AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene86421

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene86421.t1 MTR_7g023810 66.667 159 38 4 5 148 1 159 2.99e-63 192
MS.gene86421.t1 MTR_1g115315 53.846 182 53 5 1 151 1 182 5.90e-52 166
MS.gene86421.t1 MTR_1g115315 53.846 182 53 5 1 151 1 182 9.00e-52 166
MS.gene86421.t1 MTR_3g115620 47.552 143 49 2 18 134 19 161 5.31e-40 134
MS.gene86421.t1 MTR_4g084550 39.286 84 44 1 58 141 64 140 3.63e-14 66.6
MS.gene86421.t1 MTR_8g107210 38.710 93 53 2 58 150 96 184 9.20e-14 67.8
MS.gene86421.t1 MTR_2g015000 41.935 62 36 0 58 119 55 116 3.09e-12 63.5
MS.gene86421.t1 MTR_7g025010 36.145 83 52 1 37 119 27 108 9.98e-12 62.0
MS.gene86421.t1 MTR_7g060630 37.879 66 41 0 58 123 8 73 2.77e-11 59.3
MS.gene86421.t1 MTR_4g088070 37.879 66 41 0 52 117 23 88 8.20e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene86421.t1 AT4G35550 51.333 150 46 3 16 138 35 184 1.74e-39 134
MS.gene86421.t1 AT1G20700 45.600 125 43 1 18 117 30 154 6.17e-34 118
MS.gene86421.t1 AT1G20700 45.600 125 43 1 18 117 30 154 7.23e-34 118
MS.gene86421.t1 AT1G20710 42.537 134 52 1 18 126 14 147 2.64e-25 96.3
MS.gene86421.t1 AT1G20700 45.349 86 47 0 32 117 7 92 3.94e-25 94.4
MS.gene86421.t1 AT5G45980 42.424 66 38 0 54 119 51 116 1.32e-13 67.0
MS.gene86421.t1 AT3G18010 31.731 104 67 1 28 127 42 145 1.21e-12 64.3
MS.gene86421.t1 AT2G33880 41.935 62 36 0 58 119 55 116 4.83e-12 62.8
MS.gene86421.t1 AT2G33880 41.935 62 36 0 58 119 55 116 5.10e-12 62.8
MS.gene86421.t1 AT2G01500 43.636 55 31 0 58 112 61 115 1.30e-11 61.2
MS.gene86421.t1 AT2G28610 38.462 65 40 0 58 122 8 72 1.32e-11 60.8
MS.gene86421.t1 AT5G05770 31.915 94 64 0 58 151 29 122 3.82e-11 57.4

Find 23 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAACTTACTAGTGCGATTT+TGG 0.170160 2.3:-909143 None:intergenic
CTGAGACCAATGTATATAAT+TGG 0.221984 2.3:+909520 MS.gene86421:CDS
TATAAGCTACATTCTTTAGT+TGG 0.349191 2.3:-909685 None:intergenic
ACCTGTACAACTTCAAACTA+TGG 0.358508 2.3:+909410 MS.gene86421:CDS
TCCAAGCAAGGAAAAGATAA+AGG 0.385115 2.3:+909461 MS.gene86421:CDS
CTCAGAAATTTGTCCGTGCT+TGG 0.426170 2.3:-909502 None:intergenic
TTGGACTAGATATGAATTCA+AGG 0.448892 2.3:+909370 MS.gene86421:intron
GAAAGGCATGGAGAACTTGA+TGG 0.452857 2.3:+908996 None:intergenic
TATGAATTCAAGGCATCGTT+GGG 0.483810 2.3:+909380 MS.gene86421:CDS
TCCATAGTTTGAAGTTGTAC+AGG 0.489991 2.3:-909411 None:intergenic
CAAGAGAAAGCATCGGAGTA+GGG 0.507277 2.3:+909566 MS.gene86421:CDS
ACAAGAGAAAGCATCGGAGT+AGG 0.511487 2.3:+909565 MS.gene86421:CDS
GCGAATATTTGAAGCTGAGA+CGG 0.563300 2.3:+909434 MS.gene86421:CDS
CTGAAACCAATTATATACAT+TGG 0.563327 2.3:-909526 None:intergenic
GGTTTCAGAACAGACGTGCT+AGG 0.577434 2.3:+909541 MS.gene86421:CDS
GTTGTTGATTTAGCCAAGCA+CGG 0.577536 2.3:+909489 MS.gene86421:CDS
ATATGAATTCAAGGCATCGT+TGG 0.578747 2.3:+909379 MS.gene86421:CDS
GTTTGAAGTTGTACAGGTGT+TGG 0.595078 2.3:-909405 None:intergenic
GGTTAATGTTGAATCAGAAG+TGG 0.597468 2.3:+909587 MS.gene86421:CDS
TGAGACGGAGTCTCCAAGCA+AGG 0.649464 2.3:+909449 MS.gene86421:CDS
CTTATCATCAGAATCAACCT+CGG 0.655992 2.3:-909613 None:intergenic
CTAGGTACAAGAGAAAGCAT+CGG 0.670064 2.3:+909559 MS.gene86421:CDS
TGAATCAGAAGTGGAGACCG+AGG 0.711591 2.3:+909596 MS.gene86421:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAACAAAACAAAAAAGTTA+AGG + chr2.3:909231-909250 MS.gene86421:intron 15.0%
!! AAACAAAACAAAAAAGTTAA+GGG + chr2.3:909232-909251 MS.gene86421:intron 15.0%
!! AACTGAATAAAATAACAATC+TGG - chr2.3:909315-909334 None:intergenic 20.0%
! CATGATGATCACATTTAATT+AGG + chr2.3:909282-909301 MS.gene86421:intron 25.0%
! CTGAAACCAATTATATACAT+TGG - chr2.3:909529-909548 None:intergenic 25.0%
!! CAGTTACACTTTCTTTTTAT+TGG + chr2.3:909351-909370 MS.gene86421:intron 25.0%
!!! CATAAACTGCAATTTGTTTT+CGG - chr2.3:909086-909105 None:intergenic 25.0%
!!! TTTGGTTTTTATGCATTTGA+AGG - chr2.3:909128-909147 None:intergenic 25.0%
AAAATCGCACTAGTAAGTTT+AGG + chr2.3:909145-909164 MS.gene86421:intron 30.0%
AAATCGCACTAGTAAGTTTA+GGG + chr2.3:909146-909165 MS.gene86421:intron 30.0%
CTGAGACCAATGTATATAAT+TGG + chr2.3:909520-909539 MS.gene86421:CDS 30.0%
! AAGAAAGTGTAACTGAGTTT+AGG - chr2.3:909346-909365 None:intergenic 30.0%
! TAAACTTACTAGTGCGATTT+TGG - chr2.3:909146-909165 None:intergenic 30.0%
! TTGGACTAGATATGAATTCA+AGG + chr2.3:909370-909389 MS.gene86421:intron 30.0%
ACCTGTACAACTTCAAACTA+TGG + chr2.3:909410-909429 MS.gene86421:CDS 35.0%
CTTATCATCAGAATCAACCT+CGG - chr2.3:909616-909635 None:intergenic 35.0%
GGTTAATGTTGAATCAGAAG+TGG + chr2.3:909587-909606 MS.gene86421:CDS 35.0%
TCCAAGCAAGGAAAAGATAA+AGG + chr2.3:909461-909480 MS.gene86421:CDS 35.0%
! ATTCTCTCTGGTGTCAATTT+AGG + chr2.3:909188-909207 MS.gene86421:intron 35.0%
! TCCATAGTTTGAAGTTGTAC+AGG - chr2.3:909414-909433 None:intergenic 35.0%
! TCCTTTATCTTTTCCTTGCT+TGG - chr2.3:909465-909484 None:intergenic 35.0%
!! ATATGAATTCAAGGCATCGT+TGG + chr2.3:909379-909398 MS.gene86421:CDS 35.0%
!! TATGAATTCAAGGCATCGTT+GGG + chr2.3:909380-909399 MS.gene86421:CDS 35.0%
! CTAGGTACAAGAGAAAGCAT+CGG + chr2.3:909559-909578 MS.gene86421:CDS 40.0%
! GCGAATATTTGAAGCTGAGA+CGG + chr2.3:909434-909453 MS.gene86421:CDS 40.0%
! GTTTGAAGTTGTACAGGTGT+TGG - chr2.3:909408-909427 None:intergenic 40.0%
! TCTCTGGTGTCAATTTAGGT+GGG + chr2.3:909192-909211 MS.gene86421:intron 40.0%
!! GTTGTTGATTTAGCCAAGCA+CGG + chr2.3:909489-909508 MS.gene86421:CDS 40.0%
CTCAGAAATTTGTCCGTGCT+TGG - chr2.3:909505-909524 None:intergenic 45.0%
! CTCTCTGGTGTCAATTTAGG+TGG + chr2.3:909191-909210 MS.gene86421:intron 45.0%
! GTTTAGGGTTATAGCGTCTC+AGG + chr2.3:909161-909180 MS.gene86421:intron 45.0%
!! ACAAGAGAAAGCATCGGAGT+AGG + chr2.3:909565-909584 MS.gene86421:CDS 45.0%
!! CAAGAGAAAGCATCGGAGTA+GGG + chr2.3:909566-909585 MS.gene86421:CDS 45.0%
!! TGAGTTTTGTGCGTCTCAAC+TGG + chr2.3:909644-909663 MS.gene86421:CDS 45.0%
GGTTTCAGAACAGACGTGCT+AGG + chr2.3:909541-909560 MS.gene86421:CDS 50.0%
GTCTCAGGTTCGATTCTCTC+TGG + chr2.3:909176-909195 MS.gene86421:intron 50.0%
TGAATCAGAAGTGGAGACCG+AGG + chr2.3:909596-909615 MS.gene86421:CDS 50.0%
!!! GCGTCTCAACTGGCTTTTGA+TGG + chr2.3:909654-909673 MS.gene86421:CDS 50.0%
TGAGACGGAGTCTCCAAGCA+AGG + chr2.3:909449-909468 MS.gene86421:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 909003 909692 909003 ID=MS.gene86421
chr2.3 mRNA 909003 909692 909003 ID=MS.gene86421.t1;Parent=MS.gene86421
chr2.3 exon 909003 909156 909003 ID=MS.gene86421.t1.exon1;Parent=MS.gene86421.t1
chr2.3 CDS 909003 909156 909003 ID=cds.MS.gene86421.t1;Parent=MS.gene86421.t1
chr2.3 exon 909379 909692 909379 ID=MS.gene86421.t1.exon2;Parent=MS.gene86421.t1
chr2.3 CDS 909379 909692 909379 ID=cds.MS.gene86421.t1;Parent=MS.gene86421.t1
Gene Sequence

>MS.gene86421

ATGGAGAACTTGATGGAGTTGCAGATGAATGATTTGAATCAGAACGTAAATGTGATGACTGATGAACAAGTCGAAACTCTCCGAAAACAAATTGCAGTTTATGCTGTCATCTCTGAACAACTCCTTCAAATGCATAAAAACCAAAATCGCACTAGTAAGTTTAGGGTTATAGCGTCTCAGGTTCGATTCTCTCTGGTGTCAATTTAGGTGGGTTAATTTAGCTTCTTCAAAACAAAACAAAAAAGTTAAGGGTTATAGTATCACATCACTCTCTCACTACATGATGATCACATTTAATTAGGTCATACTCCAGATTGTTATTTTATTCAGTTATAGAATACCTAAACTCAGTTACACTTTCTTTTTATTGGACTAGATATGAATTCAAGGCATCGTTGGGCACCAACACCTGTACAACTTCAAACTATGGAGCGAATATTTGAAGCTGAGACGGAGTCTCCAAGCAAGGAAAAGATAAAGGAGATTGTTGTTGATTTAGCCAAGCACGGACAAATTTCTGAGACCAATGTATATAATTGGTTTCAGAACAGACGTGCTAGGTACAAGAGAAAGCATCGGAGTAGGGTTAATGTTGAATCAGAAGTGGAGACCGAGGTTGATTCTGATGATAAGAAGATCGATGAGTTTTGTGCGTCTCAACTGGCTTTTGATGGTATGCTATCCAACTAA
Protein sequence

>MS.gene86421.t1

MENLMELQMNDLNQNVNVMTDEQVETLRKQIAVYAVISEQLLQMHKNQNRTNMNSRHRWAPTPVQLQTMERIFEAETESPSKEKIKEIVVDLAKHGQISETNVYNWFQNRRARYKRKHRSRVNVESEVETEVDSDDKKIDEFCASQLAFDGMLSN