AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene85363

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85363.t1 MTR_2g044910 92.771 166 10 1 1 166 44 207 5.41e-110 311
MS.gene85363.t1 MTR_2g044910 92.771 166 10 1 1 166 1 164 1.22e-109 309
MS.gene85363.t1 MTR_2g044910 81.416 113 14 3 1 111 44 151 3.40e-56 174
MS.gene85363.t1 MTR_4g124360 58.594 128 45 3 1 125 31 153 4.14e-42 139
MS.gene85363.t1 MTR_4g124360 58.088 136 48 4 9 141 1 130 6.23e-40 132
MS.gene85363.t1 MTR_5g013515 33.846 130 55 4 14 133 13 121 6.58e-16 70.5
MS.gene85363.t1 MTR_2g042900 31.250 128 65 3 15 125 112 233 2.23e-14 68.9
MS.gene85363.t1 MTR_5g013530 29.825 114 63 2 15 128 22 118 2.17e-12 61.6
MS.gene85363.t1 MTR_5g013530 29.825 114 63 2 15 128 44 140 4.08e-12 61.2
MS.gene85363.t1 MTR_4g124960 32.231 121 45 4 7 125 91 176 4.57e-12 62.0
MS.gene85363.t1 MTR_4g124960 31.933 119 44 4 7 123 91 174 3.31e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85363.t1 AT5G20900 54.237 118 42 5 15 128 57 166 6.50e-31 110
MS.gene85363.t1 AT3G43440 37.984 129 54 4 14 140 130 234 2.60e-15 71.2
MS.gene85363.t1 AT3G43440 36.154 130 57 4 13 140 43 148 1.28e-14 67.8
MS.gene85363.t1 AT1G74950 35.484 124 51 3 16 125 120 228 1.99e-13 66.2
MS.gene85363.t1 AT1G19180 34.746 118 61 4 11 125 56 160 1.16e-12 63.2
MS.gene85363.t1 AT1G19180 34.746 118 61 4 11 125 122 226 2.60e-12 63.2
MS.gene85363.t1 AT1G19180 34.746 118 61 4 11 125 122 226 2.60e-12 63.2
MS.gene85363.t1 AT5G13220 30.894 123 63 4 3 125 92 192 4.12e-11 59.3

Find 37 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGCTTACCATCTTCTATAA+TGG 0.263317 2.1:+47244065 MS.gene85363:CDS
TTCTTTCACCTGTTCCTTCA+AGG 0.283604 2.1:+47244317 MS.gene85363:CDS
TCCTTCATTGAAACCGAATC+TGG 0.348326 2.1:-47244781 None:intergenic
TTTAGGTCAATGCCAGCATC+TGG 0.377821 2.1:+47244014 None:intergenic
TGCTGACAATTCGCCAGATT+CGG 0.379407 2.1:+47244768 MS.gene85363:CDS
AGTGAATGTCTGCGTGCTAT+TGG 0.383673 2.1:-47244553 None:intergenic
CTGCAGATAGAATTCTTTGC+AGG 0.395317 2.1:-47244397 None:intergenic
TGAGTTGTATTAGCAATCAT+TGG 0.398568 2.1:-47244044 None:intergenic
AGCTTACCATCTTCTATAAT+GGG 0.398580 2.1:+47244066 MS.gene85363:CDS
GCCAGATTCGGTTTCAATGA+AGG 0.420770 2.1:+47244780 MS.gene85363:CDS
ATTGGATTCGTTCCAGATGC+TGG 0.436562 2.1:-47244026 None:intergenic
ACAGGTGAAAGAACGGGAAC+GGG 0.457084 2.1:-47244307 None:intergenic
ATAGAATTCTTTGCAGGAAA+GGG 0.465810 2.1:-47244391 None:intergenic
CTTCTTTGTTTCACTAGACT+TGG 0.473413 2.1:-47244269 None:intergenic
TGATGGAATTCCTGCAGAAA+AGG 0.477638 2.1:+47244103 MS.gene85363:CDS
GGGAGTATTTGTATCTATGA+TGG 0.478209 2.1:+47244086 MS.gene85363:CDS
GCAGTTCCATGTGGCGAAGA+AGG 0.484372 2.1:-47244340 None:intergenic
TGTGGCGAAGAAGGCCTTGA+AGG 0.491077 2.1:-47244331 None:intergenic
CTGCAAAGAATTCTATCTGC+AGG 0.491501 2.1:+47244398 MS.gene85363:CDS
GAAGGAACAGGTGAAAGAAC+GGG 0.502028 2.1:-47244313 None:intergenic
AATACTCCCATTATAGAAGA+TGG 0.513403 2.1:-47244072 None:intergenic
TTCTTCAGAAGCGTCGAGAC+AGG 0.516859 2.1:+47244584 MS.gene85363:CDS
GATAGAATTCTTTGCAGGAA+AGG 0.520134 2.1:-47244392 None:intergenic
GAAGAAGGCCTTGAAGGAAC+AGG 0.524051 2.1:-47244325 None:intergenic
GCTCAAGATGCAGATATAGT+TGG 0.526009 2.1:-47244823 None:intergenic
GTTGGCTGAAATTCCTCCTG+TGG 0.539527 2.1:-47244805 None:intergenic
TCAAGGCCTTCTTCGCCACA+TGG 0.540794 2.1:+47244334 MS.gene85363:CDS
AATTCTATCTGCAGGCTGCA+AGG 0.555717 2.1:+47244406 MS.gene85363:CDS
TGATAATATCGCTTCACCAC+AGG 0.571663 2.1:+47244363 MS.gene85363:CDS
TGAAGGAACAGGTGAAAGAA+CGG 0.572032 2.1:-47244314 None:intergenic
AACAGGTGAAAGAACGGGAA+CGG 0.573715 2.1:-47244308 None:intergenic
GGTTTCAATGAAGGAACCAC+AGG 0.590783 2.1:+47244789 MS.gene85363:CDS
AACAAAGGTAGCTGACAACA+TGG 0.591184 2.1:+47244732 MS.gene85363:CDS
TTCAATGAAGGAACCACAGG+AGG 0.608188 2.1:+47244792 MS.gene85363:CDS
GACAACATGGAGAACAACTT+CGG 0.616517 2.1:+47244745 MS.gene85363:CDS
GCAGGAAAGGGATGTGCCTG+TGG 0.648722 2.1:-47244379 None:intergenic
ATATTATCAGCAGTTCCATG+TGG 0.739266 2.1:-47244349 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATACTATTAGTTTTCTTATT+TGG + chr2.1:47244651-47244670 MS.gene85363:intron 15.0%
!! ATAATTTATGTTTGCATTAC+AGG + chr2.1:47244674-47244693 MS.gene85363:intron 20.0%
!! TAGTTGAAGACATAATTAAT+AGG - chr2.1:47244442-47244461 None:intergenic 20.0%
! AATTCTCTCTATATACTAAC+AGG + chr2.1:47244213-47244232 MS.gene85363:intron 25.0%
!! CATACACAAAATTTGAAACA+TGG - chr2.1:47244623-47244642 None:intergenic 25.0%
AATACTCCCATTATAGAAGA+TGG - chr2.1:47244075-47244094 None:intergenic 30.0%
ACGAGACATATAAATTATGG+TGG - chr2.1:47244501-47244520 None:intergenic 30.0%
AGCTTACCATCTTCTATAAT+GGG + chr2.1:47244066-47244085 MS.gene85363:CDS 30.0%
ATAGAATTCTTTGCAGGAAA+GGG - chr2.1:47244394-47244413 None:intergenic 30.0%
CACACGAGACATATAAATTA+TGG - chr2.1:47244504-47244523 None:intergenic 30.0%
CATAATTTATATGTCTCGTG+TGG + chr2.1:47244502-47244521 MS.gene85363:intron 30.0%
TGAGTTGTATTAGCAATCAT+TGG - chr2.1:47244047-47244066 None:intergenic 30.0%
TTATGTTTGCATTACAGGTT+GGG + chr2.1:47244679-47244698 MS.gene85363:intron 30.0%
TTTATGTTTGCATTACAGGT+TGG + chr2.1:47244678-47244697 MS.gene85363:intron 30.0%
ATATTATCAGCAGTTCCATG+TGG - chr2.1:47244352-47244371 None:intergenic 35.0%
ATTTCGATTGTGACGTAACA+TGG - chr2.1:47244186-47244205 None:intergenic 35.0%
CAGCTTACCATCTTCTATAA+TGG + chr2.1:47244065-47244084 MS.gene85363:CDS 35.0%
GATAGAATTCTTTGCAGGAA+AGG - chr2.1:47244395-47244414 None:intergenic 35.0%
! CACAAAATTTGAAACATGGC+AGG - chr2.1:47244619-47244638 None:intergenic 35.0%
! CTTCTTTGTTTCACTAGACT+TGG - chr2.1:47244272-47244291 None:intergenic 35.0%
!! GGGAGTATTTGTATCTATGA+TGG + chr2.1:47244086-47244105 MS.gene85363:CDS 35.0%
!!! TTGTCAGCTACCTTTGTTTT+TGG - chr2.1:47244730-47244749 None:intergenic 35.0%
AACAAAGGTAGCTGACAACA+TGG + chr2.1:47244732-47244751 MS.gene85363:CDS 40.0%
CTGCAAAGAATTCTATCTGC+AGG + chr2.1:47244398-47244417 MS.gene85363:CDS 40.0%
CTGCAGATAGAATTCTTTGC+AGG - chr2.1:47244400-47244419 None:intergenic 40.0%
GACAACATGGAGAACAACTT+CGG + chr2.1:47244745-47244764 MS.gene85363:CDS 40.0%
TCCTTCATTGAAACCGAATC+TGG - chr2.1:47244784-47244803 None:intergenic 40.0%
TGAAGGAACAGGTGAAAGAA+CGG - chr2.1:47244317-47244336 None:intergenic 40.0%
TGATAATATCGCTTCACCAC+AGG + chr2.1:47244363-47244382 MS.gene85363:CDS 40.0%
TGATGGAATTCCTGCAGAAA+AGG + chr2.1:47244103-47244122 MS.gene85363:CDS 40.0%
TTCTTTCACCTGTTCCTTCA+AGG + chr2.1:47244317-47244336 MS.gene85363:CDS 40.0%
AACAGGTGAAAGAACGGGAA+CGG - chr2.1:47244311-47244330 None:intergenic 45.0%
AATTCTATCTGCAGGCTGCA+AGG + chr2.1:47244406-47244425 MS.gene85363:CDS 45.0%
AGTGAATGTCTGCGTGCTAT+TGG - chr2.1:47244556-47244575 None:intergenic 45.0%
ATTGGATTCGTTCCAGATGC+TGG - chr2.1:47244029-47244048 None:intergenic 45.0%
GAAGGAACAGGTGAAAGAAC+GGG - chr2.1:47244316-47244335 None:intergenic 45.0%
GGTTTCAATGAAGGAACCAC+AGG + chr2.1:47244789-47244808 MS.gene85363:CDS 45.0%
TCCTTCCTCGCCAAAAACAA+AGG + chr2.1:47244717-47244736 MS.gene85363:CDS 45.0%
TGCTGACAATTCGCCAGATT+CGG + chr2.1:47244768-47244787 MS.gene85363:CDS 45.0%
TTCAATGAAGGAACCACAGG+AGG + chr2.1:47244792-47244811 MS.gene85363:CDS 45.0%
! GCCAGATTCGGTTTCAATGA+AGG + chr2.1:47244780-47244799 MS.gene85363:CDS 45.0%
!!! ACCTTTGTTTTTGGCGAGGA+AGG - chr2.1:47244721-47244740 None:intergenic 45.0%
!!! AGCTACCTTTGTTTTTGGCG+AGG - chr2.1:47244725-47244744 None:intergenic 45.0%
!!! GTTTTTGGCGAGGAAGGATA+GGG - chr2.1:47244715-47244734 None:intergenic 45.0%
!!! TGTTTTTGGCGAGGAAGGAT+AGG - chr2.1:47244716-47244735 None:intergenic 45.0%
ACAGGTGAAAGAACGGGAAC+GGG - chr2.1:47244310-47244329 None:intergenic 50.0%
GAAGAAGGCCTTGAAGGAAC+AGG - chr2.1:47244328-47244347 None:intergenic 50.0%
GTTGGCTGAAATTCCTCCTG+TGG - chr2.1:47244808-47244827 None:intergenic 50.0%
!! TTCTTCAGAAGCGTCGAGAC+AGG + chr2.1:47244584-47244603 MS.gene85363:CDS 50.0%
CAGTGTAGCGTAGCTGCGTA+GGG - chr2.1:47244132-47244151 None:intergenic 55.0%
GCAGTTCCATGTGGCGAAGA+AGG - chr2.1:47244343-47244362 None:intergenic 55.0%
TCAAGGCCTTCTTCGCCACA+TGG + chr2.1:47244334-47244353 MS.gene85363:CDS 55.0%
TCAGTGTAGCGTAGCTGCGT+AGG - chr2.1:47244133-47244152 None:intergenic 55.0%
TGTGGCGAAGAAGGCCTTGA+AGG - chr2.1:47244334-47244353 None:intergenic 55.0%
! CGTAGGGCTACCTTTTCTGC+AGG - chr2.1:47244116-47244135 None:intergenic 55.0%
GCAGGAAAGGGATGTGCCTG+TGG - chr2.1:47244382-47244401 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 47244023 47244843 47244023 ID=MS.gene85363
chr2.1 mRNA 47244023 47244843 47244023 ID=MS.gene85363.t1;Parent=MS.gene85363
chr2.1 exon 47244023 47244124 47244023 ID=MS.gene85363.t1.exon1;Parent=MS.gene85363.t1
chr2.1 CDS 47244023 47244124 47244023 ID=cds.MS.gene85363.t1;Parent=MS.gene85363.t1
chr2.1 exon 47244235 47244427 47244235 ID=MS.gene85363.t1.exon2;Parent=MS.gene85363.t1
chr2.1 CDS 47244235 47244427 47244235 ID=cds.MS.gene85363.t1;Parent=MS.gene85363.t1
chr2.1 exon 47244548 47244605 47244548 ID=MS.gene85363.t1.exon3;Parent=MS.gene85363.t1
chr2.1 CDS 47244548 47244605 47244548 ID=cds.MS.gene85363.t1;Parent=MS.gene85363.t1
chr2.1 exon 47244696 47244843 47244696 ID=MS.gene85363.t1.exon4;Parent=MS.gene85363.t1
chr2.1 CDS 47244696 47244843 47244696 ID=cds.MS.gene85363.t1;Parent=MS.gene85363.t1
Gene Sequence

>MS.gene85363

ATGCCAGCATCTGGAACGAATCCAATGATTGCTAATACAACTCAGCTTACCATCTTCTATAATGGGAGTATTTGTATCTATGATGGAATTCCTGCAGAAAAGGTAGCCCTACGCAGCTACGCTACACTGAGATGATTAGTGAAACTTACAGCTCTATTTTCCATGTTACGTCACAATCGAAATCATATTTAATTCTCTCTATATACTAACAGGTGCAAGAAATAATGTGCATTGCTGCTGCTGCTGCCAAGTCTAGTGAAACAAAGAAGATTGTGAAACAATCTCCCGTTCCCGTTCTTTCACCTGTTCCTTCAAGGCCTTCTTCGCCACATGGAACTGCTGATAATATCGCTTCACCACAGGCACATCCCTTTCCTGCAAAGAATTCTATCTGCAGGCTGCAAGGTGTGAATTTTCCTATTAATTATGTCTTCAACTATTTACTAACTGTATGAACTTGAATAGACTCTTAATGCCACCATAATTTATATGTCTCGTGTGGTTTTTCTTGATATTTCTCTTCAGAATTTCCAATAGCACGCAGACATTCACTTCAAATGTTTCTTCAGAAGCGTCGAGACAGGTACTGTCTACCTGCCATGTTTCAAATTTTGTGTATGATTGTTATATACTATTAGTTTTCTTATTTGGATAATTTATGTTTGCATTACAGGTTGGGTAGTAAAGCTCCCTATCCTTCCTCGCCAAAAACAAAGGTAGCTGACAACATGGAGAACAACTTCGGTGCTGACAATTCGCCAGATTCGGTTTCAATGAAGGAACCACAGGAGGAATTTCAGCCAACTATATCTGCATCTTGA
Protein sequence

>MS.gene85363.t1

MPASGTNPMIANTTQLTIFYNGSICIYDGIPAEKVQEIMCIAAAAAKSSETKKIVKQSPVPVLSPVPSRPSSPHGTADNIASPQAHPFPAKNSICRLQEFPIARRHSLQMFLQKRRDRLGSKAPYPSSPKTKVADNMENNFGADNSPDSVSMKEPQEEFQPTISAS