTCGTGCCATGATATGTCTACATGAAAAAGAAGTAGATTTTGAGCTTATTCCAGTCAATGTGTTTGCTTCTGAGCATAAACAGCCTCCTTTTCTCAACAAGAACGTAAGTAAAAAAAGCACTTCTAGCTAGCTTATATATCTTTTCTTAATCACATACTAATTTTCTTTGTTCATGCAGCCCTTTGGTTTGATTCCAGTACTTGAAGATGATGATCTCACCCTCTTTGGTATGCTTTCTTTTTTTCTTTTTCAGTTGTTACATTTTATTCACTCTGCACCACCCTTTAAGTTTATTCGAAAAATATACTTTGACGCTCGCTTTCATATTTATAATCAAGCAAAAATACTACTAGGAAAAAAAAAATTATGTAATTTCAGCGCGAGAAGTGACTCTGAAATTTGAGAATTTTTGTCCTCTAATTTTTGTTACTAATTCAACATTTTCCAATCTAGACCACTAATCATGCATGCATGTCAGATAATTTGATATTGTTTTGTTCCATTTTTTGAACCTGTAATGATATGTAACCTTTTTTATGTGACTATGGACTATACAAAAAAGAGTCAAGAGCCATAACCTCATATGTAGCTGAAAAATATAAGGAAATTGGACCTGATTTGATTAGGCACAATGACACAAAAGAAGCTTCATTGGTCAAAATGTGGACAGAGGTAGAGTCTCACTACTATGACCCTGCAGTCACACCAATTATCTATGAATACTTTGTGGCTCCATTTCAAGGCCAAGAACCAAACAAGTCAGTGATTGAAAGTAACATTGAGAAGCTGAAGATTGTGCTTGATGTGTATGAGACCAAGCTAAGCACAACAAAGTACCTTGCAGGGGATTTTTATAGTCTTAGCCATATATCTTCAACTCACTATTTTATGCAGACCCCTTGTGCTTCAATGATCAATGAACGGATTCATGTTAAGGCTTGGTGGGAAGATATATCTTCTAGGTCTGCTTTCCAAAAAGTTGTGGGAGGTATGACCTTTGGTCAGAGTGATCAAAAATGA
Protein sequence

>MS.gene03034.t1

MALKIYGLPMSTNTTRAMICLHEKEVDFELIPVNVFASEHKQPPFLNKNPFGLIPVLEDDDLTLFESRAITSYVAEKYKEIGPDLIRHNDTKEASLVKMWTEVESHYYDPAVTPIIYEYFVAPFQGQEPNKSVIESNIEKLKIVLDVYETKLSTTKYLAGDFYSLSHISSTHYFMQTPCASMINERIHVKAWWEDISSRSAFQKVVGGMTFGQSDQK