AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1394030


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394030 MtrunA17_Chr4g0016701 82.591 247 18 3 6 229 1 245 2.87e-138 387
Msa1394030 MtrunA17_CPg0492981 82.591 247 18 3 6 229 1 245 2.87e-138 387
Msa1394030 MtrunA17_Chr4g0015611 82.591 247 18 3 6 229 1 245 2.87e-138 387
Msa1394030 MtrunA17_Chr3g0088491 98.324 179 3 0 51 229 36 214 4.95e-125 352
Msa1394030 MtrunA17_Chr7g0275151 73.494 166 11 1 64 229 2 134 5.61e-77 228
Msa1394030 MtrunA17_Chr4g0060751 67.273 165 8 1 65 229 11 129 7.24e-65 197
Msa1394030 MtrunA17_Chr6g0460191 74.468 94 24 0 136 229 8 101 1.77e-28 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394030 ATCG00150.1 79.518 249 26 5 6 229 1 249 4.21e-118 337

Find 41 sgRNAs with CRISPR-Local

Find 130 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCTATACCTGTTATGTTTC+TGG 0.052609 tig0021785:+1006 Msa1394030:CDS
TCAACATTCTATTGGCAAAT+AGG 0.223959 tig0021785:+442 Msa1394030:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 tig0021785:-880 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 tig0021785:+644 Msa1394030:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 tig0021785:-810 None:intergenic
CAACATTCTATTGGCAAATA+GGG 0.276147 tig0021785:+443 Msa1394030:CDS
CCTATACCTGTTATGTTTCT+GGG 0.293135 tig0021785:+1007 Msa1394030:CDS
AAATCTTCTAAGATGTTAAT+CGG 0.412258 tig0021785:-887 None:intergenic
GAAGTAGGTCAACATTCTAT+TGG 0.415279 tig0021785:+434 Msa1394030:intron
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 tig0021785:+1067 Msa1394030:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 tig0021785:-759 None:intergenic
GTAGTATTTATATCATTTGT+GGG 0.434707 tig0021785:-758 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 tig0021785:-918 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 tig0021785:-656 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 tig0021785:+623 Msa1394030:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 tig0021785:-1013 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 tig0021785:-1007 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 tig0021785:-552 None:intergenic
GGCTTATATAGGTGAATCTA+TGG 0.463562 tig0021785:+1078 Msa1394030:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 tig0021785:-595 None:intergenic
CGGTCATAGATTTATGGAAT+CGG 0.488490 tig0021785:+198 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 tig0021785:-869 None:intergenic
AGTCGAAAACTAAGTGATAA+GGG 0.500280 tig0021785:-917 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 tig0021785:+611 Msa1394030:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 tig0021785:-865 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 tig0021785:+722 Msa1394030:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 tig0021785:-1068 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 tig0021785:-875 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 tig0021785:+552 Msa1394030:CDS
TCAGTAGCCTATTTCTATGC+GGG 0.553188 tig0021785:+803 Msa1394030:CDS
AACATTCTATTGGCAAATAG+GGG 0.576894 tig0021785:+444 Msa1394030:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 tig0021785:-995 None:intergenic
AAAGAAATCTGACCGGACGT+TGG 0.600884 tig0021785:-564 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 tig0021785:+1082 Msa1394030:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 tig0021785:+631 Msa1394030:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 tig0021785:+630 Msa1394030:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 tig0021785:+1022 Msa1394030:CDS
GTTCCAATAAACGGAACCCA+CGG 0.647484 tig0021785:-647 None:intergenic
CATATTCAAAGAAATCTGAC+CGG 0.647538 tig0021785:-571 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 tig0021785:+802 Msa1394030:CDS
GGTGCAGCTAATTCTCCATG+AGG 0.714976 tig0021785:-737 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATATATATAACTTGAAA+GGG - tig0021785:334-353 None:intergenic 10.0%
!! AAATATATATATAACTTGAA+AGG - tig0021785:335-354 None:intergenic 10.0%
!! AATATATATATAACTTGAAA+GGG - tig0021785:334-353 None:intergenic 10.0%
!! AAATATATATATAACTTGAA+AGG - tig0021785:335-354 None:intergenic 10.0%
!!! ATAAATATTTTGTGATTAGT+AGG + tig0021785:250-269 Msa1394030:intron 15.0%
!!! TATTTATTTTTGTTTCGAAT+TGG + tig0021785:678-697 Msa1394030:CDS 15.0%
!!! ATAAATATTTTGTGATTAGT+AGG + tig0021785:250-269 Msa1394030:intron 15.0%
!!! TATTTATTTTTGTTTCGAAT+TGG + tig0021785:678-697 Msa1394030:CDS 15.0%
!! AAAGAAATGAAAGTCAAATA+AGG + tig0021785:286-305 Msa1394030:intron 20.0%
!! AAAATTATAAAGTTACCTCA+TGG + tig0021785:722-741 Msa1394030:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG - tig0021785:761-780 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG - tig0021785:762-781 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG - tig0021785:890-909 None:intergenic 20.0%
!! AAAGAAATGAAAGTCAAATA+AGG + tig0021785:286-305 Msa1394030:intron 20.0%
!! AAAATTATAAAGTTACCTCA+TGG + tig0021785:722-741 Msa1394030:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG - tig0021785:761-780 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG - tig0021785:762-781 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG - tig0021785:890-909 None:intergenic 20.0%
! ATGAAAGTCAAATAAGGAAA+TGG + tig0021785:292-311 Msa1394030:intron 25.0%
!!! ATATATTTTTTTTAGAGGGC+AGG + tig0021785:347-366 Msa1394030:intron 25.0%
!!! TATATTTTTTTTAGAGGGCA+GGG + tig0021785:348-367 Msa1394030:intron 25.0%
! AGAAACAAAGTTCCAATAAA+CGG - tig0021785:659-678 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG - tig0021785:719-738 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG + tig0021785:833-852 Msa1394030:CDS 25.0%
! ATGAAAGTCAAATAAGGAAA+TGG + tig0021785:292-311 Msa1394030:intron 25.0%
!!! ATATATTTTTTTTAGAGGGC+AGG + tig0021785:347-366 Msa1394030:intron 25.0%
!!! TATATTTTTTTTAGAGGGCA+GGG + tig0021785:348-367 Msa1394030:intron 25.0%
! AGAAACAAAGTTCCAATAAA+CGG - tig0021785:659-678 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG - tig0021785:719-738 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG + tig0021785:833-852 Msa1394030:CDS 25.0%
TCAACATTCTATTGGCAAAT+AGG + tig0021785:442-461 Msa1394030:CDS 30.0%
CAACATTCTATTGGCAAATA+GGG + tig0021785:443-462 Msa1394030:CDS 30.0%
AACATTCTATTGGCAAATAG+GGG + tig0021785:444-463 Msa1394030:CDS 30.0%
CATATTCAAAGAAATCTGAC+CGG - tig0021785:574-593 None:intergenic 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG + tig0021785:683-702 Msa1394030:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG + tig0021785:684-703 Msa1394030:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG + tig0021785:818-837 Msa1394030:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG + tig0021785:823-842 Msa1394030:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG - tig0021785:878-897 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG - tig0021785:883-902 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG - tig0021785:920-939 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG - tig0021785:921-940 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG + tig0021785:923-942 Msa1394030:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG - tig0021785:1016-1035 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG + tig0021785:1022-1041 Msa1394030:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG + tig0021785:1082-1101 Msa1394030:CDS 30.0%
TCAACATTCTATTGGCAAAT+AGG + tig0021785:442-461 Msa1394030:CDS 30.0%
CAACATTCTATTGGCAAATA+GGG + tig0021785:443-462 Msa1394030:CDS 30.0%
AACATTCTATTGGCAAATAG+GGG + tig0021785:444-463 Msa1394030:CDS 30.0%
CATATTCAAAGAAATCTGAC+CGG - tig0021785:574-593 None:intergenic 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG + tig0021785:683-702 Msa1394030:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG + tig0021785:684-703 Msa1394030:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG + tig0021785:818-837 Msa1394030:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG + tig0021785:823-842 Msa1394030:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG - tig0021785:878-897 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG - tig0021785:883-902 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG - tig0021785:920-939 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG - tig0021785:921-940 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG + tig0021785:923-942 Msa1394030:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG - tig0021785:1016-1035 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG + tig0021785:1022-1041 Msa1394030:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG + tig0021785:1082-1101 Msa1394030:CDS 30.0%
TGATATATTGCTGTCGAAGT+AGG + tig0021785:419-438 Msa1394030:intron 35.0%
GAAGTAGGTCAACATTCTAT+TGG + tig0021785:434-453 Msa1394030:intron 35.0%
CTCAAGTACTTATTACCTCT+TGG + tig0021785:482-501 Msa1394030:intron 35.0%
AGATAGCAATTACAACCAAG+AGG - tig0021785:500-519 None:intergenic 35.0%
CGGATTTCTAACAACTAGAA+TGG - tig0021785:535-554 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG + tig0021785:623-642 Msa1394030:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG + tig0021785:685-704 Msa1394030:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG - tig0021785:813-832 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG - tig0021785:998-1017 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG + tig0021785:1006-1025 Msa1394030:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG + tig0021785:1007-1026 Msa1394030:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG + tig0021785:1057-1076 Msa1394030:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG + tig0021785:1078-1097 Msa1394030:CDS 35.0%
TGATATATTGCTGTCGAAGT+AGG + tig0021785:419-438 Msa1394030:intron 35.0%
GAAGTAGGTCAACATTCTAT+TGG + tig0021785:434-453 Msa1394030:intron 35.0%
CTCAAGTACTTATTACCTCT+TGG + tig0021785:482-501 Msa1394030:intron 35.0%
AGATAGCAATTACAACCAAG+AGG - tig0021785:500-519 None:intergenic 35.0%
CGGATTTCTAACAACTAGAA+TGG - tig0021785:535-554 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG + tig0021785:623-642 Msa1394030:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG + tig0021785:685-704 Msa1394030:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG - tig0021785:813-832 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG - tig0021785:998-1017 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG + tig0021785:1006-1025 Msa1394030:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG + tig0021785:1007-1026 Msa1394030:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG + tig0021785:1057-1076 Msa1394030:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG + tig0021785:1078-1097 Msa1394030:CDS 35.0%
!! GTCAGTAGCCTATTTCTATG+CGG + tig0021785:802-821 Msa1394030:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG + tig0021785:803-822 Msa1394030:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG - tig0021785:868-887 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG - tig0021785:872-891 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG - tig0021785:1010-1029 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG + tig0021785:802-821 Msa1394030:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG + tig0021785:803-822 Msa1394030:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG - tig0021785:868-887 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG - tig0021785:872-891 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG - tig0021785:1010-1029 None:intergenic 40.0%
AAAGAAATCTGACCGGACGT+TGG - tig0021785:567-586 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG - tig0021785:598-617 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG - tig0021785:610-629 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG + tig0021785:611-630 Msa1394030:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG + tig0021785:630-649 Msa1394030:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG + tig0021785:631-650 Msa1394030:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG - tig0021785:650-669 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG + tig0021785:1067-1086 Msa1394030:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG - tig0021785:1071-1090 None:intergenic 45.0%
AAAGAAATCTGACCGGACGT+TGG - tig0021785:567-586 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG - tig0021785:598-617 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG - tig0021785:610-629 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG + tig0021785:611-630 Msa1394030:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG + tig0021785:630-649 Msa1394030:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG + tig0021785:631-650 Msa1394030:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG - tig0021785:650-669 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG + tig0021785:1067-1086 Msa1394030:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG - tig0021785:1071-1090 None:intergenic 45.0%
!!! TATATATATATTTTTTTTAG+AGG + tig0021785:342-361 Msa1394030:intron 5.0%
!!! ATATATATATTTTTTTTAGA+GGG + tig0021785:343-362 Msa1394030:intron 5.0%
!!! TATATATATATTTTTTTTAG+AGG + tig0021785:342-361 Msa1394030:intron 5.0%
!!! ATATATATATTTTTTTTAGA+GGG + tig0021785:343-362 Msa1394030:intron 5.0%
CCGGACGTTGGAATAGTTTG+CGG - tig0021785:555-574 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG + tig0021785:552-571 Msa1394030:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG - tig0021785:740-759 None:intergenic 50.0%
CCGGACGTTGGAATAGTTTG+CGG - tig0021785:555-574 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG + tig0021785:552-571 Msa1394030:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG - tig0021785:740-759 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG + tig0021785:644-663 Msa1394030:CDS 55.0%
GGTCCGTGGGTTCCGTTTAT+TGG + tig0021785:644-663 Msa1394030:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG + tig0021785:699-718 Msa1394030:CDS 60.0%
! GGTCAGGGGCTCTTTTGCCT+TGG + tig0021785:699-718 Msa1394030:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0021785 gene 211 1114 211 ID=Msa1394030;Name=Msa1394030
tig0021785 mRNA 211 1114 211 ID=Msa1394030-mRNA-1;Parent=Msa1394030;Name=Msa1394030-mRNA-1;_AED=0.40;_eAED=0.41;_QI=0|0|0|0.75|0|0.5|4|0|229
tig0021785 exon 211 219 211 ID=Msa1394030-mRNA-1:exon:14196;Parent=Msa1394030-mRNA-1
tig0021785 exon 369 436 369 ID=Msa1394030-mRNA-1:exon:14197;Parent=Msa1394030-mRNA-1
tig0021785 exon 441 486 441 ID=Msa1394030-mRNA-1:exon:14198;Parent=Msa1394030-mRNA-1
tig0021785 exon 548 1114 548 ID=Msa1394030-mRNA-1:exon:14199;Parent=Msa1394030-mRNA-1
tig0021785 CDS 211 219 211 ID=Msa1394030-mRNA-1:cds;Parent=Msa1394030-mRNA-1
tig0021785 CDS 369 436 369 ID=Msa1394030-mRNA-1:cds;Parent=Msa1394030-mRNA-1
tig0021785 CDS 441 486 441 ID=Msa1394030-mRNA-1:cds;Parent=Msa1394030-mRNA-1
tig0021785 CDS 548 1114 548 ID=Msa1394030-mRNA-1:cds;Parent=Msa1394030-mRNA-1
Gene Sequence

>Msa1394030

ATGGAATCGGGCAATATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATTGCTGTCGAAGTCAACATTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAAAATCCGCAAACTATTCCAACGTCCGGTCAGATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa1394030

MESGNMNVLLCYINTLNRFYDILLSKSTFYWQIGDFQVHAQKSANYSNVRSDFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*