AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene048528

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048528.t1 MTR_3g465280 54.762 84 35 2 13 96 1 81 5.36e-23 94.4
MS.gene048528.t1 MTR_3g465280 47.778 90 44 3 1 89 83 170 6.12e-18 80.5
MS.gene048528.t1 MTR_4g079500 41.053 95 56 0 108 202 194 288 3.87e-16 75.9
MS.gene048528.t1 MTR_2g090900 40.000 95 57 0 108 202 191 285 3.72e-15 73.6
MS.gene048528.t1 MTR_2g090900 40.000 95 57 0 108 202 191 285 4.85e-15 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048528.t1 AT2G42380 40.385 104 61 1 100 202 177 280 5.51e-17 78.2
MS.gene048528.t1 AT3G58120 38.053 113 69 1 90 202 185 296 1.37e-16 77.4
MS.gene048528.t1 AT2G42380 42.045 88 50 1 100 186 177 264 9.09e-15 71.6
MS.gene048528.t1 AT3G58120 39.175 97 58 1 90 186 185 280 2.20e-14 70.9
MS.gene048528.t1 AT5G07160 44.086 93 52 0 108 200 48 140 6.47e-13 64.3
MS.gene048528.t1 AT2G42380 35.577 104 55 2 100 202 177 269 9.69e-12 63.5

Find 43 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGCAATTTCAAGTCTTAAT+TGG 0.217186 3.3:-52655418 None:intergenic
ACTCGATTATATTGCAGATT+TGG 0.254957 3.3:+52654761 MS.gene048528:CDS
ACATGACCAAGATCTGATTT+TGG 0.271978 3.3:-52654120 None:intergenic
GTATACCGTTTGAGCCTCTT+TGG 0.278573 3.3:-52654219 None:intergenic
TCTGTACCAGTCATTCTCTT+TGG 0.281294 3.3:-52653907 None:intergenic
GAATAGGCTGAGGGAGCTTC+AGG 0.311474 3.3:+52655582 MS.gene048528:CDS
CTGTACCAGTCATTCTCTTT+GGG 0.324726 3.3:-52653906 None:intergenic
ATAAGAGAGCTGAGGTGAAT+AGG 0.348904 3.3:+52655566 MS.gene048528:CDS
TTCGACCATGGCAACCCTCT+TGG 0.419659 3.3:+52654010 MS.gene048528:CDS
ATGTTTGATTTCTTAGACCC+TGG 0.427163 3.3:-52653952 None:intergenic
TATTGCAGATTTGGAACAGA+TGG 0.461511 3.3:+52654770 MS.gene048528:CDS
AGTATACCAAAATCAGATCT+TGG 0.466062 3.3:+52654114 MS.gene048528:CDS
TTTCATAGGCTTCAACTTGT+GGG 0.474934 3.3:-52655364 None:intergenic
TCTTGGATGAGCATCGGCCT+TGG 0.498298 3.3:+52654027 MS.gene048528:CDS
TGGATCCAAAGAGGCTCAAA+CGG 0.512756 3.3:+52654214 MS.gene048528:CDS
CAATTTCAAGTCTTAATTGG+TGG 0.516892 3.3:-52655415 None:intergenic
GAGCTGAGGTGAATAGGCTG+AGG 0.526514 3.3:+52655572 MS.gene048528:CDS
TTGCAAACAGAAGAGGGACC+AGG 0.534478 3.3:+52653934 MS.gene048528:CDS
GGCATCCCAAAGAGAATGAC+TGG 0.538746 3.3:+52653901 MS.gene048528:CDS
CTTCATCAGCATTTCGACCA+TGG 0.539881 3.3:+52653998 MS.gene048528:CDS
TACTTTCCTCTTGTTTACCA+AGG 0.555727 3.3:-52654044 None:intergenic
AGGCTTCAACTTGTGGGCGA+AGG 0.567374 3.3:-52655358 None:intergenic
GACATGTTGCAAACAGAAGA+GGG 0.569321 3.3:+52653928 MS.gene048528:CDS
CGTAGTGCATCTGCAGATGT+TGG 0.574856 3.3:+52654165 MS.gene048528:CDS
AAACAAGAGGAAAGTAGCAG+TGG 0.582453 3.3:+52654051 MS.gene048528:CDS
CTCATCCAAGAGGGTTGCCA+TGG 0.587878 3.3:-52654015 None:intergenic
ATGGTTAGACCCTTCGCACA+TGG 0.590473 3.3:+52653973 MS.gene048528:CDS
GCATCTGCAGATGTTGGTGT+TGG 0.594426 3.3:+52654171 MS.gene048528:CDS
AGACATGTTGCAAACAGAAG+AGG 0.606246 3.3:+52653927 MS.gene048528:CDS
GATTGAGAATAAGAGAGCTG+AGG 0.610144 3.3:+52655558 MS.gene048528:CDS
TTTCTGAAGCACAAAACAAG+AGG 0.611292 3.3:+52655614 MS.gene048528:CDS
AGCTGAGGTGAATAGGCTGA+GGG 0.614102 3.3:+52655573 MS.gene048528:CDS
AGGCCGATGCTCATCCAAGA+GGG 0.614873 3.3:-52654024 None:intergenic
AAAGAAAGGATACTTCAAGA+AGG 0.624481 3.3:+52655449 MS.gene048528:CDS
CATCGGCCTTGGTAAACAAG+AGG 0.632643 3.3:+52654038 MS.gene048528:CDS
TGCAAACAGAAGAGGGACCA+GGG 0.636486 3.3:+52653935 MS.gene048528:CDS
CAACCCTCTTGGATGAGCAT+CGG 0.637743 3.3:+52654021 MS.gene048528:CDS
GATGAAGATCCATGTGCGAA+GGG 0.656221 3.3:-52653982 None:intergenic
TGATGAAGATCCATGTGCGA+AGG 0.660869 3.3:-52653983 None:intergenic
AAGGCCGATGCTCATCCAAG+AGG 0.678512 3.3:-52654025 None:intergenic
AGGGTCTAAGAAATCAAACA+TGG 0.688111 3.3:+52653954 MS.gene048528:CDS
GTTGAGAAGAAACACATCAG+TGG 0.702052 3.3:+52654141 MS.gene048528:CDS
AAGCCTATGAAAATCAGCAG+CGG 0.717215 3.3:+52655375 MS.gene048528:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTTTAAAAATTCATAATTA+AGG + chr3.3:52655712-52655731 MS.gene048528:intron 10.0%
!! ATTAAAATAAATCTATCTGT+TGG + chr3.3:52654525-52654544 MS.gene048528:intron 15.0%
!! TATTCTAATCAAATCTAAAT+CGG + chr3.3:52654622-52654641 MS.gene048528:intron 15.0%
!! TTTCAATTTCAATTTCAATT+TGG - chr3.3:52654965-52654984 None:intergenic 15.0%
!!! ATATTATATTGATTTTGTGT+AGG - chr3.3:52654658-52654677 None:intergenic 15.0%
!!! GAATTTTTAAACAACAATTT+AGG - chr3.3:52655705-52655724 None:intergenic 15.0%
!!! TTATTTTTTTTGGATAGATA+TGG - chr3.3:52655287-52655306 None:intergenic 15.0%
!! AAGCAATAAAAAAAATCAGT+TGG + chr3.3:52654261-52654280 MS.gene048528:intron 20.0%
!! CAAATCAACTATATTAGATA+GGG - chr3.3:52654594-52654613 None:intergenic 20.0%
!! TCAAATCAACTATATTAGAT+AGG - chr3.3:52654595-52654614 None:intergenic 20.0%
!! TCATGTATCAACTTATAATT+TGG + chr3.3:52655153-52655172 MS.gene048528:intron 20.0%
!!! CATTTATCGGATTTTTTTTT+AGG - chr3.3:52654376-52654395 None:intergenic 20.0%
!!! GATAGAAATTTTGATTCTTA+AGG + chr3.3:52654302-52654321 MS.gene048528:intron 20.0%
!!! TACTAATGTTATTAGTTTTG+TGG - chr3.3:52654098-52654117 None:intergenic 20.0%
!!! TCTTCACAAGTTATTTTTTT+TGG - chr3.3:52655297-52655316 None:intergenic 20.0%
!!! TTTTATCTTATCTTGTTCTT+AGG + chr3.3:52654694-52654713 MS.gene048528:intron 20.0%
!!! TTTTGACAAAAGTTCTATTT+AGG + chr3.3:52654424-52654443 MS.gene048528:intron 20.0%
! ATAGATCAATTATGATCGAA+TGG - chr3.3:52655133-52655152 None:intergenic 25.0%
!!! TTGAGATATTTTTTACATGC+AGG + chr3.3:52655322-52655341 MS.gene048528:intron 25.0%
!!! TTTTTTTGGATAGATATGGT+GGG - chr3.3:52655283-52655302 None:intergenic 25.0%
!!! TTTTTTTTGGATAGATATGG+TGG - chr3.3:52655284-52655303 None:intergenic 25.0%
AAAGAAAGGATACTTCAAGA+AGG + chr3.3:52655449-52655468 MS.gene048528:CDS 30.0%
ACACGTGAACATATAGTAAT+AGG - chr3.3:52654861-52654880 None:intergenic 30.0%
ACTCGATTATATTGCAGATT+TGG + chr3.3:52654761-52654780 MS.gene048528:CDS 30.0%
AGTATACCAAAATCAGATCT+TGG + chr3.3:52654114-52654133 MS.gene048528:CDS 30.0%
ATTGATGAACCTAAACAACA+AGG + chr3.3:52655247-52655266 MS.gene048528:intron 30.0%
CAGTTGGCAAGTTAAAAATA+TGG + chr3.3:52654277-52654296 MS.gene048528:intron 30.0%
TGATCAAGCAACACAAAAAT+TGG + chr3.3:52654194-52654213 MS.gene048528:CDS 30.0%
TTGATGAACCTAAACAACAA+GGG + chr3.3:52655248-52655267 MS.gene048528:intron 30.0%
TTGCTGTAAGAGAAAAAGAA+AGG + chr3.3:52655435-52655454 MS.gene048528:CDS 30.0%
TTGGCAAGTTAAAAATATGG+AGG + chr3.3:52654280-52654299 MS.gene048528:intron 30.0%
! CAATTTCAAGTCTTAATTGG+TGG - chr3.3:52655418-52655437 None:intergenic 30.0%
! CAGCAATTTCAAGTCTTAAT+TGG - chr3.3:52655421-52655440 None:intergenic 30.0%
! GTTCTATTTAGGCTTTATCA+TGG + chr3.3:52654435-52654454 MS.gene048528:intron 30.0%
!!! TTATTAGTTTTGTGGTCTTG+TGG - chr3.3:52654090-52654109 None:intergenic 30.0%
AAAATCCGATAAATGCGAGT+TGG + chr3.3:52654381-52654400 MS.gene048528:intron 35.0%
ACAGATGGAAAAACATTTGC+AGG + chr3.3:52654785-52654804 MS.gene048528:CDS 35.0%
ACATACTCGTGTGAAACAAA+TGG - chr3.3:52655524-52655543 None:intergenic 35.0%
AGGGTCTAAGAAATCAAACA+TGG + chr3.3:52653954-52653973 MS.gene048528:CDS 35.0%
CACAAAAATTGGATCCAAAG+AGG + chr3.3:52654205-52654224 MS.gene048528:CDS 35.0%
TAGAACCAACTCGCATTTAT+CGG - chr3.3:52654389-52654408 None:intergenic 35.0%
TTTCATAGGCTTCAACTTGT+GGG - chr3.3:52655367-52655386 None:intergenic 35.0%
! ACATGACCAAGATCTGATTT+TGG - chr3.3:52654123-52654142 None:intergenic 35.0%
! ATGTTTGATTTCTTAGACCC+TGG - chr3.3:52653955-52653974 None:intergenic 35.0%
! CAATTGCTCTAGATGTAGAA+CGG + chr3.3:52655020-52655039 MS.gene048528:intron 35.0%
! TACTTTCCTCTTGTTTACCA+AGG - chr3.3:52654047-52654066 None:intergenic 35.0%
! TATTGCAGATTTGGAACAGA+TGG + chr3.3:52654770-52654789 MS.gene048528:CDS 35.0%
! TTTTCATAGGCTTCAACTTG+TGG - chr3.3:52655368-52655387 None:intergenic 35.0%
!! AATGCGAGTTGGTTCTATTT+AGG + chr3.3:52654392-52654411 MS.gene048528:intron 35.0%
!! ATATGGATCCCTTGTTGTTT+AGG - chr3.3:52655259-52655278 None:intergenic 35.0%
!! TTTCTGAAGCACAAAACAAG+AGG + chr3.3:52655614-52655633 MS.gene048528:CDS 35.0%
AAACAAGAGGAAAGTAGCAG+TGG + chr3.3:52654051-52654070 MS.gene048528:CDS 40.0%
AAGCCTATGAAAATCAGCAG+CGG + chr3.3:52655375-52655394 MS.gene048528:CDS 40.0%
AGACATGTTGCAAACAGAAG+AGG + chr3.3:52653927-52653946 MS.gene048528:CDS 40.0%
ATAAGAGAGCTGAGGTGAAT+AGG + chr3.3:52655566-52655585 MS.gene048528:CDS 40.0%
CTGTACCAGTCATTCTCTTT+GGG - chr3.3:52653909-52653928 None:intergenic 40.0%
CTTAAGGCTAAACGTGTGAT+GGG + chr3.3:52654318-52654337 MS.gene048528:intron 40.0%
GACATGTTGCAAACAGAAGA+GGG + chr3.3:52653928-52653947 MS.gene048528:CDS 40.0%
GATTGAGAATAAGAGAGCTG+AGG + chr3.3:52655558-52655577 MS.gene048528:CDS 40.0%
GTTGAGAAGAAACACATCAG+TGG + chr3.3:52654141-52654160 MS.gene048528:CDS 40.0%
TCTGTACCAGTCATTCTCTT+TGG - chr3.3:52653910-52653929 None:intergenic 40.0%
TCTTAAGGCTAAACGTGTGA+TGG + chr3.3:52654317-52654336 MS.gene048528:intron 40.0%
! GGATAGATATGGTGGGAATA+TGG - chr3.3:52655276-52655295 None:intergenic 40.0%
ACACCATTCGCTTTCGTGAT+TGG - chr3.3:52654906-52654925 None:intergenic 45.0%
ACCATTCGCTTTCGTGATTG+GGG - chr3.3:52654904-52654923 None:intergenic 45.0%
CACCATTCGCTTTCGTGATT+GGG - chr3.3:52654905-52654924 None:intergenic 45.0%
CTTCATCAGCATTTCGACCA+TGG + chr3.3:52653998-52654017 MS.gene048528:CDS 45.0%
GATGAAGATCCATGTGCGAA+GGG - chr3.3:52653985-52654004 None:intergenic 45.0%
GTATACCGTTTGAGCCTCTT+TGG - chr3.3:52654222-52654241 None:intergenic 45.0%
TGATGAAGATCCATGTGCGA+AGG - chr3.3:52653986-52654005 None:intergenic 45.0%
TGGATCCAAAGAGGCTCAAA+CGG + chr3.3:52654214-52654233 MS.gene048528:CDS 45.0%
!!! CAACCGCTGCTGATTTTCAT+AGG - chr3.3:52655381-52655400 None:intergenic 45.0%
AGCTGAGGTGAATAGGCTGA+GGG + chr3.3:52655573-52655592 MS.gene048528:CDS 50.0%
ATGGTTAGACCCTTCGCACA+TGG + chr3.3:52653973-52653992 MS.gene048528:CDS 50.0%
CAACCCTCTTGGATGAGCAT+CGG + chr3.3:52654021-52654040 MS.gene048528:CDS 50.0%
CATCGGCCTTGGTAAACAAG+AGG + chr3.3:52654038-52654057 MS.gene048528:CDS 50.0%
CGTAGTGCATCTGCAGATGT+TGG + chr3.3:52654165-52654184 MS.gene048528:CDS 50.0%
GCATCTGCAGATGTTGGTGT+TGG + chr3.3:52654171-52654190 MS.gene048528:CDS 50.0%
GGCATCCCAAAGAGAATGAC+TGG + chr3.3:52653901-52653920 MS.gene048528:CDS 50.0%
TCCCCAATCACGAAAGCGAA+TGG + chr3.3:52654900-52654919 MS.gene048528:intron 50.0%
TGCAAACAGAAGAGGGACCA+GGG + chr3.3:52653935-52653954 MS.gene048528:CDS 50.0%
TTGCAAACAGAAGAGGGACC+AGG + chr3.3:52653934-52653953 MS.gene048528:CDS 50.0%
! TGCTCTAGATGTAGAACGGC+TGG + chr3.3:52655024-52655043 MS.gene048528:intron 50.0%
AAGGCCGATGCTCATCCAAG+AGG - chr3.3:52654028-52654047 None:intergenic 55.0%
AGGCCGATGCTCATCCAAGA+GGG - chr3.3:52654027-52654046 None:intergenic 55.0%
AGGCTTCAACTTGTGGGCGA+AGG - chr3.3:52655361-52655380 None:intergenic 55.0%
CTCATCCAAGAGGGTTGCCA+TGG - chr3.3:52654018-52654037 None:intergenic 55.0%
GAATAGGCTGAGGGAGCTTC+AGG + chr3.3:52655582-52655601 MS.gene048528:CDS 55.0%
GAGCTGAGGTGAATAGGCTG+AGG + chr3.3:52655572-52655591 MS.gene048528:CDS 55.0%
TTCGACCATGGCAACCCTCT+TGG + chr3.3:52654010-52654029 MS.gene048528:CDS 55.0%
!! TCTTGGATGAGCATCGGCCT+TGG + chr3.3:52654027-52654046 MS.gene048528:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 52653895 52655746 52653895 ID=MS.gene048528
chr3.3 mRNA 52653895 52655746 52653895 ID=MS.gene048528.t1;Parent=MS.gene048528
chr3.3 exon 52653895 52654235 52653895 ID=MS.gene048528.t1.exon1;Parent=MS.gene048528.t1
chr3.3 CDS 52653895 52654235 52653895 ID=cds.MS.gene048528.t1;Parent=MS.gene048528.t1
chr3.3 exon 52654716 52654806 52654716 ID=MS.gene048528.t1.exon2;Parent=MS.gene048528.t1
chr3.3 CDS 52654716 52654806 52654716 ID=cds.MS.gene048528.t1;Parent=MS.gene048528.t1
chr3.3 exon 52655344 52655470 52655344 ID=MS.gene048528.t1.exon3;Parent=MS.gene048528.t1
chr3.3 CDS 52655344 52655470 52655344 ID=cds.MS.gene048528.t1;Parent=MS.gene048528.t1
chr3.3 exon 52655554 52655635 52655554 ID=MS.gene048528.t1.exon4;Parent=MS.gene048528.t1
chr3.3 CDS 52655554 52655635 52655554 ID=cds.MS.gene048528.t1;Parent=MS.gene048528.t1
chr3.3 exon 52655734 52655746 52655734 ID=MS.gene048528.t1.exon5;Parent=MS.gene048528.t1
chr3.3 CDS 52655734 52655746 52655734 ID=cds.MS.gene048528.t1;Parent=MS.gene048528.t1
Gene Sequence

>MS.gene048528

ATGCAGGGCATCCCAAAGAGAATGACTGGTACAGACATGTTGCAAACAGAAGAGGGACCAGGGTCTAAGAAATCAAACATGGTTAGACCCTTCGCACATGGATCTTCATCAGCATTTCGACCATGGCAACCCTCTTGGATGAGCATCGGCCTTGGTAAACAAGAGGAAAGTAGCAGTGGAGTAAAAGAAACTCCACAAGACCACAAAACTAATAACATTAGTATACCAAAATCAGATCTTGGTCATGTTGAGAAGAAACACATCAGTGGTCGTAGTGCATCTGCAGATGTTGGTGTTGGTGATCAAGCAACACAAAAATTGGATCCAAAGAGGCTCAAACGGTATACTTGTCTTACTTATGCTTGTAAGCAATAAAAAAAATCAGTTGGCAAGTTAAAAATATGGAGGATAGAAATTTTGATTCTTAAGGCTAAACGTGTGATGGGAATAATATATTTTTTTTATTACATTTTTTTTACCTAAAAAAAAATCCGATAAATGCGAGTTGGTTCTATTTAGGTTTTTTTTTTTTTGACAAAAGTTCTATTTAGGCTTTATCATGGTCAACTGTGATTTTAATAATAAACTTAATTAATATTGTAATTGTTTTCATCTTATTTTTAATTAAAAATTAAAATAAATCTATCTGTTGGTTTAAGTTTCATGTTATTAGATTTATCATCTATGAATGTGATACCCTATCTAATATAGTTGATTTGATTTATTTTATTCTAATCAAATCTAAATCGGTTGTTTATTTCCTACACAAAATCAATATAATATATTTTAGATTTTCATCTTTTATCTTATCTTGTTCTTAGGATTGAAGCAAATCGAGTTGCTGCACAAAAATCGAGATTGAAAAAACTCGATTATATTGCAGATTTGGAACAGATGGAAAAACATTTGCAGGTTCACATCATTATTTATCATATCACGAAGATTGTAATTTATGCATTTTGTCCTATTACTATATGTTCACGTGTTTCGAAGAGACTTAAATTATCCCCAATCACGAAAGCGAATGGTGTTTAGATGAGAATCAAACAACACAAATTCTAATTTCACCAAATTGAAATTGAAATTGAAATACACTTTATGTAATTTGTGTTGTTTGATCTTCATCAATTGCTCTAGATGTAGAACGGCTGGTTACGACTTCAAAAAATTTCAATTTCTCGATTATTTGTATTAATTTGATGTAGATAAATACACTACGATCTTGTTGATTTGAACCATTCGATCATAATTGATCTATTCATGTATCAACTTATAATTTGGAATTCAATTGAAAATTTGACATGTGAGTCATTTGATCTAGATCTGATTGTTCAAATAGCATAACTCAACAAATTGATGAACCTAAACAACAAGGGATCCATATTCCCACCATATCTATCCAAAAAAAATAACTTGTGAAGATGATTTTGAGATATTTTTTACATGCAGGCTGAGTTATCTTTCCTTCGCCCACAAGTTGAAGCCTATGAAAATCAGCAGCGGTTGTTGAGTCTTGAACACCACCAATTAAGACTTGAAATTGCTGTAAGAGAAAAAGAAAGGATACTTCAAGAAGGTGATATTACTCATTTGTCTTTATATCTAGCATTTATTATCGTGTCTCTGCCATTTGTTTCACACGAGTATGTTTATTTTCAGTTGAGATTGAGAATAAGAGAGCTGAGGTGAATAGGCTGAGGGAGCTTCAGGAGAAACTAGTTTCTGAAGCACAAAACAAGAGGTATGTTGAAATGCTTACTAGTATTTTTAACAATATTTTTGTACTAATTATAATATGACTCATATGCCTAAATTGTTGTTTAAAAATTCATAATTAAGGTTTGTGTATTAA
Protein sequence

>MS.gene048528.t1

MQGIPKRMTGTDMLQTEEGPGSKKSNMVRPFAHGSSSAFRPWQPSWMSIGLGKQEESSSGVKETPQDHKTNNISIPKSDLGHVEKKHISGRSASADVGVGDQATQKLDPKRLKRIEANRVAAQKSRLKKLDYIADLEQMEKHLQAELSFLRPQVEAYENQQRLLSLEHHQLRLEIAVREKERILQEVEIENKRAEVNRLRELQEKLVSEAQNKRFVY