AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene057891

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene057891.t1 MTR_5g085390 90.955 199 15 3 1 197 37 234 1.09e-108 311
MS.gene057891.t1 MTR_6g011200 51.442 208 80 6 1 197 37 234 2.14e-52 168
MS.gene057891.t1 MTR_6g004550 55.556 126 50 2 1 123 1 123 4.74e-38 128
MS.gene057891.t1 MTR_4g099230 58.491 106 39 1 1 106 30 130 7.26e-35 120
MS.gene057891.t1 MTR_6g011230 43.216 199 71 10 1 192 39 202 2.62e-34 120
MS.gene057891.t1 MTR_6g011250 57.692 104 42 1 2 103 38 141 6.28e-34 119
MS.gene057891.t1 MTR_3g452660 40.541 74 43 1 2 75 36 108 1.09e-12 65.5
MS.gene057891.t1 MTR_8g017090 48.649 74 37 1 2 75 41 113 2.77e-12 64.3
MS.gene057891.t1 MTR_3g073690 37.838 74 45 1 2 75 38 110 3.88e-12 62.8
MS.gene057891.t1 MTR_4g107450 45.455 77 41 1 1 77 38 113 5.26e-12 63.5
MS.gene057891.t1 MTR_4g105170 36.842 76 46 2 2 76 40 114 3.96e-11 59.7
MS.gene057891.t1 MTR_5g083010 36.250 80 42 3 2 77 40 114 7.53e-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.gene057891.t1 AT3G47870 48.649 74 37 1 1 74 64 136 1.71e-15 73.6
MS.gene057891.t1 AT3G13850 41.667 84 48 1 2 85 65 147 1.09e-12 65.5
MS.gene057891.t1 AT2G40470 29.358 109 68 4 2 109 49 149 4.81e-11 59.7
MS.gene057891.t1 AT2G40470 29.358 109 68 4 2 109 74 174 8.59e-11 59.3

Find 35 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTAAATATTGGGATATT+TGG 0.141273 5.3:+69055488 None:intergenic
TCACCAACATTGTTAAATAT+TGG 0.190888 5.3:+69055479 None:intergenic
CTTGGTGTTATTATGAATTA+TGG 0.198268 5.3:-69055632 MS.gene057891:CDS
AGCTAGAACAACATTTGATT+TGG 0.264146 5.3:-69055240 MS.gene057891:CDS
TCATTGCTTGATAATCCTTT+TGG 0.267871 5.3:+69055308 None:intergenic
GGAATTTGAGAACTAGTATA+AGG 0.287802 5.3:+69055509 None:intergenic
AATATCCGACTCAATAATTA+TGG 0.288561 5.3:+69055682 None:intergenic
GCTAGAACAACATTTGATTT+GGG 0.292314 5.3:-69055239 MS.gene057891:CDS
CACCAACATTGTTAAATATT+GGG 0.294726 5.3:+69055480 None:intergenic
AGCAACGCTCATCGTTTGTT+TGG 0.383470 5.3:-69055773 MS.gene057891:CDS
GGATGACAATTCTAATTTGA+TGG 0.388591 5.3:-69055333 MS.gene057891:CDS
CCTCATGATGTTAACTATAG+TGG 0.400420 5.3:-69055371 MS.gene057891:CDS
AGATATGTTAAAGCAGTCTA+TGG 0.416875 5.3:-69055609 MS.gene057891:CDS
CTTTAGTATCCTTTGTATGT+TGG 0.435097 5.3:+69055745 None:intergenic
CGTGCAAAATCTCCCGTTCA+TGG 0.444453 5.3:-69055659 MS.gene057891:CDS
ATCCCAATATTTAACAATGT+TGG 0.449694 5.3:-69055482 MS.gene057891:CDS
GACGACCTTGACGACCTTGA+TGG 0.460725 5.3:-69055278 MS.gene057891:CDS
TCTAATTTGATGGTACCAAA+AGG 0.475215 5.3:-69055323 MS.gene057891:CDS
ACACCAAGACATCCATGAAC+GGG 0.497015 5.3:+69055647 None:intergenic
TTGAGAACTAGTATAAGGTA+AGG 0.504496 5.3:+69055514 None:intergenic
TCTCCCGTTCATGGATGTCT+TGG 0.510462 5.3:-69055650 MS.gene057891:CDS
AAAGCAGTCTATGGAAGAGT+TGG 0.512156 5.3:-69055600 MS.gene057891:CDS
AAGGATACTAAAGGAAATCA+AGG 0.515917 5.3:-69055735 MS.gene057891:CDS
CAACATACAAAGGATACTAA+AGG 0.551295 5.3:-69055744 MS.gene057891:CDS
CTAGAACAACATTTGATTTG+GGG 0.562151 5.3:-69055238 MS.gene057891:CDS
GAGATCCATAATTATTGAGT+CGG 0.580015 5.3:-69055687 MS.gene057891:CDS
CCACTATAGTTAACATCATG+AGG 0.583308 5.3:+69055371 None:intergenic
GTTCATCAACACCACCATCA+AGG 0.592727 5.3:+69055264 None:intergenic
TTGGTGTTTCCAACATACAA+AGG 0.602738 5.3:-69055754 MS.gene057891:CDS
AACACCAAGACATCCATGAA+CGG 0.603796 5.3:+69055646 None:intergenic
CACCACCATCAAGGTCGTCA+AGG 0.611148 5.3:+69055273 None:intergenic
CATGATGTTAACTATAGTGG+TGG 0.632189 5.3:-69055368 MS.gene057891:CDS
TAGTGGTGGCGACTATGTCA+TGG 0.648101 5.3:-69055354 MS.gene057891:CDS
CACTATAGTTAACATCATGA+GGG 0.659397 5.3:+69055372 None:intergenic
GACCTTGACGACCTTGATGG+TGG 0.717140 5.3:-69055275 MS.gene057891:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GGATAATAATAATAATAATT+AGG + chr5.3:69055538-69055557 None:intergenic 10.0%
!!! ATATTATTATTTTCACTATT+GGG + chr5.3:69055559-69055578 None:intergenic 10.0%
!!! CATATTATTATTTTCACTAT+TGG + chr5.3:69055560-69055579 None:intergenic 15.0%
!! TTGTTAAATATTGGGATATT+TGG + chr5.3:69055502-69055521 None:intergenic 20.0%
! AATATCCGACTCAATAATTA+TGG + chr5.3:69055308-69055327 None:intergenic 25.0%
! ATCCCAATATTTAACAATGT+TGG - chr5.3:69055505-69055524 MS.gene057891:CDS 25.0%
! CACCAACATTGTTAAATATT+GGG + chr5.3:69055510-69055529 None:intergenic 25.0%
! TCACCAACATTGTTAAATAT+TGG + chr5.3:69055511-69055530 None:intergenic 25.0%
!!! CTTGGTGTTATTATGAATTA+TGG - chr5.3:69055355-69055374 MS.gene057891:CDS 25.0%
AAGGATACTAAAGGAAATCA+AGG - chr5.3:69055252-69055271 MS.gene057891:CDS 30.0%
AGATATGTTAAAGCAGTCTA+TGG - chr5.3:69055378-69055397 MS.gene057891:CDS 30.0%
AGCTAGAACAACATTTGATT+TGG - chr5.3:69055747-69055766 MS.gene057891:CDS 30.0%
CAACATACAAAGGATACTAA+AGG - chr5.3:69055243-69055262 MS.gene057891:CDS 30.0%
CACTATAGTTAACATCATGA+GGG + chr5.3:69055618-69055637 None:intergenic 30.0%
CTTTAGTATCCTTTGTATGT+TGG + chr5.3:69055245-69055264 None:intergenic 30.0%
GAGATCCATAATTATTGAGT+CGG - chr5.3:69055300-69055319 MS.gene057891:CDS 30.0%
GGAATTTGAGAACTAGTATA+AGG + chr5.3:69055481-69055500 None:intergenic 30.0%
GGATGACAATTCTAATTTGA+TGG - chr5.3:69055654-69055673 MS.gene057891:CDS 30.0%
TTGAGAACTAGTATAAGGTA+AGG + chr5.3:69055476-69055495 None:intergenic 30.0%
! GCTAGAACAACATTTGATTT+GGG - chr5.3:69055748-69055767 MS.gene057891:CDS 30.0%
! TCTAATTTGATGGTACCAAA+AGG - chr5.3:69055664-69055683 MS.gene057891:CDS 30.0%
!! ACATTTGATTTGGGGAAAAA+AGG - chr5.3:69055757-69055776 MS.gene057891:CDS 30.0%
!! CTAGAACAACATTTGATTTG+GGG - chr5.3:69055749-69055768 MS.gene057891:CDS 30.0%
!! TCATTGCTTGATAATCCTTT+TGG + chr5.3:69055682-69055701 None:intergenic 30.0%
CATGATGTTAACTATAGTGG+TGG - chr5.3:69055619-69055638 MS.gene057891:CDS 35.0%
CCACTATAGTTAACATCATG+AGG + chr5.3:69055619-69055638 None:intergenic 35.0%
CCTCATGATGTTAACTATAG+TGG - chr5.3:69055616-69055635 MS.gene057891:CDS 35.0%
! TTGGTGTTTCCAACATACAA+AGG - chr5.3:69055233-69055252 MS.gene057891:CDS 35.0%
AAAGCAGTCTATGGAAGAGT+TGG - chr5.3:69055387-69055406 MS.gene057891:CDS 40.0%
AACACCAAGACATCCATGAA+CGG + chr5.3:69055344-69055363 None:intergenic 40.0%
ACACCAAGACATCCATGAAC+GGG + chr5.3:69055343-69055362 None:intergenic 45.0%
AGCAACGCTCATCGTTTGTT+TGG - chr5.3:69055214-69055233 MS.gene057891:CDS 45.0%
GTTCATCAACACCACCATCA+AGG + chr5.3:69055726-69055745 None:intergenic 45.0%
CGTGCAAAATCTCCCGTTCA+TGG - chr5.3:69055328-69055347 MS.gene057891:CDS 50.0%
TCTCCCGTTCATGGATGTCT+TGG - chr5.3:69055337-69055356 MS.gene057891:CDS 50.0%
! TAGTGGTGGCGACTATGTCA+TGG - chr5.3:69055633-69055652 MS.gene057891:CDS 50.0%
CACCACCATCAAGGTCGTCA+AGG + chr5.3:69055717-69055736 None:intergenic 55.0%
GACCTTGACGACCTTGATGG+TGG - chr5.3:69055712-69055731 MS.gene057891:CDS 55.0%
GACGACCTTGACGACCTTGA+TGG - chr5.3:69055709-69055728 MS.gene057891:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 69055208 69055801 69055208 ID=MS.gene057891
chr5.3 mRNA 69055208 69055801 69055208 ID=MS.gene057891.t1;Parent=MS.gene057891
chr5.3 exon 69055208 69055801 69055208 ID=MS.gene057891.t1.exon1;Parent=MS.gene057891.t1
chr5.3 CDS 69055208 69055801 69055208 ID=cds.MS.gene057891.t1;Parent=MS.gene057891.t1
Gene Sequence

>MS.gene057891

ATGTTTAGCAACGCTCATCGTTTGTTTGGTGTTTCCAACATACAAAGGATACTAAAGGAAATCAAGGACGACGATCAAAAAGATGATGCGATGAGATCCATAATTATTGAGTCGGATATTCGTGCAAAATCTCCCGTTCATGGATGTCTTGGTGTTATTATGAATTATGGAGATATGTTAAAGCAGTCTATGGAAGAGTTGGATCATGTAAAAACGTTACTAGCTTATTGTAACGATTTACAACAAAAACAACATCTTCATTCTTCCTTACCTTATACTAGTTCTCAAATTCCAAATATCCCAATATTTAACAATGTTGGTGATGTTCCTAATTATTATTATTATTATCCCAATAGTGAAAATAATAATATGATGAGAGCATCTTCTTCTTATATTAGTGACATCATCCCTCATGATGTTAACTATAGTGGTGGCGACTATGTCATGGATGACAATTCTAATTTGATGGTACCAAAAGGATTATCAAGCAATGAAGAATCAGACGACCTTGACGACCTTGATGGTGGTGTTGATGAACAAGCTAGAACAACATTTGATTTGGGGAAAAAAGGAAGATTTTCAGATAGTGATTAA
Protein sequence

>MS.gene057891.t1

MFSNAHRLFGVSNIQRILKEIKDDDQKDDAMRSIIIESDIRAKSPVHGCLGVIMNYGDMLKQSMEELDHVKTLLAYCNDLQQKQHLHSSLPYTSSQIPNIPIFNNVGDVPNYYYYYPNSENNNMMRASSSYISDIIPHDVNYSGGDYVMDDNSNLMVPKGLSSNEESDDLDDLDGGVDEQARTTFDLGKKGRFSDSD