AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene77636

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene77636.t1 MTR_1g060700 89.274 317 16 9 1 306 178 487 0.0 535
MS.gene77636.t1 MTR_2g067000 86.817 311 23 5 1 306 1 298 1.35e-179 497
MS.gene77636.t1 MTR_8g093500 58.491 53 22 0 176 228 125 177 9.83e-13 67.4
MS.gene77636.t1 MTR_3g101810 58.491 53 22 0 176 228 182 234 3.60e-12 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene77636.t1 AT1G30670 36.564 227 125 6 87 299 41 262 1.25e-28 111
MS.gene77636.t1 AT2G34820 39.662 237 106 7 87 299 66 289 5.83e-28 110
MS.gene77636.t1 AT3G21330 60.377 53 21 0 176 228 280 332 4.95e-13 69.3
MS.gene77636.t1 AT5G01305 50.000 58 29 0 176 233 48 105 4.80e-12 63.9

Find 46 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCATTATGATTGCTCAATT+TGG 0.191234 2.3:+29777816 None:intergenic
AGTTGGAATGCTTCAACTTA+TGG 0.195386 2.3:-29778728 MS.gene77636:CDS
ATCTCTGCTGTGTTCATCTT+TGG 0.238213 2.3:+29778793 None:intergenic
AAAATGAAATCTTCCTCATT+TGG 0.263570 2.3:+29779108 None:intergenic
AATTTGGTGACAAACTCTTT+TGG 0.289383 2.3:+29777832 None:intergenic
CCTCATAGTATAGCAGCTTT+TGG 0.317037 2.3:+29779055 None:intergenic
AAATGAAATCTTCCTCATTT+GGG 0.325640 2.3:+29779109 None:intergenic
TACAATTTCTCTTGAACAAA+TGG 0.348402 2.3:+29777877 None:intergenic
GAGAAGCTTCATTGAAATAG+TGG 0.359894 2.3:+29779271 None:intergenic
ATCAAAACCTACCATCCTTA+AGG 0.361760 2.3:-29777788 MS.gene77636:CDS
AAATAACACTATTCTTGCTT+TGG 0.365183 2.3:+29777727 None:intergenic
GCAGTTTGAATAGGTTGATA+AGG 0.385279 2.3:+29779357 None:intergenic
TCGAAGGAAGCAAAAGGGTT+AGG 0.397832 2.3:+29778961 None:intergenic
TTGATTATTTCAGGAAGAAA+AGG 0.418378 2.3:-29777941 MS.gene77636:intron
GAGCTAGGGAAGTTGGTTCC+TGG 0.426916 2.3:-29778820 MS.gene77636:CDS
CAAGCTGTTTCAGACCCTTA+AGG 0.427556 2.3:+29777773 None:intergenic
GACACAAGAGCTAGGGAAGT+TGG 0.431491 2.3:-29778827 MS.gene77636:CDS
TCAAAACCTACCATCCTTAA+GGG 0.456430 2.3:-29777787 MS.gene77636:CDS
AAGGGTCTGAAACAGCTTGT+TGG 0.460418 2.3:-29777769 MS.gene77636:CDS
TTGTGTAGATCTTCACTTGG+AGG 0.465635 2.3:+29777913 None:intergenic
AGTGGTGATTTCTGAGTTGT+TGG 0.472171 2.3:+29779332 None:intergenic
CGAAGGAAGCAAAAGGGTTA+GGG 0.473469 2.3:+29778962 None:intergenic
CAGTTTGAATAGGTTGATAA+GGG 0.475268 2.3:+29779358 None:intergenic
TTGTTGGTAGCAGTTTGAAT+AGG 0.476845 2.3:+29779348 None:intergenic
TCTGTCTCGAAGGAAGCAAA+AGG 0.486756 2.3:+29778955 None:intergenic
GTTCAATATGAGAAGAAAGT+TGG 0.493290 2.3:-29778913 MS.gene77636:CDS
TGTAGATCTTCACTTGGAGG+AGG 0.494574 2.3:+29777916 None:intergenic
GTGTTCATCTTTGGTCCACC+AGG 0.499817 2.3:+29778802 None:intergenic
AGAGTATCGCGGCTCGAGAA+AGG 0.514420 2.3:-29778870 MS.gene77636:CDS
ACTGAGAAGACACAAGAGCT+AGG 0.516284 2.3:-29778835 MS.gene77636:CDS
CCAAAAGCTGCTATACTATG+AGG 0.553268 2.3:-29779055 MS.gene77636:CDS
AGTTTGTGTAGATCTTCACT+TGG 0.558027 2.3:+29777910 None:intergenic
TTGTTCATGATGTTGAAAAG+TGG 0.560071 2.3:+29779314 None:intergenic
TCGCGGCTCGAGAAAGGAGA+AGG 0.564993 2.3:-29778864 MS.gene77636:CDS
AAGTTTCTTCAAGCTCAAGT+TGG 0.567049 2.3:-29778745 MS.gene77636:CDS
GAGTTCAAAAGCTCTTGTTG+TGG 0.567814 2.3:+29779018 None:intergenic
ACTTATGGAAACATTTAGCA+AGG 0.569731 2.3:-29778713 MS.gene77636:intron
ATGAGAAGAAAGTTGGTGAA+AGG 0.571730 2.3:-29778906 MS.gene77636:CDS
TTCAGACCCTTAAGGATGGT+AGG 0.578594 2.3:+29777781 None:intergenic
CTGAGAAGACACAAGAGCTA+GGG 0.585998 2.3:-29778834 MS.gene77636:CDS
CTGTCTCGAAGGAAGCAAAA+GGG 0.604732 2.3:+29778956 None:intergenic
CTAGGGAAGTTGGTTCCTGG+TGG 0.615915 2.3:-29778817 MS.gene77636:CDS
CTGTTTCAGACCCTTAAGGA+TGG 0.616344 2.3:+29777777 None:intergenic
AGTAGTTGTTGATCTTGACA+AGG 0.634276 2.3:+29779189 None:intergenic
TATATCGTCGCAGAGTATCG+CGG 0.664379 2.3:-29778881 MS.gene77636:CDS
GTAGTTGTTGATCTTGACAA+GGG 0.670997 2.3:+29779190 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCTTTGTAAATATCTAAAA+TGG - chr2.3:29778620-29778639 MS.gene77636:intron 15.0%
!!! CACTATTAATTTTATTTTCT+AGG + chr2.3:29779072-29779091 None:intergenic 15.0%
!! ACTAACTAAATCTACAATAA+TGG + chr2.3:29778655-29778674 None:intergenic 20.0%
!! GAATATTTAAAAACAAAGAG+TGG + chr2.3:29778962-29778981 None:intergenic 20.0%
!! TCATTTGAGTAAAAACAATT+AGG + chr2.3:29777915-29777934 None:intergenic 20.0%
!! TTATTGTATAAAGTTACACT+AGG + chr2.3:29779119-29779138 None:intergenic 20.0%
!!! AATATTTTCAGAGTAAAAGT+AGG + chr2.3:29778758-29778777 None:intergenic 20.0%
!!! ATATGATCATTGATTATTTC+AGG - chr2.3:29779181-29779200 MS.gene77636:CDS 20.0%
!!! CAATAAAAAAGAGAGTATTT+AGG - chr2.3:29778881-29778900 MS.gene77636:CDS 20.0%
!!! CTTTTACTCTGAAAATATTT+AGG - chr2.3:29778759-29778778 MS.gene77636:CDS 20.0%
! AAAATGAAATCTTCCTCATT+TGG + chr2.3:29778026-29778045 None:intergenic 25.0%
! AAACTCATCCACAAAAAAAT+TGG + chr2.3:29778141-29778160 None:intergenic 25.0%
! AAATGAAATCTTCCTCATTT+GGG + chr2.3:29778025-29778044 None:intergenic 25.0%
! ATCATTATGATTGCTCAATT+TGG + chr2.3:29779318-29779337 None:intergenic 25.0%
! TACAATTTCTCTTGAACAAA+TGG + chr2.3:29779257-29779276 None:intergenic 25.0%
! TTAGGAACAACAATTGTATA+TGG - chr2.3:29778899-29778918 MS.gene77636:CDS 25.0%
! TTGATTATTTCAGGAAGAAA+AGG - chr2.3:29779190-29779209 MS.gene77636:CDS 25.0%
!! TGAACAACATCAACAATTTT+TGG + chr2.3:29778203-29778222 None:intergenic 25.0%
!! TTTTATCAACATAAGACCTA+AGG + chr2.3:29778555-29778574 None:intergenic 25.0%
!!! ATCATTTTGAGAAGAAAAAG+TGG + chr2.3:29777976-29777995 None:intergenic 25.0%
ACTTATGGAAACATTTAGCA+AGG - chr2.3:29778418-29778437 MS.gene77636:intron 30.0%
CAATTGTATATGGAATGAGA+TGG - chr2.3:29778909-29778928 MS.gene77636:CDS 30.0%
GTTCAATATGAGAAGAAAGT+TGG - chr2.3:29778218-29778237 MS.gene77636:intron 30.0%
TAATATCCTTCCAAGTGTTT+GGG + chr2.3:29779017-29779036 None:intergenic 30.0%
TTAATATCCTTCCAAGTGTT+TGG + chr2.3:29779018-29779037 None:intergenic 30.0%
TTGTTCATGATGTTGAAAAG+TGG + chr2.3:29777820-29777839 None:intergenic 30.0%
! GAATGAAATTTTCCCAAATG+AGG - chr2.3:29778010-29778029 MS.gene77636:intron 30.0%
! TATTTAGTTTCCCAAACACT+TGG - chr2.3:29779004-29779023 MS.gene77636:CDS 30.0%
!! AATTTGGTGACAAACTCTTT+TGG + chr2.3:29779302-29779321 None:intergenic 30.0%
!! CAGTTTGAATAGGTTGATAA+GGG + chr2.3:29777776-29777795 None:intergenic 30.0%
!!! GAACTCAACCAATTTTTTTG+TGG - chr2.3:29778130-29778149 MS.gene77636:intron 30.0%
AAGTTTCTTCAAGCTCAAGT+TGG - chr2.3:29778386-29778405 MS.gene77636:intron 35.0%
AGTAGTTGTTGATCTTGACA+AGG + chr2.3:29777945-29777964 None:intergenic 35.0%
AGTTGGAATGCTTCAACTTA+TGG - chr2.3:29778403-29778422 MS.gene77636:intron 35.0%
AGTTTGTGTAGATCTTCACT+TGG + chr2.3:29779224-29779243 None:intergenic 35.0%
ATCAAAACCTACCATCCTTA+AGG - chr2.3:29779343-29779362 MS.gene77636:CDS 35.0%
ATCAACATAAGACCTAAGGA+AGG + chr2.3:29778551-29778570 None:intergenic 35.0%
CGGTTAATAAGAAGAGGAAA+TGG - chr2.3:29778857-29778876 MS.gene77636:CDS 35.0%
GAGAAGCTTCATTGAAATAG+TGG + chr2.3:29777863-29777882 None:intergenic 35.0%
GTAGTTGTTGATCTTGACAA+GGG + chr2.3:29777944-29777963 None:intergenic 35.0%
TCAAAACCTACCATCCTTAA+GGG - chr2.3:29779344-29779363 MS.gene77636:CDS 35.0%
! TTTTCAGAGTAAAAGTAGGC+AGG + chr2.3:29778754-29778773 None:intergenic 35.0%
!! ATGAGAAGAAAGTTGGTGAA+AGG - chr2.3:29778225-29778244 MS.gene77636:intron 35.0%
!! GCAGTTTGAATAGGTTGATA+AGG + chr2.3:29777777-29777796 None:intergenic 35.0%
!! TTGTTGGTAGCAGTTTGAAT+AGG + chr2.3:29777786-29777805 None:intergenic 35.0%
!!! AATTTTTGGTTCTGTCTCGA+AGG + chr2.3:29778189-29778208 None:intergenic 35.0%
AGTGGTGATTTCTGAGTTGT+TGG + chr2.3:29777802-29777821 None:intergenic 40.0%
ATCTCTGCTGTGTTCATCTT+TGG + chr2.3:29778341-29778360 None:intergenic 40.0%
CCAAAAGCTGCTATACTATG+AGG - chr2.3:29778076-29778095 MS.gene77636:intron 40.0%
GAGTTCAAAAGCTCTTGTTG+TGG + chr2.3:29778116-29778135 None:intergenic 40.0%
GGCTATGTAACTGTTCAACA+AGG - chr2.3:29778930-29778949 MS.gene77636:CDS 40.0%
GGGAAACGGTTAATAAGAAG+AGG - chr2.3:29778851-29778870 MS.gene77636:CDS 40.0%
TAGTTTCCCAAACACTTGGA+AGG - chr2.3:29779008-29779027 MS.gene77636:CDS 40.0%
TTGTGTAGATCTTCACTTGG+AGG + chr2.3:29779221-29779240 None:intergenic 40.0%
! ACTGTTTTGTGTCCTTCCTT+AGG - chr2.3:29778536-29778555 MS.gene77636:intron 40.0%
! CCTCATAGTATAGCAGCTTT+TGG + chr2.3:29778079-29778098 None:intergenic 40.0%
! TATAGCAGCTTTTGGCGTTT+TGG + chr2.3:29778071-29778090 None:intergenic 40.0%
!! TAGGTGCTGAATCATGTCAT+GGG + chr2.3:29779053-29779072 None:intergenic 40.0%
ACTGAGAAGACACAAGAGCT+AGG - chr2.3:29778296-29778315 MS.gene77636:intron 45.0%
AGAGAGAGAGAGAGAGGTTA+GGG - chr2.3:29778831-29778850 MS.gene77636:CDS 45.0%
AGAGAGAGAGGTTAGGGAAA+CGG - chr2.3:29778837-29778856 MS.gene77636:CDS 45.0%
CGAAGGAAGCAAAAGGGTTA+GGG + chr2.3:29778172-29778191 None:intergenic 45.0%
CTGAGAAGACACAAGAGCTA+GGG - chr2.3:29778297-29778316 MS.gene77636:intron 45.0%
CTGTCTCGAAGGAAGCAAAA+GGG + chr2.3:29778178-29778197 None:intergenic 45.0%
CTGTTTCAGACCCTTAAGGA+TGG + chr2.3:29779357-29779376 None:intergenic 45.0%
TCGAAGGAAGCAAAAGGGTT+AGG + chr2.3:29778173-29778192 None:intergenic 45.0%
TCTGTCTCGAAGGAAGCAAA+AGG + chr2.3:29778179-29778198 None:intergenic 45.0%
TGTAGATCTTCACTTGGAGG+AGG + chr2.3:29779218-29779237 None:intergenic 45.0%
TTCAGACCCTTAAGGATGGT+AGG + chr2.3:29779353-29779372 None:intergenic 45.0%
! AAGGGTCTGAAACAGCTTGT+TGG - chr2.3:29779362-29779381 MS.gene77636:CDS 45.0%
! CAAGCTGTTTCAGACCCTTA+AGG + chr2.3:29779361-29779380 None:intergenic 45.0%
!! AGCTTTTGGCGTTTTGGACA+TGG + chr2.3:29778065-29778084 None:intergenic 45.0%
!! CTAGGTGCTGAATCATGTCA+TGG + chr2.3:29779054-29779073 None:intergenic 45.0%
!! TATATCGTCGCAGAGTATCG+CGG - chr2.3:29778250-29778269 MS.gene77636:intron 45.0%
AGAGAGAGAGAGAGAGAGAG+AGG - chr2.3:29778799-29778818 MS.gene77636:CDS 50.0%
GACACAAGAGCTAGGGAAGT+TGG - chr2.3:29778304-29778323 MS.gene77636:intron 50.0%
GAGAGAGAGAGAGAGAGGTT+AGG - chr2.3:29778830-29778849 MS.gene77636:CDS 50.0%
GTGTTCATCTTTGGTCCACC+AGG + chr2.3:29778332-29778351 None:intergenic 50.0%
! CTAGGGAAGTTGGTTCCTGG+TGG - chr2.3:29778314-29778333 MS.gene77636:intron 55.0%
! GAGCTAGGGAAGTTGGTTCC+TGG - chr2.3:29778311-29778330 MS.gene77636:intron 55.0%
!! AGAGTATCGCGGCTCGAGAA+AGG - chr2.3:29778261-29778280 MS.gene77636:intron 55.0%
!! GGCGTTTTGGACATGGAAGC+TGG + chr2.3:29778058-29778077 None:intergenic 55.0%
TCGCGGCTCGAGAAAGGAGA+AGG - chr2.3:29778267-29778286 MS.gene77636:intron 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 29777735 29779418 29777735 ID=MS.gene77636
chr2.3 mRNA 29777735 29779418 29777735 ID=MS.gene77636.t1;Parent=MS.gene77636
chr2.3 exon 29778714 29779418 29778714 ID=MS.gene77636.t1.exon1;Parent=MS.gene77636.t1
chr2.3 CDS 29778714 29779418 29778714 ID=cds.MS.gene77636.t1;Parent=MS.gene77636.t1
chr2.3 exon 29777735 29777950 29777735 ID=MS.gene77636.t1.exon2;Parent=MS.gene77636.t1
chr2.3 CDS 29777735 29777950 29777735 ID=cds.MS.gene77636.t1;Parent=MS.gene77636.t1
Gene Sequence

>MS.gene77636

ATGGGAGCACTTAGCACATACTTTAACTATAATTGTTACCCTTATCAACCTATTCAAACTGCTACCAACAACTCAGAAATCACCACTTTTCAACATCATGAACAAGAACAACTTGTGCAACAAAACCACTATTTCAATGAAGCTTCTCTTTTAGATGAAAGCTTCATTTTTCAAACTCCTAATTGTTTTTACTCAAATGAGACTTACCCTTGTCAAGATCAACAACTACTTGTTGACTCCACTTTTTCTTCTCAAAATGATTGCTTTGTTTCAATGAATGAAATTTTCCCAAATGAGGAAGATTTCATTTTCAACAACTACCAGCTTCCATGTCCAAAACGCCAAAAGCTGCTATACTATGAGGAGAAAAGAGAAGAGCCACAACAAGAGCTTTTGAACTCAACCAATTTTTTTGTGGATGAGTTTATGACTAACCCTAACCCTTTTGCTTCCTTCGAGACAGAACCAAAAATTGTTGATGTTGTTCAATATGAGAAGAAAGTTGGTGAAAGGACTATATCGTCGCAGAGTATCGCGGCTCGAGAAAGGAGAAGGAAGATAACTGAGAAGACACAAGAGCTAGGGAAGTTGGTTCCTGGTGGACCAAAGATGAACACAGCAGAGATGCTTCATGCTGCTGCTAATTATGTCAAGTTTCTTCAAGCTCAAGTTGGAATGCTTCAACTTATGGAAACATTTAGCAAGGTAACTGTTTTTGCTTTTTTATTGTTGCAATGTTCTTATATTATTAGAGCTCATAATTGAAGTTAATTACTTTTCTTCACTTGAGTTTCGATTTCAACTGTTTTGTGTCCTTCCTTAGGTCTTATGTTGATAAAAAAAAAAATGATTATATGTCATTTTTCGTAGTGTGATTATGTATGTATCTTTGTAAATATCTAAAATGGATATTAATGCCATTATTGTAGATTTAGTTAGTTTTCTCATTTATGTGTGTAAAATAATCTATGACTAACTATTGTCTCAATGTTGTCTTTTTCACATTTATTTTTTTTCCTGCCTACTTTTACTCTGAAAATATTTAGGAATTGTTAAAAAAATTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGTTAGGGAAACGGTTAATAAGAAGAGGAAATGGTCAATAAAAAAGAGAGTATTTAGGAACAACAATTGTATATGGAATGAGATGGCTATGTAACTGTTCAACAAGGAATTATCCACTCTTTGTTTTTAAATATTCATTATTTTTACTTTCTTTATTATATTTAGTTTCCCAAACACTTGGAAGGATATTAAAAAATTTATAATCCCATGACATGATTCAGCACCTAGAAAATAAAATTAATAGTGTAACATTTTTGTAAAAGCTAAATTCCTAGTGTAACTTTATACAATAAAATTAATTAATGCTTAGAATATTCATTCTCTTTTGTTTATATATATGATCATTGATTATTTCAGGAAGAAAAGGAACCTCCTCCAAGTGAAGATCTACACAAACTAGTTGTTTCTCCATTTGTTCAAGAGAAATTGTATTCAGAAGAAAAGTGCTTTGTTCCAAAAGAGTTTGTCACCAAATTGAGCAATCATAATGATGTTCAATCAAAACCTACCATCCTTAAGGGTCTGAAACAGCTTGTTGGAACTGAGATTGAGAAGAAACCAAAGCAAGAATAG
Protein sequence

>MS.gene77636.t1

MGALSTYFNYNCYPYQPIQTATNNSEITTFQHHEQEQLVQQNHYFNEASLLDESFIFQTPNCFYSNETYPCQDQQLLVDSTFSSQNDCFVSMNEIFPNEEDFIFNNYQLPCPKRQKLLYYEEKREEPQQELLNSTNFFVDEFMTNPNPFASFETEPKIVDVVQYEKKVGERTISSQSIAARERRRKITEKTQELGKLVPGGPKMNTAEMLHAAANYVKFLQAQVGMLQLMETFSKEEKEPPPSEDLHKLVVSPFVQEKLYSEEKCFVPKEFVTKLSNHNDVQSKPTILKGLKQLVGTEIEKKPKQE