AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene050088

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene050088.t1 MTR_4g057800 89.706 136 12 1 1 134 1 136 6.84e-87 249
MS.gene050088.t1 MTR_4g057810 83.333 108 18 0 1 108 1 108 1.61e-64 192
MS.gene050088.t1 MTR_2g095430 56.190 105 40 2 5 107 16 116 1.69e-36 122
MS.gene050088.t1 MTR_1g063330 46.667 75 40 0 26 100 20 94 1.52e-20 80.5
MS.gene050088.t1 MTR_1g063340 45.333 75 41 0 26 100 20 94 9.20e-20 78.6
MS.gene050088.t1 MTR_1g063300 44.318 88 49 0 13 100 14 101 1.01e-19 78.6
MS.gene050088.t1 MTR_1g063290 42.045 88 51 0 13 100 14 101 3.08e-19 77.4
MS.gene050088.t1 MTR_1g063310 41.772 79 46 0 33 111 21 99 5.10e-18 73.9
MS.gene050088.t1 MTR_1g063280 50.746 67 33 0 34 100 38 104 2.90e-17 72.4
MS.gene050088.t1 MTR_1g063260 50.746 67 33 0 34 100 37 103 5.62e-17 71.6
MS.gene050088.t1 MTR_7g101920 43.836 73 41 0 33 105 30 102 1.83e-16 70.5
MS.gene050088.t1 MTR_7g101890 44.444 63 35 0 38 100 52 114 1.18e-14 65.9
MS.gene050088.t1 MTR_8g076040 43.243 74 40 1 26 99 29 100 1.83e-14 65.1
MS.gene050088.t1 MTR_5g021820 45.455 66 34 1 26 91 28 91 2.90e-14 64.7
MS.gene050088.t1 MTR_3g117610 54.545 55 23 1 37 91 44 96 3.30e-13 62.0
MS.gene050088.t1 MTR_4g072190 43.902 82 38 3 11 91 13 87 3.94e-13 61.6
MS.gene050088.t1 MTR_3g113310 46.032 63 32 1 37 99 41 101 2.08e-12 59.7
MS.gene050088.t1 MTR_4g072910 36.364 88 46 3 6 92 10 88 3.30e-12 59.3
MS.gene050088.t1 MTR_3g117640 51.786 56 25 2 37 91 33 87 6.97e-11 55.8
MS.gene050088.t1 MTR_4g124750 36.458 96 58 2 5 100 37 129 9.35e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene050088.t1 AT2G28085 46.296 108 51 3 4 104 16 123 1.53e-24 91.7
MS.gene050088.t1 AT3G09870 46.269 67 36 0 34 100 41 107 1.19e-15 68.6
MS.gene050088.t1 AT2G21220 56.364 55 22 1 37 91 39 91 1.20e-13 63.2
MS.gene050088.t1 AT4G34760 45.070 71 37 1 29 99 34 102 2.14e-12 59.7
MS.gene050088.t1 AT4G34780 46.667 60 30 2 37 94 27 86 4.28e-12 58.9
MS.gene050088.t1 AT4G38860 48.438 64 30 2 29 91 31 92 5.70e-12 58.5
MS.gene050088.t1 AT5G53590 37.662 77 43 2 37 110 45 119 7.50e-12 59.3
MS.gene050088.t1 AT3G61900 43.548 62 34 1 31 91 23 84 9.74e-12 58.9
MS.gene050088.t1 AT1G19830 43.478 69 37 1 37 105 47 113 1.70e-11 57.8
MS.gene050088.t1 AT4G34800 43.421 76 41 2 27 100 10 85 1.77e-11 57.0
MS.gene050088.t1 AT1G75580 50.909 55 25 1 37 91 43 95 2.40e-11 57.0
MS.gene050088.t1 AT5G66260 44.444 63 33 1 38 100 34 94 2.55e-11 57.0
MS.gene050088.t1 AT2G37030 41.270 63 35 1 30 92 41 101 3.15e-11 57.4
MS.gene050088.t1 AT4G12410 39.189 74 41 2 19 91 60 130 6.26e-11 57.0

Find 24 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATAACATCTGAAGTTTATT+AGG 0.136214 4.2:-45544902 None:intergenic
AATCATTTCTTCCCATTAAT+AGG 0.172378 4.2:-45544688 None:intergenic
TCCAATAGACTCACAAATAT+TGG 0.185171 4.2:-45544821 None:intergenic
TAATAAACTTCAGATGTTAT+TGG 0.222466 4.2:+45544904 MS.gene050088:CDS
CCCAATATTTGTGAGTCTAT+TGG 0.275274 4.2:+45544820 MS.gene050088:CDS
ATCATTTCTTCCCATTAATA+GGG 0.284308 4.2:-45544687 None:intergenic
GCTGAAAAGTATGGATTTAA+TGG 0.293311 4.2:+45544851 MS.gene050088:CDS
TGTGGCAAAGGATGTGAAAA+AGG 0.316950 4.2:+45544724 MS.gene050088:CDS
CCAATAGACTCACAAATATT+GGG 0.324415 4.2:-45544820 None:intergenic
AATATCCACTCGGTCGTCTT+TGG 0.344650 4.2:-45544985 None:intergenic
ATAACATCTGAAGTTTATTA+GGG 0.357631 4.2:-45544901 None:intergenic
GAACAAGCAGCTGAAAAGTA+TGG 0.387212 4.2:+45544842 MS.gene050088:CDS
GTTATTGGTGCAGCAATTGC+AGG 0.408441 4.2:+45544919 MS.gene050088:CDS
GAAATCAAAATGGTTGTTGT+AGG 0.433297 4.2:+45544617 None:intergenic
GGGTTTGTTAAACAACTCAA+TGG 0.477349 4.2:-45544800 None:intergenic
ATCAAAATGGTTGTTGTAGG+TGG 0.492707 4.2:+45544620 None:intergenic
TGAAGTTTATTAGGGCTACA+AGG 0.523865 4.2:-45544893 None:intergenic
GTGCAGCAATTGCAGGAAGA+AGG 0.534889 4.2:+45544926 MS.gene050088:CDS
TAAATCAAGGTATGTGGCAA+AGG 0.539872 4.2:+45544712 MS.gene050088:CDS
TGATTATAAATCAAGGTATG+TGG 0.558755 4.2:+45544706 MS.gene050088:CDS
GAAGAAATGATTATAAATCA+AGG 0.558976 4.2:+45544699 MS.gene050088:CDS
AAGTATGGATTTAATGGAGA+TGG 0.588044 4.2:+45544857 MS.gene050088:CDS
TTTAACTTGAAATATCCACT+CGG 0.674988 4.2:-45544995 None:intergenic
TGTTACCAAAGACGACCGAG+TGG 0.714375 4.2:+45544980 MS.gene050088:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAAGAAATGATTATAAATCA+AGG + chr4.2:45544699-45544718 MS.gene050088:CDS 20.0%
!! TAATAAACTTCAGATGTTAT+TGG + chr4.2:45544904-45544923 MS.gene050088:CDS 20.0%
!!! AATAACATCTGAAGTTTATT+AGG - chr4.2:45544905-45544924 None:intergenic 20.0%
!!! ATAACATCTGAAGTTTATTA+GGG - chr4.2:45544904-45544923 None:intergenic 20.0%
! AATCATTTCTTCCCATTAAT+AGG - chr4.2:45544691-45544710 None:intergenic 25.0%
! ATCATTTCTTCCCATTAATA+GGG - chr4.2:45544690-45544709 None:intergenic 25.0%
! TGATTATAAATCAAGGTATG+TGG + chr4.2:45544706-45544725 MS.gene050088:CDS 25.0%
!!! TTTAACTTGAAATATCCACT+CGG - chr4.2:45544998-45545017 None:intergenic 25.0%
AAGTATGGATTTAATGGAGA+TGG + chr4.2:45544857-45544876 MS.gene050088:CDS 30.0%
CCAATAGACTCACAAATATT+GGG - chr4.2:45544823-45544842 None:intergenic 30.0%
CTCCAAAAAACCCTATTAAT+GGG + chr4.2:45544677-45544696 MS.gene050088:CDS 30.0%
TCCAATAGACTCACAAATAT+TGG - chr4.2:45544824-45544843 None:intergenic 30.0%
! GCTGAAAAGTATGGATTTAA+TGG + chr4.2:45544851-45544870 MS.gene050088:CDS 30.0%
!!! TTCCCATTAATAGGGTTTTT+TGG - chr4.2:45544682-45544701 None:intergenic 30.0%
CCCAATATTTGTGAGTCTAT+TGG + chr4.2:45544820-45544839 MS.gene050088:CDS 35.0%
CCTCCAAAAAACCCTATTAA+TGG + chr4.2:45544676-45544695 MS.gene050088:CDS 35.0%
TAAATCAAGGTATGTGGCAA+AGG + chr4.2:45544712-45544731 MS.gene050088:CDS 35.0%
TGAAGTTTATTAGGGCTACA+AGG - chr4.2:45544896-45544915 None:intergenic 35.0%
! GAAAAAGGGACATTTTGTTG+TGG + chr4.2:45544739-45544758 MS.gene050088:CDS 35.0%
!! ACATTTTGTTGTGGTTGCTA+AGG + chr4.2:45544748-45544767 MS.gene050088:CDS 35.0%
!! GGGTTTGTTAAACAACTCAA+TGG - chr4.2:45544803-45544822 None:intergenic 35.0%
!!! CCATTAATAGGGTTTTTTGG+AGG - chr4.2:45544679-45544698 None:intergenic 35.0%
GAACAAGCAGCTGAAAAGTA+TGG + chr4.2:45544842-45544861 MS.gene050088:CDS 40.0%
GTGGCAAAGGATGTGAAAAA+GGG + chr4.2:45544725-45544744 MS.gene050088:CDS 40.0%
TGTGGCAAAGGATGTGAAAA+AGG + chr4.2:45544724-45544743 MS.gene050088:CDS 40.0%
AATATCCACTCGGTCGTCTT+TGG - chr4.2:45544988-45545007 None:intergenic 45.0%
GTTATTGGTGCAGCAATTGC+AGG + chr4.2:45544919-45544938 MS.gene050088:CDS 45.0%
GTGCAGCAATTGCAGGAAGA+AGG + chr4.2:45544926-45544945 MS.gene050088:CDS 50.0%
TGTTACCAAAGACGACCGAG+TGG + chr4.2:45544980-45544999 MS.gene050088:CDS 50.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 45544626 45545039 45544626 ID=MS.gene050088
chr4.2 mRNA 45544626 45545039 45544626 ID=MS.gene050088.t1;Parent=MS.gene050088
chr4.2 exon 45544626 45545039 45544626 ID=MS.gene050088.t1.exon1;Parent=MS.gene050088.t1
chr4.2 CDS 45544626 45545039 45544626 ID=cds.MS.gene050088.t1;Parent=MS.gene050088.t1
Gene Sequence

>MS.gene050088

ATGGTTGTTGTAGGTGGAATTTTGAAGCTCAAGAATAATGTCTTCAAAAACCTCCAAAAAACCCTATTAATGGGAAGAAATGATTATAAATCAAGGTATGTGGCAAAGGATGTGAAAAAGGGACATTTTGTTGTGGTTGCTAAGGATGAAGATGAAGCAAAGAGATTTATTGTGCCATTGAGTTGTTTAACAAACCCAATATTTGTGAGTCTATTGGAACAAGCAGCTGAAAAGTATGGATTTAATGGAGATGGTGCACTAACTATTCCTTGTAGCCCTAATAAACTTCAGATGTTATTGGTGCAGCAATTGCAGGAAGAAGGAAGCTATTGCTCTGATCAAGTCATGTTTAAATGTTACCAAAGACGACCGAGTGGATATTTCAAGTTAAAGCAAATTGTATCTCAACATTAA
Protein sequence

>MS.gene050088.t1

MVVVGGILKLKNNVFKNLQKTLLMGRNDYKSRYVAKDVKKGHFVVVAKDEDEAKRFIVPLSCLTNPIFVSLLEQAAEKYGFNGDGALTIPCSPNKLQMLLVQQLQEEGSYCSDQVMFKCYQRRPSGYFKLKQIVSQH