AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene029328

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene029328.t1 MTR_1g112030 97.403 154 4 0 1 154 3 156 2.99e-109 307
MS.gene029328.t1 MTR_1g112030 97.403 154 4 0 1 154 7 160 4.28e-109 307
MS.gene029328.t1 MTR_1g112050 90.196 153 15 0 1 153 1 153 1.15e-100 286
MS.gene029328.t1 MTR_2g086510 72.727 132 35 1 24 154 24 155 3.62e-67 201
MS.gene029328.t1 MTR_4g053120 65.385 156 48 3 1 154 4 155 1.22e-65 197
MS.gene029328.t1 MTR_2g006290 55.102 147 60 3 12 153 3 148 7.50e-50 157
MS.gene029328.t1 MTR_8g088720 55.556 144 61 3 12 153 4 146 1.06e-49 156
MS.gene029328.t1 MTR_5g006320 31.757 148 96 3 6 153 1 143 1.86e-19 79.7
MS.gene029328.t1 MTR_4g098490 39.535 86 52 0 69 154 74 159 1.19e-18 78.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene029328.t1 AT2G27510 60.000 155 56 3 6 154 1 155 2.91e-60 184
MS.gene029328.t1 AT1G60950 56.209 153 56 5 6 153 1 147 7.46e-50 157
MS.gene029328.t1 AT1G10960 58.915 129 47 3 30 153 20 147 6.59e-47 149
MS.gene029328.t1 AT5G10000 52.381 126 57 2 31 153 22 147 8.26e-40 131
MS.gene029328.t1 AT4G14890 44.554 101 53 3 53 153 47 144 6.33e-20 81.3
MS.gene029328.t1 AT1G32550 39.535 86 52 0 69 154 69 154 3.45e-18 77.4
MS.gene029328.t1 AT1G32550 37.255 102 45 3 69 154 69 167 8.19e-13 63.5

Find 33 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAATCACAGTATCTGATTT+TGG 0.126493 1.4:+86071028 None:intergenic
TTCACAGATCTCAAACTTGA+TGG 0.324898 1.4:+86071349 None:intergenic
TTGTGCTGGCCAAGTGGTTA+CGG 0.329557 1.4:-86071131 MS.gene029328:CDS
CCCTGATGACTCTTACATTC+TGG 0.354348 1.4:-86071215 MS.gene029328:CDS
GCACCCGCTCTGCATGAATA+AGG 0.356204 1.4:+86071163 None:intergenic
TGTGCTGGCCAAGTGGTTAC+GGG 0.411836 1.4:-86071130 MS.gene029328:CDS
AAGAATGTGTCCAAAACATT+TGG 0.421132 1.4:-86071328 MS.gene029328:CDS
AATTCGTTCTCTGTTCCATC+TGG 0.449513 1.4:+86071244 None:intergenic
TCCAGAATGTAAGAGTCATC+AGG 0.451621 1.4:+86071214 None:intergenic
CTTTCAACAGCTTCATTGTA+CGG 0.469663 1.4:-86071412 MS.gene029328:CDS
CTGGATTCAGCTGAAGATGC+TGG 0.504908 1.4:-86071196 MS.gene029328:CDS
GGTGCATGTTCTACTTGTGC+TGG 0.505031 1.4:-86071145 MS.gene029328:CDS
GTATACAAAGTGAAACTGAT+TGG 0.509553 1.4:-86071268 MS.gene029328:CDS
CTACCTTATTCATGCAGAGC+GGG 0.513286 1.4:-86071166 MS.gene029328:CDS
CGACAGAACCCGTAACCACT+TGG 0.534235 1.4:+86071122 None:intergenic
GTGAAACTGATTGGACCAGA+TGG 0.549003 1.4:-86071259 MS.gene029328:CDS
TGTACGGAACAGTGCCCTCT+CGG 0.555453 1.4:-86071396 MS.gene029328:CDS
CGATGAGCAGCAAATCGAGA+AGG 0.589494 1.4:-86071077 MS.gene029328:CDS
CCAGAATGTAAGAGTCATCA+GGG 0.593554 1.4:+86071215 None:intergenic
TCTCACGGTGGACATATTCA+CGG 0.595716 1.4:+86071435 None:intergenic
ATCATTTAGAGTATCTGCAA+TGG 0.596293 1.4:-86071293 MS.gene029328:CDS
TTCTACTTGTGCTGGCCAAG+TGG 0.605670 1.4:-86071137 MS.gene029328:CDS
TTCAGCTGAAGATGCTGGAG+TGG 0.623617 1.4:-86071191 MS.gene029328:CDS
GATGAGCAGCAAATCGAGAA+GGG 0.629753 1.4:-86071076 MS.gene029328:CDS
TACTGTGATTTACACACACA+AGG 0.647153 1.4:-86071017 MS.gene029328:CDS
TCTCGATTTGCTGCTCATCG+AGG 0.652018 1.4:+86071080 None:intergenic
TGAAGCTGTTGAAAGTCTCA+CGG 0.659563 1.4:+86071420 None:intergenic
AGAGCACAAGATGTCCGAGA+GGG 0.687025 1.4:+86071382 None:intergenic
GCTACCTTATTCATGCAGAG+CGG 0.717700 1.4:-86071167 MS.gene029328:CDS
TGTGATTTACACACACAAGG+AGG 0.721823 1.4:-86071014 MS.gene029328:CDS
CAGAGCACAAGATGTCCGAG+AGG 0.730685 1.4:+86071381 None:intergenic
CAGAATGTAAGAGTCATCAG+GGG 0.754480 1.4:+86071216 None:intergenic
AGCTGTTGAAAGTCTCACGG+TGG 0.759008 1.4:+86071423 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATCACAGTATCTGATTTT+GGG + chr1.4:86071416-86071435 None:intergenic 25.0%
!! TAAATCACAGTATCTGATTT+TGG + chr1.4:86071417-86071436 None:intergenic 25.0%
!!! AGATTTTAGTCCAAATGTTT+TGG + chr1.4:86071127-86071146 None:intergenic 25.0%
AAGAATGTGTCCAAAACATT+TGG - chr1.4:86071114-86071133 MS.gene029328:CDS 30.0%
GTATACAAAGTGAAACTGAT+TGG - chr1.4:86071174-86071193 MS.gene029328:CDS 30.0%
! ATCATTTAGAGTATCTGCAA+TGG - chr1.4:86071149-86071168 MS.gene029328:CDS 30.0%
CTTTCAACAGCTTCATTGTA+CGG - chr1.4:86071030-86071049 MS.gene029328:CDS 35.0%
TACTGTGATTTACACACACA+AGG - chr1.4:86071425-86071444 MS.gene029328:CDS 35.0%
TTCACAGATCTCAAACTTGA+TGG + chr1.4:86071096-86071115 None:intergenic 35.0%
AATTCGTTCTCTGTTCCATC+TGG + chr1.4:86071201-86071220 None:intergenic 40.0%
CAGAATGTAAGAGTCATCAG+GGG + chr1.4:86071229-86071248 None:intergenic 40.0%
CCAGAATGTAAGAGTCATCA+GGG + chr1.4:86071230-86071249 None:intergenic 40.0%
TCCAGAATGTAAGAGTCATC+AGG + chr1.4:86071231-86071250 None:intergenic 40.0%
TGAAGCTGTTGAAAGTCTCA+CGG + chr1.4:86071025-86071044 None:intergenic 40.0%
TGTGATTTACACACACAAGG+AGG - chr1.4:86071428-86071447 MS.gene029328:CDS 40.0%
CCCTGATGACTCTTACATTC+TGG - chr1.4:86071227-86071246 MS.gene029328:CDS 45.0%
CTACCTTATTCATGCAGAGC+GGG - chr1.4:86071276-86071295 MS.gene029328:CDS 45.0%
GATGAGCAGCAAATCGAGAA+GGG - chr1.4:86071366-86071385 MS.gene029328:CDS 45.0%
GCTACCTTATTCATGCAGAG+CGG - chr1.4:86071275-86071294 MS.gene029328:CDS 45.0%
GTGAAACTGATTGGACCAGA+TGG - chr1.4:86071183-86071202 MS.gene029328:CDS 45.0%
TCTCACGGTGGACATATTCA+CGG + chr1.4:86071010-86071029 None:intergenic 45.0%
AGAGCACAAGATGTCCGAGA+GGG + chr1.4:86071063-86071082 None:intergenic 50.0%
AGCTGTTGAAAGTCTCACGG+TGG + chr1.4:86071022-86071041 None:intergenic 50.0%
CGATGAGCAGCAAATCGAGA+AGG - chr1.4:86071365-86071384 MS.gene029328:CDS 50.0%
CTGGATTCAGCTGAAGATGC+TGG - chr1.4:86071246-86071265 MS.gene029328:CDS 50.0%
GGTGCATGTTCTACTTGTGC+TGG - chr1.4:86071297-86071316 MS.gene029328:CDS 50.0%
TTCAGCTGAAGATGCTGGAG+TGG - chr1.4:86071251-86071270 MS.gene029328:CDS 50.0%
! TTCTACTTGTGCTGGCCAAG+TGG - chr1.4:86071305-86071324 MS.gene029328:CDS 50.0%
! TTGTGCTGGCCAAGTGGTTA+CGG - chr1.4:86071311-86071330 MS.gene029328:CDS 50.0%
!! TCTCGATTTGCTGCTCATCG+AGG + chr1.4:86071365-86071384 None:intergenic 50.0%
CAGAGCACAAGATGTCCGAG+AGG + chr1.4:86071064-86071083 None:intergenic 55.0%
CGACAGAACCCGTAACCACT+TGG + chr1.4:86071323-86071342 None:intergenic 55.0%
GCACCCGCTCTGCATGAATA+AGG + chr1.4:86071282-86071301 None:intergenic 55.0%
TGTACGGAACAGTGCCCTCT+CGG - chr1.4:86071046-86071065 MS.gene029328:CDS 55.0%
! TGTGCTGGCCAAGTGGTTAC+GGG - chr1.4:86071312-86071331 MS.gene029328:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 86071000 86071464 86071000 ID=MS.gene029328
chr1.4 mRNA 86071000 86071464 86071000 ID=MS.gene029328.t1;Parent=MS.gene029328
chr1.4 exon 86071000 86071464 86071000 ID=MS.gene029328.t1.exon1;Parent=MS.gene029328.t1
chr1.4 CDS 86071000 86071464 86071000 ID=cds.MS.gene029328.t1;Parent=MS.gene029328.t1
Gene Sequence

>MS.gene029328

ATGTCAGCCGTGAATATGTCCACCGTGAGACTTTCAACAGCTTCATTGTACGGAACAGTGCCCTCTCGGACATCTTGTGCTCTGATGAAGAGTCCATCAAGTTTGAGATCTGTGAAGAATGTGTCCAAAACATTTGGACTAAAATCTTCATCATTTAGAGTATCTGCAATGGCAGTATACAAAGTGAAACTGATTGGACCAGATGGAACAGAGAACGAATTTGATGCCCCTGATGACTCTTACATTCTGGATTCAGCTGAAGATGCTGGAGTGGAGCTACCTTATTCATGCAGAGCGGGTGCATGTTCTACTTGTGCTGGCCAAGTGGTTACGGGTTCTGTCGATCAGTCTGATCAATCTTTCCTCGATGAGCAGCAAATCGAGAAGGGTTATCTTCTCACTTGTGTCTCATACCCAAAATCAGATACTGTGATTTACACACACAAGGAGGAAGAACTCTACTAA
Protein sequence

>MS.gene029328.t1

MSAVNMSTVRLSTASLYGTVPSRTSCALMKSPSSLRSVKNVSKTFGLKSSSFRVSAMAVYKVKLIGPDGTENEFDAPDDSYILDSAEDAGVELPYSCRAGACSTCAGQVVTGSVDQSDQSFLDEQQIEKGYLLTCVSYPKSDTVIYTHKEEELY