AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53312

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53312.t1 MTR_4g027800 80.682 88 17 0 1 88 20 107 3.25e-45 142
MS.gene53312.t1 MTR_4g027840 80.682 88 17 0 1 88 20 107 5.06e-45 142
MS.gene53312.t1 MTR_4g428370 78.409 88 19 0 1 88 77 164 2.54e-44 141
MS.gene53312.t1 MTR_4g029390 63.636 88 31 1 1 88 22 108 8.26e-33 110
MS.gene53312.t1 MTR_4g029350 63.636 88 31 1 1 88 22 108 2.08e-31 107
MS.gene53312.t1 MTR_7g072930 50.538 93 43 2 1 91 23 114 1.16e-27 98.6
MS.gene53312.t1 MTR_4g029210 50.575 87 43 0 5 91 24 110 3.62e-25 91.7
MS.gene53312.t1 MTR_7g073150 47.312 93 46 2 1 91 23 114 3.67e-24 89.4
MS.gene53312.t1 MTR_7g073170 46.237 93 46 3 1 91 23 113 4.89e-23 86.3
MS.gene53312.t1 MTR_4g028190 49.398 83 41 1 5 86 29 111 1.23e-21 82.8
MS.gene53312.t1 MTR_2g062600 47.126 87 44 2 2 87 21 106 3.90e-21 81.3
MS.gene53312.t1 MTR_7g072730 41.935 93 52 2 1 91 23 115 1.05e-20 81.3
MS.gene53312.t1 MTR_4g028180 46.237 93 43 3 2 87 25 117 2.23e-20 79.3
MS.gene53312.t1 MTR_7g072830 39.785 93 54 1 1 91 23 115 2.30e-20 79.3
MS.gene53312.t1 MTR_7g072960 42.391 92 38 2 1 91 23 100 1.07e-17 72.8
MS.gene53312.t1 MTR_7g073120 41.667 84 47 1 1 82 24 107 1.51e-17 72.8
MS.gene53312.t1 MTR_7g451500 37.778 90 55 1 5 93 7 96 8.78e-17 69.7
MS.gene53312.t1 MTR_7g072993 41.489 94 52 1 1 91 23 116 2.63e-15 66.6
MS.gene53312.t1 MTR_7g072900 43.011 93 50 2 1 91 23 114 6.85e-15 65.1
MS.gene53312.t1 MTR_7g073100 38.947 95 51 2 1 91 23 114 1.16e-13 62.8
MS.gene53312.t1 MTR_4g028310 36.559 93 56 1 2 91 21 113 1.75e-13 62.0
MS.gene53312.t1 MTR_7g073130 38.043 92 55 2 1 91 23 113 3.02e-13 61.2
MS.gene53312.t1 MTR_7g073060 38.043 92 56 1 1 91 23 114 3.04e-13 61.2
MS.gene53312.t1 MTR_7g072980 36.559 93 57 1 1 91 23 115 9.68e-13 60.1
MS.gene53312.t1 MTR_1g040335 43.011 93 50 2 1 91 23 114 4.49e-12 58.2
MS.gene53312.t1 MTR_3g467100 32.941 85 57 0 2 86 20 104 5.87e-12 57.8
MS.gene53312.t1 MTR_4g028250 40.964 83 48 1 8 89 29 111 8.47e-12 57.4
MS.gene53312.t1 MTR_7g072987 47.059 68 33 2 6 71 57 123 3.36e-11 56.6
MS.gene53312.t1 MTR_3g046350 34.940 83 51 2 6 86 31 112 4.63e-11 55.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53312.t1 AT5G59320 60.465 86 34 0 2 87 21 106 1.93e-30 104
MS.gene53312.t1 AT5G59310 58.621 87 33 1 2 88 21 104 1.03e-28 100
MS.gene53312.t1 AT2G38540 60.674 89 32 3 2 88 23 110 1.44e-28 100
MS.gene53312.t1 AT2G38530 56.818 88 37 1 2 88 23 110 1.25e-25 92.8
MS.gene53312.t1 AT4G33355 56.410 78 34 0 5 82 28 105 2.10e-24 89.7
MS.gene53312.t1 AT4G33355 56.410 78 34 0 5 82 28 105 2.13e-24 89.4
MS.gene53312.t1 AT3G51590 47.312 93 47 2 2 93 22 113 4.21e-23 86.3
MS.gene53312.t1 AT3G51600 55.056 89 37 3 2 88 23 110 2.45e-22 84.3
MS.gene53312.t1 AT2G15050 48.837 86 41 2 2 84 23 108 2.87e-22 84.3
MS.gene53312.t1 AT2G15050 48.837 86 41 2 2 84 23 108 3.42e-22 84.0
MS.gene53312.t1 AT2G15050 48.837 86 41 2 2 84 23 108 3.78e-22 84.0
MS.gene53312.t1 AT5G01870 42.529 87 48 1 2 86 20 106 6.25e-18 73.2
MS.gene53312.t1 AT3G08770 43.617 94 49 3 3 93 18 110 3.83e-17 70.9
MS.gene53312.t1 AT3G08770 43.617 94 49 3 3 93 18 110 4.82e-17 70.9
MS.gene53312.t1 AT2G18370 44.578 83 44 2 2 83 22 103 2.97e-16 68.9

Find 30 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTGCTGCTCGTGCTATTTC+TGG 0.185000 4.3:-70930713 MS.gene53312:CDS
GGCGCAGCTTCTTCTCTTCC+TGG 0.339122 4.3:-70930680 MS.gene53312:CDS
ACTTAAAATTTCCATAACTT+TGG 0.352472 4.3:+70930155 None:intergenic
CCATGCATTGGATATCTTAG+AGG 0.354250 4.3:-70930836 MS.gene53312:CDS
GCTATTTCTGGTTTGAATAC+AGG 0.359485 4.3:-70930701 MS.gene53312:CDS
CCATCTCCAGCATGCTGTGC+TGG 0.375274 4.3:-70930803 MS.gene53312:CDS
TTGCAAGCAGCCTGACGGTC+AGG 0.421711 4.3:+70930746 None:intergenic
CACCACCACGCCTGACCGTC+AGG 0.443141 4.3:-70930756 MS.gene53312:CDS
ACGGTCAGGCGTGGTGGTGG+CGG 0.445777 4.3:+70930760 None:intergenic
GTCAGGCGTGGTGGTGGCGG+CGG 0.446691 4.3:+70930763 None:intergenic
GGTGCTCTTTCTCCATGCAT+TGG 0.474474 4.3:-70930848 MS.gene53312:CDS
ATATTGCAGCTCCAAAGTTA+TGG 0.477723 4.3:-70930166 MS.gene53312:CDS
TTCACTCCAGCACAGCATGC+TGG 0.485039 4.3:+70930797 None:intergenic
GTGGAGGTACTGATCTTGTA+TGG 0.494316 4.3:+70930638 None:intergenic
GGATATCTTAGAGGTGGTGC+TGG 0.504129 4.3:-70930827 MS.gene53312:CDS
CTGACGGTCAGGCGTGGTGG+TGG 0.517462 4.3:+70930757 None:intergenic
ATGTTAACACCACATTTGCC+AGG 0.525937 4.3:+70930662 None:intergenic
TGCTGGAGTGAAGAGACTTA+AGG 0.538170 4.3:-70930786 MS.gene53312:CDS
TCTTCTCTTCCTGGCAAATG+TGG 0.544086 4.3:-70930671 MS.gene53312:CDS
CCAGCACAGCATGCTGGAGA+TGG 0.550113 4.3:+70930803 None:intergenic
GAGATTGCAGCCTCTGCCAT+TGG 0.562691 4.3:+70930887 None:intergenic
AGCAGCCTGACGGTCAGGCG+TGG 0.565783 4.3:+70930751 None:intergenic
AGCCTGACGGTCAGGCGTGG+TGG 0.576862 4.3:+70930754 None:intergenic
TGGTCATATTTACAGCATCA+GGG 0.592414 4.3:-70930199 MS.gene53312:intron
CCTCTAAGATATCCAATGCA+TGG 0.598915 4.3:+70930836 None:intergenic
GATTGTTGCACCAATGGCAG+AGG 0.608779 4.3:-70930897 None:intergenic
TGCATTGGATATCTTAGAGG+TGG 0.623803 4.3:-70930833 MS.gene53312:CDS
AGCAGTTGCAAGCAGCCTGA+CGG 0.624471 4.3:+70930741 None:intergenic
GCAGAGGCTGCAATCTCATG+TGG 0.630304 4.3:-70930881 MS.gene53312:CDS
ATCTCATGTGGACAAGTGAG+TGG 0.724614 4.3:-70930869 MS.gene53312:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTTATTTATATTTTT+TGG + chr4.3:70930541-70930560 None:intergenic 0.0%
!! TTAAATTAGTCCACTTAAAA+TGG - chr4.3:70930513-70930532 MS.gene53312:intron 20.0%
!!! GTTGCTGATTTTTTTTTTGT+TGG - chr4.3:70930822-70930841 MS.gene53312:CDS 25.0%
!!! TTTTTTGGTGCCATTTTAAG+TGG + chr4.3:70930526-70930545 None:intergenic 30.0%
ATATTGCAGCTCCAAAGTTA+TGG - chr4.3:70930875-70930894 MS.gene53312:CDS 35.0%
TGGTCATATTTACAGCATCA+GGG - chr4.3:70930842-70930861 MS.gene53312:CDS 35.0%
TTGGTCATATTTACAGCATC+AGG - chr4.3:70930841-70930860 MS.gene53312:CDS 35.0%
!! GCTATTTCTGGTTTGAATAC+AGG - chr4.3:70930340-70930359 MS.gene53312:intron 35.0%
ATGAACATACGTAGCACAGT+TGG + chr4.3:70930428-70930447 None:intergenic 40.0%
ATGTTAACACCACATTTGCC+AGG + chr4.3:70930382-70930401 None:intergenic 40.0%
CCATGCATTGGATATCTTAG+AGG - chr4.3:70930205-70930224 MS.gene53312:intron 40.0%
TGCATTGGATATCTTAGAGG+TGG - chr4.3:70930208-70930227 MS.gene53312:intron 40.0%
!! CCTCTAAGATATCCAATGCA+TGG + chr4.3:70930208-70930227 None:intergenic 40.0%
AACATACGTAGCACAGTTGG+TGG + chr4.3:70930425-70930444 None:intergenic 45.0%
ATCTCATGTGGACAAGTGAG+TGG - chr4.3:70930172-70930191 MS.gene53312:CDS 45.0%
TCTTCTCTTCCTGGCAAATG+TGG - chr4.3:70930370-70930389 MS.gene53312:intron 45.0%
TGCTGGAGTGAAGAGACTTA+AGG - chr4.3:70930255-70930274 MS.gene53312:intron 45.0%
!! GTGGAGGTACTGATCTTGTA+TGG + chr4.3:70930406-70930425 None:intergenic 45.0%
!!! AATTTCATTATTTTAATTTT+TGG - chr4.3:70930623-70930642 MS.gene53312:intron 5.0%
GGATATCTTAGAGGTGGTGC+TGG - chr4.3:70930214-70930233 MS.gene53312:intron 50.0%
GGTGCTCTTTCTCCATGCAT+TGG - chr4.3:70930193-70930212 MS.gene53312:intron 50.0%
!! AGTGCTGCTCGTGCTATTTC+TGG - chr4.3:70930328-70930347 MS.gene53312:intron 50.0%
!! ATACGTAGCACAGTTGGTGG+AGG + chr4.3:70930422-70930441 None:intergenic 50.0%
AGCAGTTGCAAGCAGCCTGA+CGG + chr4.3:70930303-70930322 None:intergenic 55.0%
GCAGAGGCTGCAATCTCATG+TGG - chr4.3:70930160-70930179 MS.gene53312:CDS 55.0%
TTCACTCCAGCACAGCATGC+TGG + chr4.3:70930247-70930266 None:intergenic 55.0%
CCAGCACAGCATGCTGGAGA+TGG + chr4.3:70930241-70930260 None:intergenic 60.0%
CCATCTCCAGCATGCTGTGC+TGG - chr4.3:70930238-70930257 MS.gene53312:intron 60.0%
GGCGCAGCTTCTTCTCTTCC+TGG - chr4.3:70930361-70930380 MS.gene53312:intron 60.0%
TTGCAAGCAGCCTGACGGTC+AGG + chr4.3:70930298-70930317 None:intergenic 60.0%
AGCAGCCTGACGGTCAGGCG+TGG + chr4.3:70930293-70930312 None:intergenic 70.0%
AGCCTGACGGTCAGGCGTGG+TGG + chr4.3:70930290-70930309 None:intergenic 70.0%
CACCACCACGCCTGACCGTC+AGG - chr4.3:70930285-70930304 MS.gene53312:intron 70.0%
CTGACGGTCAGGCGTGGTGG+TGG + chr4.3:70930287-70930306 None:intergenic 70.0%
!! ACGGTCAGGCGTGGTGGTGG+CGG + chr4.3:70930284-70930303 None:intergenic 70.0%
!! GTCAGGCGTGGTGGTGGCGG+CGG + chr4.3:70930281-70930300 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 70930157 70930906 70930157 ID=MS.gene53312
chr4.3 mRNA 70930157 70930906 70930157 ID=MS.gene53312.t1;Parent=MS.gene53312
chr4.3 exon 70930648 70930906 70930648 ID=MS.gene53312.t1.exon1;Parent=MS.gene53312.t1
chr4.3 CDS 70930648 70930906 70930648 ID=cds.MS.gene53312.t1;Parent=MS.gene53312.t1
chr4.3 exon 70930157 70930206 70930157 ID=MS.gene53312.t1.exon2;Parent=MS.gene53312.t1
chr4.3 CDS 70930157 70930206 70930157 ID=cds.MS.gene53312.t1;Parent=MS.gene53312.t1
Gene Sequence

>MS.gene53312

ATGGCAGAGGCTGCAATCTCATGTGGACAAGTGAGTGGTGCTCTTTCTCCATGCATTGGATATCTTAGAGGTGGTGCTGGTCCATCTCCAGCATGCTGTGCTGGAGTGAAGAGACTTAAGGCCGCCGCCACCACCACGCCTGACCGTCAGGCTGCTTGCAACTGCTTGAAAAGTGCTGCTCGTGCTATTTCTGGTTTGAATACAGGCGCAGCTTCTTCTCTTCCTGGCAAATGTGGTGTTAACATTCCATACAAGATCAGTACCTCCACCAACTGTGCTACGTATGTTCATCTATTTTTCACTTCATTTTCAATCTTTAATTAAAAAATATCAACTATATTCTTTTTTTGAAGAAGTTAAATTAGTCCACTTAAAATGGCACCAAAAAATATAAATAAAAAAAAATTCGTTGTTATTTTAGTCTTTTTATAGACTATTGTGATAACATTTGAATTTTTATAGAACTAATTTCATTATTTTAATTTTTGGACATTAATATTATGAATAAACTGTTTCATTTTCTAAGAAAATTTTATATATACACTATATGTTCAGTTTTTTAGATTATTTTTATATTCTATAATATAATCTTTGTTTTTGAATTTTTATGTTTTAGATTACATCACTACTAATCTACTGTTTCTTTACTAGTTTATTTTTTAATAGTTGCTGATTTTTTTTTTGTTGGTCATATTTACAGCATCAGGGCTTGAAGATGATATTGCAGCTCCAAAGTTATGGAAATTTTAA
Protein sequence

>MS.gene53312.t1

MAEAAISCGQVSGALSPCIGYLRGGAGPSPACCAGVKRLKAAATTTPDRQAACNCLKSAARAISGLNTGAASSLPGKCGVNIPYKITSGLEDDIAAPKLWKF