AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene29608

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29608.t1 MTR_5g081990 98.378 185 1 2 1 184 1 184 5.40e-135 375
MS.gene29608.t1 MTR_7g060630 68.254 63 20 0 33 95 8 70 6.86e-27 101
MS.gene29608.t1 MTR_4g084550 60.294 68 27 0 33 100 64 131 7.49e-26 98.2
MS.gene29608.t1 MTR_8g107210 63.380 71 26 0 25 95 88 158 1.52e-25 101
MS.gene29608.t1 MTR_1g019130 63.636 66 24 0 33 98 90 155 7.16e-25 96.7
MS.gene29608.t1 MTR_1g019130 63.636 66 24 0 33 98 90 155 7.62e-25 97.1
MS.gene29608.t1 MTR_5g021930 58.108 74 27 2 33 105 30 100 1.04e-23 95.1
MS.gene29608.t1 MTR_4g063735 56.061 66 29 0 33 98 25 90 9.56e-23 92.0
MS.gene29608.t1 MTR_8g095580 67.273 55 18 0 44 98 93 147 2.79e-19 80.5
MS.gene29608.t1 MTR_3g088485 65.455 55 19 0 44 98 91 145 5.67e-19 79.7
MS.gene29608.t1 MTR_7g025010 42.188 64 37 0 33 96 47 110 1.51e-14 71.2
MS.gene29608.t1 MTR_2g015000 43.750 64 36 0 33 96 55 118 1.60e-14 70.9
MS.gene29608.t1 MTR_4g088070 39.344 61 37 0 33 93 29 89 1.87e-12 65.1
MS.gene29608.t1 MTR_1g115315 43.333 60 34 0 33 92 85 144 4.58e-11 60.5
MS.gene29608.t1 MTR_1g115315 43.333 60 34 0 33 92 85 144 5.50e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29608.t1 AT3G11260 57.459 181 62 5 14 184 7 182 3.52e-60 186
MS.gene29608.t1 AT5G05770 64.602 113 32 3 4 110 2 112 7.23e-40 132
MS.gene29608.t1 AT3G18010 69.841 63 19 0 33 95 76 138 5.32e-26 102
MS.gene29608.t1 AT2G28610 63.492 63 23 0 33 95 8 70 5.48e-25 97.4
MS.gene29608.t1 AT5G59340 56.000 75 28 1 21 95 7 76 1.85e-24 96.7
MS.gene29608.t1 AT1G46480 61.905 63 24 0 33 95 90 152 9.07e-24 93.2
MS.gene29608.t1 AT1G46480 61.905 63 24 0 33 95 90 152 5.09e-23 92.4
MS.gene29608.t1 AT2G17950 65.079 63 21 1 33 94 38 100 6.06e-23 93.2
MS.gene29608.t1 AT2G01500 65.455 55 19 0 33 87 61 115 8.57e-21 87.0
MS.gene29608.t1 AT2G33880 43.548 62 35 0 33 94 55 116 3.93e-14 69.7
MS.gene29608.t1 AT2G33880 43.548 62 35 0 33 94 55 116 4.41e-14 69.7
MS.gene29608.t1 AT5G45980 45.161 62 34 0 33 94 55 116 9.14e-14 68.6
MS.gene29608.t1 AT1G20700 35.556 90 55 2 19 106 20 108 2.62e-11 59.3
MS.gene29608.t1 AT4G35550 42.623 61 35 0 33 93 99 159 2.98e-11 60.8
MS.gene29608.t1 AT1G20700 35.556 90 55 2 19 106 82 170 5.70e-11 59.3
MS.gene29608.t1 AT1G20700 38.667 75 45 1 19 93 82 155 6.03e-11 59.3

Find 24 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTTTAACTTGTTCTGTTGT+TGG 0.328649 5.2:+70048929 None:intergenic
GATTCACCAAATGAGTTCAA+TGG 0.392997 5.2:+70048359 None:intergenic
AGAGCAAGAATGTGTTGTAT+TGG 0.397222 5.2:-70048814 MS.gene29608:CDS
AGAGTCTCAATCACTCTATC+AGG 0.412077 5.2:+70048392 None:intergenic
ATGTACAATGGGAGAACAAA+TGG 0.428304 5.2:-70048273 MS.gene29608:CDS
AACACCCACCATTGGACTTA+CGG 0.439714 5.2:-70048250 MS.gene29608:CDS
GGTTTCAGAATCACAAAGCT+AGG 0.453724 5.2:-70048793 MS.gene29608:CDS
TTCTGAATTTGATCGGTGCT+TGG 0.463204 5.2:+70048872 None:intergenic
AGTGGAAGCAGCAGCAGCAC+TGG 0.493876 5.2:-70048974 MS.gene29608:CDS
AATATGGAAGAGAGCATGTC+AGG 0.497698 5.2:-70049037 MS.gene29608:CDS
TTTGCATACACATGTACAAT+GGG 0.499345 5.2:-70048284 MS.gene29608:CDS
AGTAGTTTCCATGGTAAAAG+TGG 0.503916 5.2:-70048992 MS.gene29608:CDS
ACAAATGGAACACCCACCAT+TGG 0.543359 5.2:-70048258 MS.gene29608:CDS
TCATCTGGAAGTAGTTTCCA+TGG 0.556114 5.2:-70049001 MS.gene29608:CDS
GTTTCAGAATCACAAAGCTA+GGG 0.556495 5.2:-70048792 MS.gene29608:CDS
GTATGCATGCAAATGAATGC+AGG 0.569996 5.2:-70048319 MS.gene29608:CDS
AGCAGCACTGGCACAAAGTG+TGG 0.575447 5.2:-70048962 MS.gene29608:CDS
CTCAACCGTAAGTCCAATGG+TGG 0.576156 5.2:+70048245 None:intergenic
GTGAATCAGAATCAGAGAAG+TGG 0.590084 5.2:-70048343 MS.gene29608:CDS
CTGGCACAAAGTGTGGTCGT+TGG 0.591246 5.2:-70048955 MS.gene29608:CDS
AAACTCAACCGTAAGTCCAA+TGG 0.615710 5.2:+70048242 None:intergenic
GTTTGCATACACATGTACAA+TGG 0.618786 5.2:-70048285 MS.gene29608:CDS
TATGCATGCAAATGAATGCA+GGG 0.627141 5.2:-70048318 MS.gene29608:CDS
TCAACCGTAAGTCCAATGGT+GGG 0.711399 5.2:+70048246 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTATTAAATTTTTTGCTTT+AGG - chr5.2:70048757-70048776 MS.gene29608:CDS 15.0%
!!! AAATTATTTTTCTAACGAGA+TGG + chr5.2:70048712-70048731 None:intergenic 20.0%
!! GGATATTTTCTGAATTTGAT+CGG + chr5.2:70048407-70048426 None:intergenic 25.0%
!!! ACCATAAAAACTAAGTTGAT+TGG + chr5.2:70048428-70048447 None:intergenic 25.0%
!!! TCCAATCAACTTAGTTTTTA+TGG - chr5.2:70048424-70048443 MS.gene29608:intron 25.0%
AATGAATAAATGAGTTGCGT+CGG + chr5.2:70048618-70048637 None:intergenic 30.0%
AGTATCAGATCAAAGTTTCA+AGG + chr5.2:70048658-70048677 None:intergenic 30.0%
TTTGCATACACATGTACAAT+GGG - chr5.2:70048985-70049004 MS.gene29608:CDS 30.0%
! CTTTTTCCATTGAACTCATT+TGG - chr5.2:70048904-70048923 MS.gene29608:CDS 30.0%
! TCTTTTCCTCATATATTGCA+GGG - chr5.2:70048833-70048852 MS.gene29608:CDS 30.0%
! TTCTTTTCCTCATATATTGC+AGG - chr5.2:70048832-70048851 MS.gene29608:CDS 30.0%
!! AGTTTAACTTGTTCTGTTGT+TGG + chr5.2:70048343-70048362 None:intergenic 30.0%
AGAGCAAGAATGTGTTGTAT+TGG - chr5.2:70048455-70048474 MS.gene29608:intron 35.0%
AGTAGTTTCCATGGTAAAAG+TGG - chr5.2:70048277-70048296 MS.gene29608:CDS 35.0%
ATACATGTTACATCATCGTC+AGG + chr5.2:70048805-70048824 None:intergenic 35.0%
ATGTACAATGGGAGAACAAA+TGG - chr5.2:70048996-70049015 MS.gene29608:CDS 35.0%
GATTCACCAAATGAGTTCAA+TGG + chr5.2:70048913-70048932 None:intergenic 35.0%
GTTTCAGAATCACAAAGCTA+GGG - chr5.2:70048477-70048496 MS.gene29608:intron 35.0%
GTTTGCATACACATGTACAA+TGG - chr5.2:70048984-70049003 MS.gene29608:CDS 35.0%
TACATGTTACATCATCGTCA+GGG + chr5.2:70048804-70048823 None:intergenic 35.0%
TATGCATGCAAATGAATGCA+GGG - chr5.2:70048951-70048970 MS.gene29608:CDS 35.0%
!!! GGTTTCTTTTGATGATGACA+AGG - chr5.2:70048519-70048538 MS.gene29608:intron 35.0%
AAACTCAACCGTAAGTCCAA+TGG + chr5.2:70049030-70049049 None:intergenic 40.0%
AGAGTCTCAATCACTCTATC+AGG + chr5.2:70048880-70048899 None:intergenic 40.0%
AGCAAACCCTGCAATATATG+AGG + chr5.2:70048842-70048861 None:intergenic 40.0%
CTTTAGGCCTCTTAATGCAT+TGG - chr5.2:70048773-70048792 MS.gene29608:CDS 40.0%
GGAAAGACAAAAACGTCGTA+AGG - chr5.2:70048498-70048517 MS.gene29608:intron 40.0%
GGTTTCAGAATCACAAAGCT+AGG - chr5.2:70048476-70048495 MS.gene29608:intron 40.0%
GTATGCATGCAAATGAATGC+AGG - chr5.2:70048950-70048969 MS.gene29608:CDS 40.0%
GTGAATCAGAATCAGAGAAG+TGG - chr5.2:70048926-70048945 MS.gene29608:CDS 40.0%
TCATCTGGAAGTAGTTTCCA+TGG - chr5.2:70048268-70048287 MS.gene29608:CDS 40.0%
! GGCTTTTGCATGAAATCATC+TGG - chr5.2:70048253-70048272 MS.gene29608:CDS 40.0%
! TGACTGAACTTTTCAGAGCA+GGG - chr5.2:70048365-70048384 MS.gene29608:CDS 40.0%
! TTCTGAATTTGATCGGTGCT+TGG + chr5.2:70048400-70048419 None:intergenic 40.0%
AACACCCACCATTGGACTTA+CGG - chr5.2:70049019-70049038 MS.gene29608:CDS 45.0%
ACAAATGGAACACCCACCAT+TGG - chr5.2:70049011-70049030 MS.gene29608:CDS 45.0%
TCAACCGTAAGTCCAATGGT+GGG + chr5.2:70049026-70049045 None:intergenic 45.0%
! CTGACTGAACTTTTCAGAGC+AGG - chr5.2:70048364-70048383 MS.gene29608:CDS 45.0%
!! TGCTGCTTCCACTTTTACCA+TGG + chr5.2:70048288-70048307 None:intergenic 45.0%
!!! GTTAAAAAAATTATTTTAAA+AGG - chr5.2:70048733-70048752 MS.gene29608:CDS 5.0%
CTCAACCGTAAGTCCAATGG+TGG + chr5.2:70049027-70049046 None:intergenic 50.0%
GGCCTCTTAATGCATTGGAC+CGG - chr5.2:70048778-70048797 MS.gene29608:CDS 50.0%
TGTTACATCATCGTCAGGGC+CGG + chr5.2:70048800-70048819 None:intergenic 50.0%
CTGGCACAAAGTGTGGTCGT+TGG - chr5.2:70048314-70048333 MS.gene29608:CDS 55.0%
GGCCGGTCCAATGCATTAAG+AGG + chr5.2:70048783-70048802 None:intergenic 55.0%
!! AGCAGCACTGGCACAAAGTG+TGG - chr5.2:70048307-70048326 MS.gene29608:CDS 55.0%
AGTGGAAGCAGCAGCAGCAC+TGG - chr5.2:70048295-70048314 MS.gene29608:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 70048235 70049056 70048235 ID=MS.gene29608
chr5.2 mRNA 70048235 70049056 70048235 ID=MS.gene29608.t1;Parent=MS.gene29608
chr5.2 exon 70048705 70049056 70048705 ID=MS.gene29608.t1.exon1;Parent=MS.gene29608.t1
chr5.2 CDS 70048705 70049056 70048705 ID=cds.MS.gene29608.t1;Parent=MS.gene29608.t1
chr5.2 exon 70048235 70048437 70048235 ID=MS.gene29608.t1.exon2;Parent=MS.gene29608.t1
chr5.2 CDS 70048235 70048437 70048235 ID=cds.MS.gene29608.t1;Parent=MS.gene29608.t1
Gene Sequence

>MS.gene29608

ATGGAAGAGAGCATGTCAGGCTTTTGCATGAAATCATCTGGAAGTAGTTTCCATGGTAAAAGTGGAAGCAGCAGCAGCACTGGCACAAAGTGTGGTCGTTGGAATCCAACAACAGAACAAGTTAAACTTCTGACTGAACTTTTCAGAGCAGGGCTCAGAACTCCAAGCACCGATCAAATTCAGAAAATATCCAATCAACTTAGTTTTTATGGTAAGATAGAGAGCAAGAATGTGTTGTATTGGTTTCAGAATCACAAAGCTAGGGAAAGACAAAAACGTCGTAAGGTTTCTTTTGATGATGACAAGGATGTCATAGTTCATAGAGACAACTCTATGAATGCTTCAACACAAAGTAAGTCAAAAATCACTTACTCTATTTACCGACGCAACTCATTTATTCATTTACTTTCGTATCAATTTCCTTGAAACTTTGATCTGATACTATGTTAATCACAAGATCTAAGAGATAAAGATCCATCTCGTTAGAAAAATAATTTTGTTAAAAAAATTATTTTAAAAGGTCTTATTAAATTTTTTGCTTTAGGCCTCTTAATGCATTGGACCGGCCCTGACGATGATGTAACATGTATTTGACACTTCTTTTCCTCATATATTGCAGGGTTTGCTGAGATGTACTCAGAGCCTGATAGAGTGATTGAGACTCTCGAACTTTTTCCATTGAACTCATTTGGTGAATCAGAATCAGAGAAGTGGAGTATGCATGCAAATGAATGCAGGGAAAATACAATGTTTGCATACACATGTACAATGGGAGAACAAATGGAACACCCACCATTGGACTTACGGTTGAGTTTTGTGTAA
Protein sequence

>MS.gene29608.t1

MEESMSGFCMKSSGSSFHGKSGSSSSTGTKCGRWNPTTEQVKLLTELFRAGLRTPSTDQIQKISNQLSFYGKIESKNVLYWFQNHKARERQKRRKVSFDDDKDVIVHRDNSMNASTQRFAEMYSEPDRVIETLELFPLNSFGESESEKWSMHANECRENTMFAYTCTMGEQMEHPPLDLRLSFV