AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene63324


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63324.t1 MTR_3g067870 60.000 140 30 4 1 127 1 127 1.18e-45 147
MS.gene63324.t1 MTR_5g045560 63.235 68 22 1 83 150 16 80 1.61e-21 87.8
MS.gene63324.t1 MTR_2g085250 61.194 67 23 1 83 149 16 79 2.55e-20 84.7
MS.gene63324.t1 MTR_2g085280 61.194 67 23 1 83 149 16 79 2.68e-20 84.7
MS.gene63324.t1 MTR_1g012570 64.615 65 20 1 83 147 16 77 4.00e-20 84.0
MS.gene63324.t1 MTR_1g105905 63.492 63 20 1 85 147 1 60 8.84e-20 82.8
MS.gene63324.t1 MTR_1g105910 61.538 65 22 1 83 147 16 77 8.87e-20 83.2
MS.gene63324.t1 MTR_1g077360 60.000 65 23 1 83 147 16 77 1.16e-19 82.8
MS.gene63324.t1 MTR_8g043650 61.538 65 22 1 83 147 16 77 1.28e-19 82.8
MS.gene63324.t1 MTR_3g052920 82.222 45 8 0 83 127 16 60 1.39e-19 82.8
MS.gene63324.t1 MTR_3g067875 83.721 43 7 0 85 127 1 43 1.53e-19 78.2
MS.gene63324.t1 MTR_3g052870 61.538 65 22 1 83 147 16 77 1.93e-19 82.0
MS.gene63324.t1 MTR_1g075600 60.000 65 23 1 83 147 16 77 2.03e-19 82.4
MS.gene63324.t1 MTR_1g105920 61.538 65 22 1 83 147 16 77 2.45e-19 82.0
MS.gene63324.t1 MTR_5g053390 80.000 45 9 0 83 127 16 60 3.08e-19 81.6
MS.gene63324.t1 MTR_5g055100 80.000 45 9 0 83 127 16 60 3.35e-19 81.6
MS.gene63324.t1 MTR_1g106070 75.556 45 11 0 83 127 16 60 2.22e-18 78.2
MS.gene63324.t1 MTR_2g030740 58.462 65 24 1 83 147 16 77 1.23e-17 77.4
MS.gene63324.t1 MTR_1g075570 76.744 43 10 0 85 127 1 43 3.54e-17 74.7
MS.gene63324.t1 MTR_1g108510 54.412 68 28 1 83 150 16 80 6.52e-17 75.5
MS.gene63324.t1 MTR_3g030770 54.412 68 28 1 83 150 16 80 7.08e-17 75.5
MS.gene63324.t1 MTR_0121s0080 53.846 65 27 1 83 147 16 77 3.44e-15 70.9
MS.gene63324.t1 MTR_3g067910 82.500 40 7 0 88 127 2 41 9.32e-15 67.0
MS.gene63324.t1 MTR_3g080940 65.909 44 15 0 85 128 18 61 1.01e-14 69.3
MS.gene63324.t1 MTR_2g093190 51.471 68 30 1 83 150 16 80 1.10e-14 69.3
MS.gene63324.t1 MTR_1g108580 68.889 45 14 0 83 127 16 60 1.24e-14 69.3
MS.gene63324.t1 MTR_0121s0100 50.746 67 30 1 83 149 16 79 1.29e-14 67.4
MS.gene63324.t1 MTR_3g030780 49.231 65 30 1 83 147 16 77 5.20e-14 65.5
MS.gene63324.t1 MTR_8g086290 49.231 65 30 1 83 147 19 80 5.76e-14 66.6
MS.gene63324.t1 MTR_7g028448 52.542 59 25 1 89 147 25 80 6.51e-14 66.2
MS.gene63324.t1 MTR_4g036915 52.542 59 25 1 89 147 25 80 6.51e-14 66.2
MS.gene63324.t1 MTR_1g108500 74.359 39 10 0 89 127 110 148 1.72e-13 67.4
MS.gene63324.t1 MTR_4g127140 50.000 60 27 1 89 148 25 81 3.64e-13 64.7
MS.gene63324.t1 MTR_2g105290 45.455 66 33 1 83 148 19 81 5.43e-13 63.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63324.t1 AT5G60440 76.744 43 10 0 85 127 16 58 2.75e-17 77.4
MS.gene63324.t1 AT1G01530 68.182 44 14 0 85 128 16 59 6.03e-15 70.5
MS.gene63324.t1 AT4G36590 58.333 60 22 1 83 142 14 70 1.16e-14 69.7
MS.gene63324.t1 AT1G65360 45.714 70 34 2 85 154 16 81 4.56e-13 65.1
MS.gene63324.t1 AT2G24840 62.791 43 16 0 85 127 72 114 5.75e-13 65.5

Find 24 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGAATTCTTCATCTGCATTT+AGG 0.178670 3.3:-60020152 None:intergenic
AGATGAAGAATTCGCAAATA+TGG 0.383002 3.3:+60020161 MS.gene63324:CDS
GCTTCGAGAAAGTCACTTGC+AGG 0.384026 3.3:-60020573 None:intergenic
GCTTCGAGAAAGTCACTTGC+AGG 0.392864 3.3:+60021159 MS.gene63324:CDS
CGTTAAGCTTGTAAGACAAC+TGG 0.405172 3.3:+60020330 MS.gene63324:CDS
ATCTCTTCAGATCGCTGCTC+TGG 0.413157 3.3:+60020125 MS.gene63324:CDS
AAATATGGTTGAAAATCATA+AGG 0.438033 3.3:+60020176 MS.gene63324:CDS
TGGATGAAGAAGCAAGAGGT+TGG 0.466733 3.3:+60019917 None:intergenic
TGAAGGACAAAATCATCATA+TGG 0.474780 3.3:+60019967 MS.gene63324:CDS
AATTTATATACAGGGAGAAA+AGG 0.506795 3.3:+60020288 MS.gene63324:intron
CTTTCTCGAAGCGCCGCAGT+GGG 0.517223 3.3:+60020584 MS.gene63324:CDS
AGCAAGCTTTGCACCCTCTG+TGG 0.545328 3.3:+60020622 MS.gene63324:CDS
ACTTTCTCGAAGCGCCGCAG+TGG 0.564118 3.3:+60020583 MS.gene63324:CDS
TATATTCTCACCTGGTGAGA+AGG 0.565372 3.3:+60020663 MS.gene63324:CDS
ACTTTCTCGAAGCGTCGTAG+TGG 0.570157 3.3:-60021149 None:intergenic
GATGAAATGCAAAATTCTGA+AGG 0.573656 3.3:+60019950 MS.gene63324:CDS
GCTCTAATTATATTCTCACC+TGG 0.609848 3.3:+60020655 MS.gene63324:CDS
AATGAAAATACCTTCTCACC+AGG 0.623617 3.3:-60020673 None:intergenic
AGCAACATATGCACCACAGA+GGG 0.625524 3.3:-60020635 None:intergenic
TGTGCTTCAGCCATGTCGAG+CGG 0.630136 3.3:-60021239 None:intergenic
TCGAGCGGAAAGAAAACTCG+AGG 0.680063 3.3:-60021224 None:intergenic
AAAGTGGATGAAGAAGCAAG+AGG 0.708930 3.3:+60019913 None:intergenic
GAGCAACATATGCACCACAG+AGG 0.750197 3.3:-60020636 None:intergenic
CTTTCGTGAAGAGCCCACTG+CGG 0.762759 3.3:-60020597 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAATATCAATTTATATACA+GGG + chr3.3:60020280-60020299 MS.gene63324:intron 15.0%
!! TTGAATATCAATTTATATAC+AGG + chr3.3:60020279-60020298 MS.gene63324:intron 15.0%
!! AAATATGGTTGAAAATCATA+AGG + chr3.3:60020176-60020195 MS.gene63324:CDS 20.0%
!! TTCTTGAATAATTCAAAAGT+TGG + chr3.3:60020874-60020893 MS.gene63324:intron 20.0%
! AATTTATATACAGGGAGAAA+AGG + chr3.3:60020288-60020307 MS.gene63324:intron 25.0%
! AGTAACAAAACAAAAGGAAA+GGG - chr3.3:60020210-60020229 None:intergenic 25.0%
! ATATGAAACAAAAGTTGGAA+TGG + chr3.3:60020353-60020372 MS.gene63324:intron 25.0%
! ATCATATTCATCATACCAAT+GGG + chr3.3:60020897-60020916 MS.gene63324:intron 25.0%
! TATGAAACAAAAGTTGGAAT+GGG + chr3.3:60020354-60020373 MS.gene63324:intron 25.0%
! TGATCAAAATTGTGTTTGTT+AGG + chr3.3:60020229-60020248 MS.gene63324:intron 25.0%
! TTATGTAACTGTTTATTCCA+TGG - chr3.3:60020006-60020025 None:intergenic 25.0%
! TTGATCAGTAACAAAACAAA+AGG - chr3.3:60020216-60020235 None:intergenic 25.0%
! TTTATGACTGTTTCAACATT+TGG + chr3.3:60021028-60021047 MS.gene63324:intron 25.0%
!!! TCTTTTTCATCACAATCTTT+TGG + chr3.3:60021198-60021217 MS.gene63324:CDS 25.0%
ACTGGATATGAAACAAAAGT+TGG + chr3.3:60020348-60020367 MS.gene63324:intron 30.0%
AGATGAAGAATTCGCAAATA+TGG + chr3.3:60020161-60020180 MS.gene63324:CDS 30.0%
ATCATATTCATCCCATCAAT+GGG + chr3.3:60020427-60020446 MS.gene63324:intron 30.0%
CAGTAACAAAACAAAAGGAA+AGG - chr3.3:60020211-60020230 None:intergenic 30.0%
CTGTGTTGAATAATTCAAGT+TGG + chr3.3:60020404-60020423 MS.gene63324:intron 30.0%
GATCATATTCATCATACCAA+TGG + chr3.3:60020896-60020915 MS.gene63324:intron 30.0%
GATGAAATGCAAAATTCTGA+AGG + chr3.3:60019950-60019969 MS.gene63324:CDS 30.0%
TGAAGGACAAAATCATCATA+TGG + chr3.3:60019967-60019986 MS.gene63324:CDS 30.0%
! ATTTTTCATTGCATTCTGCA+TGG - chr3.3:60020103-60020122 None:intergenic 30.0%
AAAAGTTGGAATGGGAGATT+GGG + chr3.3:60020362-60020381 MS.gene63324:intron 35.0%
AATGAAAATACCTTCTCACC+AGG - chr3.3:60020676-60020695 None:intergenic 35.0%
AATGAAATTACCTTCTCACC+AGG + chr3.3:60021058-60021077 MS.gene63324:intron 35.0%
AGCAACATATGCACCATAAA+AGG + chr3.3:60021096-60021115 MS.gene63324:intron 35.0%
ATCATATTCGACCCATCAAT+GGG - chr3.3:60020831-60020850 None:intergenic 35.0%
ATGGTATGTATTGTTGACCA+TGG + chr3.3:60019986-60020005 MS.gene63324:intron 35.0%
CATAAATCGTTATCTCTCTC+AGG - chr3.3:60021014-60021033 None:intergenic 35.0%
CGAATTCTTCATCTGCATTT+AGG - chr3.3:60020155-60020174 None:intergenic 35.0%
GATCATATTCATCCCATCAA+TGG + chr3.3:60020426-60020445 MS.gene63324:intron 35.0%
GCAACATATGCACCATAAAA+GGG + chr3.3:60021097-60021116 MS.gene63324:intron 35.0%
GCTCTAATTATATTCTCACC+TGG + chr3.3:60020655-60020674 MS.gene63324:CDS 35.0%
GCTCTAATTATATTCTCACC+TGG - chr3.3:60020674-60020655 None:intergenic 35.0%
GGTGAGAAGGTAATTTCATT+TGG - chr3.3:60021058-60021077 None:intergenic 35.0%
TGGACAATAAGTAACATCAG+AGG - chr3.3:60020083-60020102 None:intergenic 35.0%
TTTATGACCGTTTCAACACT+TGG - chr3.3:60020706-60020725 None:intergenic 35.0%
! TTGCATCATGCCATTGTTTT+AGG + chr3.3:60020982-60021001 MS.gene63324:intron 35.0%
! TTTTTGTAGACTCTTCCCAT+TGG - chr3.3:60020915-60020934 None:intergenic 35.0%
!! TGCATCATGCCATTGTTTTA+GGG + chr3.3:60020983-60021002 MS.gene63324:intron 35.0%
!!! AGAATGAGGCTCATTTTTTG+TGG - chr3.3:60020459-60020478 None:intergenic 35.0%
!!! GGTGAGAAGGTATTTTCATT+TGG + chr3.3:60020676-60020695 MS.gene63324:intron 35.0%
CAAAAGTTGGAATGGGAGAT+TGG + chr3.3:60020361-60020380 MS.gene63324:intron 40.0%
CAGTTTCCACCCTAAAACAA+TGG + chr3.3:60020739-60020758 MS.gene63324:intron 40.0%
CGTTAAGCTTGTAAGACAAC+TGG + chr3.3:60020330-60020349 MS.gene63324:CDS 40.0%
GATCATATTCGACCCATCAA+TGG - chr3.3:60020832-60020851 None:intergenic 40.0%
TAGACATCGAGAAGAACCAT+TGG - chr3.3:60020507-60020526 None:intergenic 40.0%
TATATTCTCACCTGGTGAGA+AGG + chr3.3:60020663-60020682 MS.gene63324:CDS 40.0%
TATATTCTCACCTGGTGAGA+AGG - chr3.3:60020682-60020663 None:intergenic 40.0%
TCAGTTGCGAAAGAAGAATG+AGG - chr3.3:60020473-60020492 None:intergenic 40.0%
TGGCATGATGCAATTCATTG+AGG - chr3.3:60020975-60020994 None:intergenic 40.0%
! ACTGACTCAGCTTATTCCAA+TGG + chr3.3:60020488-60020507 MS.gene63324:intron 40.0%
! TTGCATCACGCCATTGTTTT+AGG - chr3.3:60020752-60020771 None:intergenic 40.0%
!! TGCATCACGCCATTGTTTTA+GGG - chr3.3:60020751-60020770 None:intergenic 40.0%
!! TGGTCAACCAAGTGTTGAAA+CGG + chr3.3:60020696-60020715 MS.gene63324:intron 40.0%
!!! ATCATGCCATTGTTTTAGGG+TGG + chr3.3:60020986-60021005 MS.gene63324:intron 40.0%
AAAAACGAGCTTGCGCACTT+TGG - chr3.3:60020797-60020816 None:intergenic 45.0%
AGCAACATATGCACCACAGA+GGG - chr3.3:60020638-60020657 None:intergenic 45.0%
CAGGTTCCACCCTAAAACAA+TGG - chr3.3:60020995-60021014 None:intergenic 45.0%
TGGCGTGATGCAATTCATTG+AGG + chr3.3:60020759-60020778 MS.gene63324:intron 45.0%
TGGGAGATTGGGCAACTAAA+AGG + chr3.3:60020373-60020392 MS.gene63324:intron 45.0%
TGTGGAGTTGTCCCATTGAT+GGG - chr3.3:60020441-60020460 None:intergenic 45.0%
TTGTGGAGTTGTCCCATTGA+TGG - chr3.3:60020442-60020461 None:intergenic 45.0%
! AAAGTGCGCAAGCTCGTTTT+TGG + chr3.3:60020796-60020815 MS.gene63324:intron 45.0%
! AGTTTTCTTTCCGCTCGACA+TGG + chr3.3:60021229-60021248 MS.gene63324:CDS 45.0%
! GAATTGAGCTTGCCCACTTT+TGG + chr3.3:60020937-60020956 MS.gene63324:intron 45.0%
!!! ATCACGCCATTGTTTTAGGG+TGG - chr3.3:60020748-60020767 None:intergenic 45.0%
ATCTCTTCAGATCGCTGCTC+TGG + chr3.3:60020125-60020144 MS.gene63324:CDS 50.0%
CATACCGTAGCGCCAAAAGT+GGG - chr3.3:60020952-60020971 None:intergenic 50.0%
GAGCAACATATGCACCACAG+AGG - chr3.3:60020639-60020658 None:intergenic 50.0%
GCTTCGAGAAAGTCACTTGC+AGG + chr3.3:60021159-60021178 MS.gene63324:CDS 50.0%
GCTTCGAGAAAGTCACTTGC+AGG - chr3.3:60021178-60021159 None:intergenic 50.0%
GGTGGAGTTGTCCCATTGAT+GGG + chr3.3:60020817-60020836 MS.gene63324:intron 50.0%
TCGAGCGGAAAGAAAACTCG+AGG - chr3.3:60021227-60021246 None:intergenic 50.0%
TGGTGGAGTTGTCCCATTGA+TGG + chr3.3:60020816-60020835 MS.gene63324:intron 50.0%
! GCGAGCTTTGCACCCTTTTA+TGG - chr3.3:60021112-60021131 None:intergenic 50.0%
!! ACTTTCTCGAAGCGTCGTAG+TGG - chr3.3:60021152-60021171 None:intergenic 50.0%
AGCAAGCTTTGCACCCTCTG+TGG + chr3.3:60020622-60020641 MS.gene63324:CDS 55.0%
CTTTCGTGAAGAGCCCACTG+CGG - chr3.3:60020600-60020619 None:intergenic 55.0%
GCATACCGTAGCGCCAAAAG+TGG - chr3.3:60020953-60020972 None:intergenic 55.0%
!! CTTGCCCACTTTTGGCGCTA+CGG + chr3.3:60020945-60020964 MS.gene63324:intron 55.0%
!! GTGCGCAAGCTCGTTTTTGG+TGG + chr3.3:60020799-60020818 MS.gene63324:intron 55.0%
!! ACTTTCTCGAAGCGCCGCAG+TGG + chr3.3:60020583-60020602 MS.gene63324:CDS 60.0%
!! CTTTCTCGAAGCGCCGCAGT+GGG + chr3.3:60020584-60020603 MS.gene63324:CDS 60.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 60019920 60021255 60019920 ID=MS.gene63324
chr3.3 mRNA 60019920 60021255 60019920 ID=MS.gene63324.t1;Parent=MS.gene63324
chr3.3 exon 60019920 60019988 60019920 ID=MS.gene63324.t1.exon1;Parent=MS.gene63324.t1
chr3.3 CDS 60019920 60019988 60019920 ID=cds.MS.gene63324.t1;Parent=MS.gene63324.t1
chr3.3 exon 60020108 60020197 60020108 ID=MS.gene63324.t1.exon2;Parent=MS.gene63324.t1
chr3.3 CDS 60020108 60020197 60020108 ID=cds.MS.gene63324.t1;Parent=MS.gene63324.t1
chr3.3 exon 60020301 60020365 60020301 ID=MS.gene63324.t1.exon3;Parent=MS.gene63324.t1
chr3.3 CDS 60020301 60020365 60020301 ID=cds.MS.gene63324.t1;Parent=MS.gene63324.t1
chr3.3 exon 60020528 60020684 60020528 ID=MS.gene63324.t1.exon4;Parent=MS.gene63324.t1
chr3.3 CDS 60020528 60020684 60020528 ID=cds.MS.gene63324.t1;Parent=MS.gene63324.t1
chr3.3 exon 60021118 60021255 60021118 ID=MS.gene63324.t1.exon5;Parent=MS.gene63324.t1
chr3.3 CDS 60021118 60021255 60021118 ID=cds.MS.gene63324.t1;Parent=MS.gene63324.t1
Gene Sequence

>MS.gene63324

ATGAAGAAGCAAGAGGTTGGAAAGAACAATGATGAAATGCAAAATTCTGAAGGACAAAATCATCATATGGTATGTATTGTTGACCATGGAATAAACAGTTACATAATAATTTCTGTAATTGAATTCATTTATTTTGTTGCTAAAATGTGATTTCATGCTTCCTCTGATGTTACTTATTGTCCATGCAGAATGCAATGAAAAATATATCTCTTCAGATCGCTGCTCTGGATAACCTAAATGCAGATGAAGAATTCGCAAATATGGTTGAAAATCATAAGGTTTATATTCCCTTTCCTTTTGTTTTGTTACTGATCAAAATTGTGTTTGTTAGGTTAACATTAGCATAATATTTATGTCATTTGAATATCAATTTATATACAGGGAGAAAAGGAACAACTTCATGTTGAATTCGTTAAGCTTGTAAGACAACTGGATATGAAACAAAAGTTGGAATGGGAGATTGGGCAACTAAAAGGATCATTAACTGTGTTGAATAATTCAAGTTGGATCATATTCATCCCATCAATGGGACAACTCCACAAAAAATGAGCCTCATTCTTCTTTCGCAACTGACTCAGCTTATTCCAATGGTTCTTCTCGATGTCTAGTGCATCGTTCATACAAGTCAGCAGAGCATTAAGCAATAAAAGCAACCTGCAAGTGACTTTCTCGAAGCGCCGCAGTGGGCTCTTCACGAAAGCTAGCAAGCTTTGCACCCTCTGTGGTGCATATGTTGCTCTAATTATATTCTCACCTGGTGAGAAGGTATTTTCATTTGGTCAACCAAGTGTTGAAACGGTCATAAATTGTTATTTCTCTCAGTTTCCACCCTAAAACAATGGCGTGATGCAATTCATTGAGGCATAACGTATCACCAAAGTGCGCAAGCTCGTTTTTGGTGGAGTTGTCCCATTGATGGGTCGAATATGATCACACTTGAATTATTCAAGAAGATTCTTGAATAATTCAAAAGTTGGATCATATTCATCATACCAATGGGAAGAGTCTACAAAAAATGAATTGAGCTTGCCCACTTTTGGCGCTACGGTATGCCTCAATGAATTGCATCATGCCATTGTTTTAGGGTGGAACCTGAGAGAGATAACGATTTATGACTGTTTCAACATTTGGCTGTCCAAATGAAATTACCTTCTCACCAGGTGAGAATATAATTAGAGCAACATATGCACCATAAAAGGGTGCAAAGCTCGCTAGCTTTCTTGAAGAGTCCACTACGACGCTTCGAGAAAGTCACTTGCAGGTTGCTTTCATTGCTCATCTTTTTCATCACAATCTTTTGGCGACCTCGAGTTTTCTTTCCGCTCGACATGGCTGA

Protein sequence

>MS.gene63324.t1

MKKQEVGKNNDEMQNSEGQNHHMNAMKNISLQIAALDNLNADEEFANMVENHKGEKEQLHVEFVKLVRQLDMKQNASFIQVSRALSNKSNLQVTFSKRRSGLFTKASKLCTLCGAYVALIIFSPGEKGAKLASFLEESTTTLRESHLQVAFIAHLFHHNLLATSSFLSARHG