AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1293390

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1293390 MtrunA17_Chr8g0368861 97.500 120 3 0 1 120 1 120 3.87e-80 231
Msa1293390 MtrunA17_Chr8g0368831 96.667 120 4 0 1 120 9 128 1.96e-79 229
Msa1293390 MtrunA17_Chr7g0240471 51.515 99 46 2 23 120 20 117 9.17e-27 95.9
Msa1293390 MtrunA17_Chr7g0240451 51.579 95 44 2 27 120 24 117 2.54e-25 92.4
Msa1293390 MtrunA17_Chr7g0240441 57.407 54 22 1 63 116 38 90 9.98e-15 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1293390 AT2G37870.1 68.644 118 34 1 3 120 1 115 2.17e-50 155
Msa1293390 AT5G05960.1 45.902 122 58 3 1 120 1 116 7.57e-29 101
Msa1293390 AT3G53980.2 46.809 94 49 1 27 120 22 114 1.83e-27 97.8
Msa1293390 AT3G53980.1 46.809 94 49 1 27 120 22 114 1.83e-27 97.8

Find 36 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATAAATCAAATTTAAATAT+TGG 0.179260 8_3:-50496576 Msa1293390:three_prime_UTR
GGCATCAAGTGTGTTAATTT+TGG 0.227059 8_3:-50497363 Msa1293390:CDS
ATAAATCAAATTTAAATATT+GGG 0.278134 8_3:-50496575 Msa1293390:three_prime_UTR
ATCACTGACTAGTTTGTATA+TGG 0.303785 8_3:+50497471 None:intergenic
AGCTAGTCTAAGTCCATGTT+TGG 0.350440 8_3:-50497291 Msa1293390:CDS
TTCCTAATGTTGCATCTCTT+AGG 0.372829 8_3:+50497116 None:intergenic
ATCTTAGCTTGTTTAGCAAT+AGG 0.376748 8_3:+50497164 None:intergenic
TGGGTGCTGTACGTAATGTT+AGG 0.392658 8_3:-50497271 Msa1293390:CDS
ATGAGAAACCGCAACTGAAT+TGG 0.398627 8_3:+50496528 None:intergenic
GATTCTCAAAACAATACTAA+TGG 0.412873 8_3:-50497432 Msa1293390:exon
AATTAAATCATAATAGAAGT+TGG 0.445956 8_3:+50496676 None:intergenic
AGAACAGAACAAAGACATCT+TGG 0.469439 8_3:+50497194 None:intergenic
CCAACTCTAGCACAACAAAC+TGG 0.478057 8_3:+50497236 None:intergenic
CTTCCACATTTCTTTCCAGC+AGG 0.484036 8_3:+50497089 None:intergenic
CTAGCTGCTGCTGACCCAAT+TGG 0.492373 8_3:+50497308 None:intergenic
TTCCTAAGAGATGCAACATT+AGG 0.493031 8_3:-50497118 Msa1293390:CDS
TATTTCTGAGTGTTGTTGCA+TGG 0.493052 8_3:-50496756 Msa1293390:three_prime_UTR
AATGAAGTTATTGACTCAAG+TGG 0.499496 8_3:-50496629 Msa1293390:three_prime_UTR
AACATTAGGAACCGTCCTGC+TGG 0.500548 8_3:-50497104 Msa1293390:CDS
AACAGTGGTGATGTTTCTGT+TGG 0.504837 8_3:-50497384 Msa1293390:CDS
GGGTGCTGTACGTAATGTTA+GGG 0.506383 8_3:-50497270 Msa1293390:CDS
CCAGTTTGTTGTGCTAGAGT+TGG 0.508251 8_3:-50497236 Msa1293390:CDS
GAATGTGGAAGGACACCAAT+TGG 0.510582 8_3:-50497323 Msa1293390:CDS
CACATTTCTTTCCAGCAGGA+CGG 0.516461 8_3:+50497093 None:intergenic
AATGTGGAAGGACACCAATT+GGG 0.520212 8_3:-50497322 Msa1293390:CDS
TCAGAAATACAAAATGCTAC+AGG 0.524894 8_3:+50496770 None:intergenic
GCTAGTCTAAGTCCATGTTT+GGG 0.544347 8_3:-50497290 Msa1293390:CDS
AGTGAGGCAGCTGGTGAATG+TGG 0.580104 8_3:-50497338 Msa1293390:CDS
GGAACAGTGATAGCAATAGC+AGG 0.582273 8_3:+50497137 None:intergenic
GCTAAATAAATTCTGTAACA+TGG 0.587936 8_3:-50496824 Msa1293390:three_prime_UTR
TTACGTACAGCACCCAAACA+TGG 0.602239 8_3:+50497278 None:intergenic
CGTCCTGCTGGAAAGAAATG+TGG 0.607476 8_3:-50497092 Msa1293390:CDS
GAAACATCACCACTGTTGCA+AGG 0.618573 8_3:+50497390 None:intergenic
ACTCTAGCACAACAAACTGG+TGG 0.633479 8_3:+50497239 None:intergenic
AAGAACTTTCCTTGCAACAG+TGG 0.633689 8_3:-50497399 Msa1293390:CDS
AGGCAGCTGGTGAATGTGGA+AGG 0.638837 8_3:-50497334 Msa1293390:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTTTTTATTTTATTTACA+GGG - chr8_3:50497107-50497126 Msa1293390:CDS 10.0%
!!! CTTTTTTTATTTTATTTACA+GGG - chr8_3:50497107-50497126 Msa1293390:CDS 10.0%
!! ATTAATATCTACTAAGTTTA+TGG - chr8_3:50496994-50497013 Msa1293390:intron 15.0%
!! AATAAAATAAAAAAAGGACA+AGG + chr8_3:50497103-50497122 None:intergenic 15.0%
!! CCTGTAAATAAAATAAAAAA+AGG + chr8_3:50497109-50497128 None:intergenic 15.0%
!!! CCTTTTTTTATTTTATTTAC+AGG - chr8_3:50497106-50497125 Msa1293390:CDS 15.0%
!! AATTAAATCATAATAGAAGT+TGG + chr8_3:50497346-50497365 None:intergenic 15.0%
!! ATTAATATCTACTAAGTTTA+TGG - chr8_3:50496994-50497013 Msa1293390:intron 15.0%
!! AATAAAATAAAAAAAGGACA+AGG + chr8_3:50497103-50497122 None:intergenic 15.0%
!! CCTGTAAATAAAATAAAAAA+AGG + chr8_3:50497109-50497128 None:intergenic 15.0%
!!! CCTTTTTTTATTTTATTTAC+AGG - chr8_3:50497106-50497125 Msa1293390:CDS 15.0%
!! AATTAAATCATAATAGAAGT+TGG + chr8_3:50497346-50497365 None:intergenic 15.0%
! GATTCTCAAAACAATACTAA+TGG - chr8_3:50496587-50496606 Msa1293390:three_prime_UTR 25.0%
!!! ATTATTTTCCTGCTTTTTCA+AGG + chr8_3:50497142-50497161 None:intergenic 25.0%
! GCTAAATAAATTCTGTAACA+TGG - chr8_3:50497195-50497214 Msa1293390:CDS 25.0%
! GATTCTCAAAACAATACTAA+TGG - chr8_3:50496587-50496606 Msa1293390:three_prime_UTR 25.0%
!!! ATTATTTTCCTGCTTTTTCA+AGG + chr8_3:50497142-50497161 None:intergenic 25.0%
! GCTAAATAAATTCTGTAACA+TGG - chr8_3:50497195-50497214 Msa1293390:CDS 25.0%
!! ATCACTGACTAGTTTGTATA+TGG + chr8_3:50496551-50496570 None:intergenic 30.0%
!! TGTGTTAATTTTGGAAAGTG+AGG - chr8_3:50496665-50496684 Msa1293390:three_prime_UTR 30.0%
!! ATCTTAGCTTGTTTAGCAAT+AGG + chr8_3:50496858-50496877 None:intergenic 30.0%
TCAGAAATACAAAATGCTAC+AGG + chr8_3:50497252-50497271 None:intergenic 30.0%
!! AATGAAGTTATTGACTCAAG+TGG - chr8_3:50497390-50497409 Msa1293390:CDS 30.0%
!! ATCACTGACTAGTTTGTATA+TGG + chr8_3:50496551-50496570 None:intergenic 30.0%
!! TGTGTTAATTTTGGAAAGTG+AGG - chr8_3:50496665-50496684 Msa1293390:three_prime_UTR 30.0%
!! ATCTTAGCTTGTTTAGCAAT+AGG + chr8_3:50496858-50496877 None:intergenic 30.0%
TCAGAAATACAAAATGCTAC+AGG + chr8_3:50497252-50497271 None:intergenic 30.0%
!! AATGAAGTTATTGACTCAAG+TGG - chr8_3:50497390-50497409 Msa1293390:CDS 30.0%
! GGCATCAAGTGTGTTAATTT+TGG - chr8_3:50496656-50496675 Msa1293390:three_prime_UTR 35.0%
AGAACAGAACAAAGACATCT+TGG + chr8_3:50496828-50496847 None:intergenic 35.0%
TTCCTAAGAGATGCAACATT+AGG - chr8_3:50496901-50496920 Msa1293390:intron 35.0%
TTCCTAATGTTGCATCTCTT+AGG + chr8_3:50496906-50496925 None:intergenic 35.0%
! GTAACATGGCATTTTCTACT+TGG - chr8_3:50497209-50497228 Msa1293390:CDS 35.0%
! TATTTCTGAGTGTTGTTGCA+TGG - chr8_3:50497263-50497282 Msa1293390:CDS 35.0%
! GGCATCAAGTGTGTTAATTT+TGG - chr8_3:50496656-50496675 Msa1293390:three_prime_UTR 35.0%
AGAACAGAACAAAGACATCT+TGG + chr8_3:50496828-50496847 None:intergenic 35.0%
TTCCTAAGAGATGCAACATT+AGG - chr8_3:50496901-50496920 Msa1293390:intron 35.0%
TTCCTAATGTTGCATCTCTT+AGG + chr8_3:50496906-50496925 None:intergenic 35.0%
! GTAACATGGCATTTTCTACT+TGG - chr8_3:50497209-50497228 Msa1293390:CDS 35.0%
! TATTTCTGAGTGTTGTTGCA+TGG - chr8_3:50497263-50497282 Msa1293390:CDS 35.0%
AAGAACTTTCCTTGCAACAG+TGG - chr8_3:50496620-50496639 Msa1293390:three_prime_UTR 40.0%
! AACAGTGGTGATGTTTCTGT+TGG - chr8_3:50496635-50496654 Msa1293390:three_prime_UTR 40.0%
AATGTGGAAGGACACCAATT+GGG - chr8_3:50496697-50496716 Msa1293390:three_prime_UTR 40.0%
! AGCTAGTCTAAGTCCATGTT+TGG - chr8_3:50496728-50496747 Msa1293390:three_prime_UTR 40.0%
! GCTAGTCTAAGTCCATGTTT+GGG - chr8_3:50496729-50496748 Msa1293390:three_prime_UTR 40.0%
ACACACTTCCTTGAAAAAGC+AGG - chr8_3:50497131-50497150 Msa1293390:CDS 40.0%
AAGAACTTTCCTTGCAACAG+TGG - chr8_3:50496620-50496639 Msa1293390:three_prime_UTR 40.0%
! AACAGTGGTGATGTTTCTGT+TGG - chr8_3:50496635-50496654 Msa1293390:three_prime_UTR 40.0%
AATGTGGAAGGACACCAATT+GGG - chr8_3:50496697-50496716 Msa1293390:three_prime_UTR 40.0%
! AGCTAGTCTAAGTCCATGTT+TGG - chr8_3:50496728-50496747 Msa1293390:three_prime_UTR 40.0%
! GCTAGTCTAAGTCCATGTTT+GGG - chr8_3:50496729-50496748 Msa1293390:three_prime_UTR 40.0%
ACACACTTCCTTGAAAAAGC+AGG - chr8_3:50497131-50497150 Msa1293390:CDS 40.0%
GAAACATCACCACTGTTGCA+AGG + chr8_3:50496632-50496651 None:intergenic 45.0%
!! ATTTTGGAAAGTGAGGCAGC+TGG - chr8_3:50496672-50496691 Msa1293390:three_prime_UTR 45.0%
GAATGTGGAAGGACACCAAT+TGG - chr8_3:50496696-50496715 Msa1293390:three_prime_UTR 45.0%
TTACGTACAGCACCCAAACA+TGG + chr8_3:50496744-50496763 None:intergenic 45.0%
! TGGGTGCTGTACGTAATGTT+AGG - chr8_3:50496748-50496767 Msa1293390:three_prime_UTR 45.0%
! GGGTGCTGTACGTAATGTTA+GGG - chr8_3:50496749-50496768 Msa1293390:three_prime_UTR 45.0%
ACTCTAGCACAACAAACTGG+TGG + chr8_3:50496783-50496802 None:intergenic 45.0%
CCAACTCTAGCACAACAAAC+TGG + chr8_3:50496786-50496805 None:intergenic 45.0%
!! CCAGTTTGTTGTGCTAGAGT+TGG - chr8_3:50496783-50496802 Msa1293390:three_prime_UTR 45.0%
GGAACAGTGATAGCAATAGC+AGG + chr8_3:50496885-50496904 None:intergenic 45.0%
CACATTTCTTTCCAGCAGGA+CGG + chr8_3:50496929-50496948 None:intergenic 45.0%
CTTCCACATTTCTTTCCAGC+AGG + chr8_3:50496933-50496952 None:intergenic 45.0%
GAAACATCACCACTGTTGCA+AGG + chr8_3:50496632-50496651 None:intergenic 45.0%
!! ATTTTGGAAAGTGAGGCAGC+TGG - chr8_3:50496672-50496691 Msa1293390:three_prime_UTR 45.0%
GAATGTGGAAGGACACCAAT+TGG - chr8_3:50496696-50496715 Msa1293390:three_prime_UTR 45.0%
TTACGTACAGCACCCAAACA+TGG + chr8_3:50496744-50496763 None:intergenic 45.0%
! TGGGTGCTGTACGTAATGTT+AGG - chr8_3:50496748-50496767 Msa1293390:three_prime_UTR 45.0%
! GGGTGCTGTACGTAATGTTA+GGG - chr8_3:50496749-50496768 Msa1293390:three_prime_UTR 45.0%
ACTCTAGCACAACAAACTGG+TGG + chr8_3:50496783-50496802 None:intergenic 45.0%
CCAACTCTAGCACAACAAAC+TGG + chr8_3:50496786-50496805 None:intergenic 45.0%
!! CCAGTTTGTTGTGCTAGAGT+TGG - chr8_3:50496783-50496802 Msa1293390:three_prime_UTR 45.0%
GGAACAGTGATAGCAATAGC+AGG + chr8_3:50496885-50496904 None:intergenic 45.0%
CACATTTCTTTCCAGCAGGA+CGG + chr8_3:50496929-50496948 None:intergenic 45.0%
CTTCCACATTTCTTTCCAGC+AGG + chr8_3:50496933-50496952 None:intergenic 45.0%
!! AATAAATCAAATTTAAATAT+TGG - chr8_3:50497443-50497462 Msa1293390:five_prime_UTR 5.0%
!! ATAAATCAAATTTAAATATT+GGG - chr8_3:50497444-50497463 Msa1293390:five_prime_UTR 5.0%
!! AATAAATCAAATTTAAATAT+TGG - chr8_3:50497443-50497462 Msa1293390:five_prime_UTR 5.0%
!! ATAAATCAAATTTAAATATT+GGG - chr8_3:50497444-50497463 Msa1293390:five_prime_UTR 5.0%
AACATTAGGAACCGTCCTGC+TGG - chr8_3:50496915-50496934 Msa1293390:intron 50.0%
CGTCCTGCTGGAAAGAAATG+TGG - chr8_3:50496927-50496946 Msa1293390:intron 50.0%
AACATTAGGAACCGTCCTGC+TGG - chr8_3:50496915-50496934 Msa1293390:intron 50.0%
CGTCCTGCTGGAAAGAAATG+TGG - chr8_3:50496927-50496946 Msa1293390:intron 50.0%
AGTGAGGCAGCTGGTGAATG+TGG - chr8_3:50496681-50496700 Msa1293390:three_prime_UTR 55.0%
AGGCAGCTGGTGAATGTGGA+AGG - chr8_3:50496685-50496704 Msa1293390:three_prime_UTR 55.0%
CTAGCTGCTGCTGACCCAAT+TGG + chr8_3:50496714-50496733 None:intergenic 55.0%
AGTGAGGCAGCTGGTGAATG+TGG - chr8_3:50496681-50496700 Msa1293390:three_prime_UTR 55.0%
AGGCAGCTGGTGAATGTGGA+AGG - chr8_3:50496685-50496704 Msa1293390:three_prime_UTR 55.0%
CTAGCTGCTGCTGACCCAAT+TGG + chr8_3:50496714-50496733 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 50496542 50497499 50496542 ID=Msa1293390;Name=Msa1293390
chr8_3 mRNA 50496542 50497499 50496542 ID=Msa1293390-mRNA-1;Parent=Msa1293390;Name=Msa1293390-mRNA-1;_AED=0.25;_eAED=0.25;_QI=64|1|1|1|1|1|2|355|120
chr8_3 exon 50496542 50496913 50496542 ID=Msa1293390-mRNA-1:exon:14086;Parent=Msa1293390-mRNA-1
chr8_3 exon 50497090 50497499 50497090 ID=Msa1293390-mRNA-1:exon:14085;Parent=Msa1293390-mRNA-1
chr8_3 five_prime_UTR 50497436 50497499 50497436 ID=Msa1293390-mRNA-1:five_prime_utr;Parent=Msa1293390-mRNA-1
chr8_3 CDS 50497090 50497435 50497090 ID=Msa1293390-mRNA-1:cds;Parent=Msa1293390-mRNA-1
chr8_3 CDS 50496897 50496913 50496897 ID=Msa1293390-mRNA-1:cds;Parent=Msa1293390-mRNA-1
chr8_3 three_prime_UTR 50496542 50496896 50496542 ID=Msa1293390-mRNA-1:three_prime_utr;Parent=Msa1293390-mRNA-1
Gene Sequence

>Msa1293390

ATGGAGTTCAAAGTAAGAACTTTCCTTGCAACAGTGGTGATGTTTCTGTTGGCATCAAGTGTGTTAATTTTGGAAAGTGAGGCAGCTGGTGAATGTGGAAGGACACCAATTGGGTCAGCAGCAGCTAGTCTAAGTCCATGTTTGGGTGCTGTACGTAATGTTAGGGCAAAAGTTCCACCAGTTTGTTGTGCTAGAGTTGGTGCTTTGATTAGAACTTCTCCAAGATGTCTTTGTTCTGTTCTTTTGTCACCTATTGCTAAACAAGCTAAGATTAATCCTGCTATTGCTATCACTGTTCCTAAGAGATGCAACATTAGGAACCGTCCTGCTGGAAAGAAATGTGGAAGGTACACACTTCCTTGA
Protein sequence

>Msa1293390

MEFKVRTFLATVVMFLLASSVLILESEAAGECGRTPIGSAAASLSPCLGAVRNVRAKVPPVCCARVGALIRTSPRCLCSVLLSPIAKQAKINPAIAITVPKRCNIRNRPAGKKCGRYTLP*