AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1275940


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1275940 MtrunA17_Chr8g0343151 98.419 253 4 0 12 264 3657 3909 7.06e-166 509
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1275940 AT1G67120.2 49.615 260 124 1 12 264 3687 3946 1.00e-68 231
Msa1275940 AT1G67120.1 49.615 260 124 1 12 264 3680 3939 1.08e-68 231

Find 43 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTCTTCCCACTCATTTAAA+AGG 0.154249 8_3:-10283806 None:intergenic
CTTCCAGCTTTGGGGAATTC+AGG 0.194184 8_3:+10284820 Msa1275940:CDS
TTATTCAGACTTCCAGCTTT+GGG 0.305959 8_3:+10284811 Msa1275940:CDS
AAAAGATGGAACTGGGTTCT+TGG 0.325602 8_3:+10284273 Msa1275940:CDS
CAGCTTCTTTATGCTTTCCT+TGG 0.331555 8_3:+10284852 Msa1275940:CDS
TTCGACTGAACTGAAAGATT+TGG 0.333586 8_3:+10285336 Msa1275940:CDS
ACATTCTTGTACAATATGTT+TGG 0.340503 8_3:+10285153 Msa1275940:CDS
TTTATTCAGACTTCCAGCTT+TGG 0.412758 8_3:+10284810 Msa1275940:CDS
CTGGACACTGCAGCTGTTGT+CGG 0.434729 8_3:+10285118 Msa1275940:intron
CTCTTCCCACTCATTTAAAA+GGG 0.451523 8_3:-10283805 None:intergenic
CATGCCTGAAAATTAATTCC+AGG 0.455535 8_3:+10284892 Msa1275940:CDS
TCTCATGAGCATTTGAATCC+TGG 0.461464 8_3:-10283734 None:intergenic
TTTCCTGAATTCCCCAAAGC+TGG 0.473734 8_3:-10284823 None:intergenic
ATCATGGCAAAAGATGGAAC+TGG 0.475501 8_3:+10284265 Msa1275940:CDS
GAAACTATGTCGGTGGGAGC+AGG 0.478121 8_3:+10285360 Msa1275940:CDS
GATGTCATCATGGCAAAAGA+TGG 0.489535 8_3:+10284259 Msa1275940:CDS
AAGAAAATTCATACTTGAGA+AGG 0.494227 8_3:-10284143 None:intergenic
GGATATCAGATGGAAGAGTC+AGG 0.503377 8_3:-10283869 None:intergenic
CCTTTGGAAAATTGATTGAT+CGG 0.505093 8_3:-10284675 None:intergenic
GATAGAAGAAGAGAGTACAA+AGG 0.534850 8_3:-10284644 None:intergenic
ATCTGATATCCCTCTAGCTA+AGG 0.537770 8_3:+10283881 Msa1275940:CDS
GCTTTGGGGAATTCAGGAAA+CGG 0.546918 8_3:+10284826 Msa1275940:CDS
AATTGATTGATCGGAAGTAG+TGG 0.548771 8_3:-10284666 None:intergenic
CGTGTTGCTTGATGAGGTGA+TGG 0.551638 8_3:+10284298 Msa1275940:CDS
AAGTCTGAATAAAGTCCTCC+AGG 0.554221 8_3:-10284800 None:intergenic
CGAAGCACATTGATGCTAGT+AGG 0.557924 8_3:+10285305 Msa1275940:CDS
TACATATAAAACTAAACCAC+AGG 0.561255 8_3:-10285479 None:intergenic
AGCATTACTCTGCCTGCCTG+TGG 0.563244 8_3:+10285463 Msa1275940:CDS
GATATGATCTGCTGTCTTAG+CGG 0.565254 8_3:-10283783 None:intergenic
TTAGCTAGAGGGATATCAGA+TGG 0.572898 8_3:-10283879 None:intergenic
TATTCAGACTTCCAGCTTTG+GGG 0.581710 8_3:+10284812 Msa1275940:CDS
TTGGCCCGTGTTGCTTGATG+AGG 0.582535 8_3:+10284292 Msa1275940:CDS
AATTGCTCACCTTAGCTAGA+GGG 0.597638 8_3:-10283890 None:intergenic
TATAAAACTAAACCACAGGC+AGG 0.597755 8_3:-10285475 None:intergenic
ACACTGCAGCTGTTGTCGGA+CGG 0.599254 8_3:+10285122 Msa1275940:intron
ATTTGGTGAAACTATGTCGG+TGG 0.611375 8_3:+10285353 Msa1275940:CDS
TAATTGCTCACCTTAGCTAG+AGG 0.617212 8_3:-10283891 None:intergenic
TTTGGTGAAACTATGTCGGT+GGG 0.619701 8_3:+10285354 Msa1275940:CDS
ATCACCTCATCAAGCAACAC+GGG 0.621276 8_3:-10284296 None:intergenic
CATCACCTCATCAAGCAACA+CGG 0.626281 8_3:-10284297 None:intergenic
TCATGGCAAAAGATGGAACT+GGG 0.630972 8_3:+10284266 Msa1275940:CDS
ATATGAATCTTGTAGCCTGG+AGG 0.658277 8_3:+10284785 Msa1275940:intron
AAGATTTGGTGAAACTATGT+CGG 0.671476 8_3:+10285350 Msa1275940:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTAACTAATATTATCTAT+TGG - chr8_3:10284983-10285002 None:intergenic 10.0%
!!! GTTTTATATGTAAATATAAT+TGG + chr8_3:10285490-10285509 Msa1275940:CDS 10.0%
!!! TTTTAAGATACAAATAAGAA+GGG - chr8_3:10284461-10284480 None:intergenic 15.0%
!!! ATTTTAAGATACAAATAAGA+AGG - chr8_3:10284462-10284481 None:intergenic 15.0%
!! ATAAATAAAAGACAAGATAT+TGG - chr8_3:10285229-10285248 None:intergenic 15.0%
!!! CTTTTATTTATTGTTTTCAT+TGG + chr8_3:10285238-10285257 Msa1275940:intron 15.0%
!!! TGTGTTTTTACCAATTTTTA+TGG + chr8_3:10284195-10284214 Msa1275940:intron 20.0%
!! GTCATTAAAACCATAAAAAT+TGG - chr8_3:10284208-10284227 None:intergenic 20.0%
!! TTTGTTAATAGTTGTATTGT+AGG + chr8_3:10284381-10284400 Msa1275940:intron 20.0%
!! CAAAAAGAATTAAGTTATTG+CGG - chr8_3:10284598-10284617 None:intergenic 20.0%
!! TGTTAATTATAGATTACCTT+TGG - chr8_3:10284694-10284713 None:intergenic 20.0%
! AAGAAAATTCATACTTGAGA+AGG - chr8_3:10284146-10284165 None:intergenic 25.0%
! AACAATGCTAAAAAAGTAAG+CGG + chr8_3:10284332-10284351 Msa1275940:intron 25.0%
! CAAATAAGAAGGGAAAAAAA+AGG - chr8_3:10284451-10284470 None:intergenic 25.0%
! AATGCACTTATAAAGACTAA+AGG + chr8_3:10284534-10284553 Msa1275940:intron 25.0%
!! CTTCATCTTTTTAGATTATG+TGG + chr8_3:10284734-10284753 Msa1275940:intron 25.0%
!! TATACCTGGAATTAATTTTC+AGG - chr8_3:10284899-10284918 None:intergenic 25.0%
!! TCTAGAACTATAAATATACC+TGG - chr8_3:10284913-10284932 None:intergenic 25.0%
! CTAAACATTTGCAACAAAAT+GGG - chr8_3:10285020-10285039 None:intergenic 25.0%
! TCTAAACATTTGCAACAAAA+TGG - chr8_3:10285021-10285040 None:intergenic 25.0%
!!! ATAGTTTTTTTCTTCATTGC+TGG + chr8_3:10285099-10285118 Msa1275940:intron 25.0%
! ACATTCTTGTACAATATGTT+TGG + chr8_3:10285153-10285172 Msa1275940:CDS 25.0%
! TACATATAAAACTAAACCAC+AGG - chr8_3:10285482-10285501 None:intergenic 25.0%
CAAAGAACAAAAAGATACAC+AGG - chr8_3:10283709-10283728 None:intergenic 30.0%
! GTGTATCTTTTTGTTCTTTG+TGG + chr8_3:10283709-10283728 Msa1275940:CDS 30.0%
! TCATATCCCTTTTAAATGAG+TGG + chr8_3:10283799-10283818 Msa1275940:CDS 30.0%
! CATATCCCTTTTAAATGAGT+GGG + chr8_3:10283800-10283819 Msa1275940:CDS 30.0%
! GACAACTTCATTTTCATTAG+AGG - chr8_3:10283938-10283957 None:intergenic 30.0%
! TTAACTGAAAAAGTGTGCTA+GGG - chr8_3:10283974-10283993 None:intergenic 30.0%
! ATTAACTGAAAAAGTGTGCT+AGG - chr8_3:10283975-10283994 None:intergenic 30.0%
! TTTTTGATCTGATGTCATCA+TGG + chr8_3:10284249-10284268 Msa1275940:CDS 30.0%
ATTGCGGCTTAAAATAAATC+AGG - chr8_3:10284582-10284601 None:intergenic 30.0%
! CCTTTGGAAAATTGATTGAT+CGG - chr8_3:10284678-10284697 None:intergenic 30.0%
!! AAGATTTGGTGAAACTATGT+CGG + chr8_3:10285350-10285369 Msa1275940:CDS 30.0%
! TTTTTGTTCTTTGTGGATCC+AGG + chr8_3:10283716-10283735 Msa1275940:CDS 35.0%
CTCTTCCCACTCATTTAAAA+GGG - chr8_3:10283808-10283827 None:intergenic 35.0%
! GAATGATCTGCAGAGATTTT+TGG + chr8_3:10283830-10283849 Msa1275940:CDS 35.0%
TGAGCAATTACTGTCTAGAA+CGG + chr8_3:10283904-10283923 Msa1275940:intron 35.0%
AAGAATAGACAGTTGAGTCA+TGG - chr8_3:10284035-10284054 None:intergenic 35.0%
TCATCTATTCTCTCCTCTTT+AGG + chr8_3:10284054-10284073 Msa1275940:intron 35.0%
! GTTGCAGTTTTTACTTCACA+AGG + chr8_3:10284087-10284106 Msa1275940:CDS 35.0%
TTCATGCTACAAACCATTGT+GGG - chr8_3:10284408-10284427 None:intergenic 35.0%
TTTCATGCTACAAACCATTG+TGG - chr8_3:10284409-10284428 None:intergenic 35.0%
! CATGAAAGCTTTATAGCACT+AGG + chr8_3:10284422-10284441 Msa1275940:intron 35.0%
TTATAAGTGCATTCCTAGCA+GGG - chr8_3:10284527-10284546 None:intergenic 35.0%
TTTATAAGTGCATTCCTAGC+AGG - chr8_3:10284528-10284547 None:intergenic 35.0%
ATCAGGATATCACCAAAAGT+GGG - chr8_3:10284565-10284584 None:intergenic 35.0%
AATCAGGATATCACCAAAAG+TGG - chr8_3:10284566-10284585 None:intergenic 35.0%
! GATAGAAGAAGAGAGTACAA+AGG - chr8_3:10284647-10284666 None:intergenic 35.0%
AATTGATTGATCGGAAGTAG+TGG - chr8_3:10284669-10284688 None:intergenic 35.0%
! CCGATCAATCAATTTTCCAA+AGG + chr8_3:10284675-10284694 Msa1275940:CDS 35.0%
TTCATATGAATCTTGTAGCC+TGG + chr8_3:10284782-10284801 Msa1275940:intron 35.0%
TTTATTCAGACTTCCAGCTT+TGG + chr8_3:10284810-10284829 Msa1275940:CDS 35.0%
TTATTCAGACTTCCAGCTTT+GGG + chr8_3:10284811-10284830 Msa1275940:CDS 35.0%
!! CACTTGTATGATTTTGACCA+AGG - chr8_3:10284872-10284891 None:intergenic 35.0%
CATGCCTGAAAATTAATTCC+AGG + chr8_3:10284892-10284911 Msa1275940:CDS 35.0%
TTGGATAAACAACAACCGAA+AGG - chr8_3:10285210-10285229 None:intergenic 35.0%
TTCGACTGAACTGAAAGATT+TGG + chr8_3:10285336-10285355 Msa1275940:CDS 35.0%
TATAAAACTAAACCACAGGC+AGG - chr8_3:10285478-10285497 None:intergenic 35.0%
TCTCATGAGCATTTGAATCC+TGG - chr8_3:10283737-10283756 None:intergenic 40.0%
GATATGATCTGCTGTCTTAG+CGG - chr8_3:10283786-10283805 None:intergenic 40.0%
GCTCTTCCCACTCATTTAAA+AGG - chr8_3:10283809-10283828 None:intergenic 40.0%
TTAGCTAGAGGGATATCAGA+TGG - chr8_3:10283882-10283901 None:intergenic 40.0%
ATCTGATATCCCTCTAGCTA+AGG + chr8_3:10283881-10283900 Msa1275940:CDS 40.0%
AATTGCTCACCTTAGCTAGA+GGG - chr8_3:10283893-10283912 None:intergenic 40.0%
TAATTGCTCACCTTAGCTAG+AGG - chr8_3:10283894-10283913 None:intergenic 40.0%
!! TCTCCTCTTTAGGCTTTTTC+AGG + chr8_3:10284064-10284083 Msa1275940:intron 40.0%
!!! CTCCTCTTTAGGCTTTTTCA+GGG + chr8_3:10284065-10284084 Msa1275940:intron 40.0%
AACCCTGAAAAAGCCTAAAG+AGG - chr8_3:10284070-10284089 None:intergenic 40.0%
GATGTCATCATGGCAAAAGA+TGG + chr8_3:10284259-10284278 Msa1275940:CDS 40.0%
ATCATGGCAAAAGATGGAAC+TGG + chr8_3:10284265-10284284 Msa1275940:CDS 40.0%
TCATGGCAAAAGATGGAACT+GGG + chr8_3:10284266-10284285 Msa1275940:CDS 40.0%
AAAAGATGGAACTGGGTTCT+TGG + chr8_3:10284273-10284292 Msa1275940:CDS 40.0%
TTGTATTGTAGGACCCACAA+TGG + chr8_3:10284392-10284411 Msa1275940:intron 40.0%
TATAAGTGCATTCCTAGCAG+GGG - chr8_3:10284526-10284545 None:intergenic 40.0%
! CTAAAGGCTTTTCCCACTTT+TGG + chr8_3:10284550-10284569 Msa1275940:intron 40.0%
!! TCTTGCTTTTGTTGCAGTTG+TGG + chr8_3:10284618-10284637 Msa1275940:intron 40.0%
! AGATGAAGCATCAAATGAGC+AGG - chr8_3:10284722-10284741 None:intergenic 40.0%
ATATGAATCTTGTAGCCTGG+AGG + chr8_3:10284785-10284804 Msa1275940:intron 40.0%
AAGTCTGAATAAAGTCCTCC+AGG - chr8_3:10284803-10284822 None:intergenic 40.0%
TATTCAGACTTCCAGCTTTG+GGG + chr8_3:10284812-10284831 Msa1275940:CDS 40.0%
CAGCTTCTTTATGCTTTCCT+TGG + chr8_3:10284852-10284871 Msa1275940:CDS 40.0%
TTACCAACGTGAGTTCCTTT+CGG + chr8_3:10285192-10285211 Msa1275940:intron 40.0%
! ATTTGGTGAAACTATGTCGG+TGG + chr8_3:10285353-10285372 Msa1275940:CDS 40.0%
TTTGGTGAAACTATGTCGGT+GGG + chr8_3:10285354-10285373 Msa1275940:CDS 40.0%
GGATATCAGATGGAAGAGTC+AGG - chr8_3:10283872-10283891 None:intergenic 45.0%
ATCACCTCATCAAGCAACAC+GGG - chr8_3:10284299-10284318 None:intergenic 45.0%
CATCACCTCATCAAGCAACA+CGG - chr8_3:10284300-10284319 None:intergenic 45.0%
TTTCCTGAATTCCCCAAAGC+TGG - chr8_3:10284826-10284845 None:intergenic 45.0%
!! GCTTTGGGGAATTCAGGAAA+CGG + chr8_3:10284826-10284845 Msa1275940:CDS 45.0%
CGAAGCACATTGATGCTAGT+AGG + chr8_3:10285305-10285324 Msa1275940:CDS 45.0%
!! CGTGTTGCTTGATGAGGTGA+TGG + chr8_3:10284298-10284317 Msa1275940:CDS 50.0%
!! CTTCCAGCTTTGGGGAATTC+AGG + chr8_3:10284820-10284839 Msa1275940:CDS 50.0%
CAACCGAAAGGAACTCACGT+TGG - chr8_3:10285198-10285217 None:intergenic 50.0%
TGTGCTTCGATACACTGCTC+AGG - chr8_3:10285294-10285313 None:intergenic 50.0%
!! TTGGCCCGTGTTGCTTGATG+AGG + chr8_3:10284292-10284311 Msa1275940:CDS 55.0%
!! ATTCCTAGCAGGGGCATCAC+TGG - chr8_3:10284517-10284536 None:intergenic 55.0%
CTGGACACTGCAGCTGTTGT+CGG + chr8_3:10285118-10285137 Msa1275940:intron 55.0%
ACACTGCAGCTGTTGTCGGA+CGG + chr8_3:10285122-10285141 Msa1275940:intron 55.0%
GAAACTATGTCGGTGGGAGC+AGG + chr8_3:10285360-10285379 Msa1275940:CDS 55.0%
AGCATTACTCTGCCTGCCTG+TGG + chr8_3:10285463-10285482 Msa1275940:CDS 55.0%
ACGCCAGTGATGCCCCTGCT+AGG + chr8_3:10284511-10284530 Msa1275940:intron 65.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 10283702 10285519 10283702 ID=Msa1275940;Name=Msa1275940
chr8_3 mRNA 10283702 10285519 10283702 ID=Msa1275940-mRNA-1;Parent=Msa1275940;Name=Msa1275940-mRNA-1;_AED=0.10;_eAED=0.10;_QI=0|1|0.71|1|1|1|7|0|284
chr8_3 exon 10283702 10283902 10283702 ID=Msa1275940-mRNA-1:exon:4242;Parent=Msa1275940-mRNA-1
chr8_3 exon 10284076 10284151 10284076 ID=Msa1275940-mRNA-1:exon:4243;Parent=Msa1275940-mRNA-1
chr8_3 exon 10284234 10284346 10284234 ID=Msa1275940-mRNA-1:exon:4244;Parent=Msa1275940-mRNA-1
chr8_3 exon 10284635 10284696 10284635 ID=Msa1275940-mRNA-1:exon:4245;Parent=Msa1275940-mRNA-1
chr8_3 exon 10284800 10284913 10284800 ID=Msa1275940-mRNA-1:exon:4246;Parent=Msa1275940-mRNA-1
chr8_3 exon 10285131 10285199 10285131 ID=Msa1275940-mRNA-1:exon:4247;Parent=Msa1275940-mRNA-1
chr8_3 exon 10285300 10285519 10285300 ID=Msa1275940-mRNA-1:exon:4248;Parent=Msa1275940-mRNA-1
chr8_3 CDS 10283702 10283902 10283702 ID=Msa1275940-mRNA-1:cds;Parent=Msa1275940-mRNA-1
chr8_3 CDS 10284076 10284151 10284076 ID=Msa1275940-mRNA-1:cds;Parent=Msa1275940-mRNA-1
chr8_3 CDS 10284234 10284346 10284234 ID=Msa1275940-mRNA-1:cds;Parent=Msa1275940-mRNA-1
chr8_3 CDS 10284635 10284696 10284635 ID=Msa1275940-mRNA-1:cds;Parent=Msa1275940-mRNA-1
chr8_3 CDS 10284800 10284913 10284800 ID=Msa1275940-mRNA-1:cds;Parent=Msa1275940-mRNA-1
chr8_3 CDS 10285131 10285199 10285131 ID=Msa1275940-mRNA-1:cds;Parent=Msa1275940-mRNA-1
chr8_3 CDS 10285300 10285519 10285300 ID=Msa1275940-mRNA-1:cds;Parent=Msa1275940-mRNA-1
Gene Sequence

>Msa1275940

ATGACCTGTGTATCTTTTTGTTCTTTGTGGATCCAGGATTCAAATGCTCATGAGATTGAACAAATGCTGAAAGTACTTGCACCGCTAAGACAGCAGATCATATCCCTTTTAAATGAGTGGGAAGAGCAGAATGATCTGCAGAGATTTTTGGATGTCATTGACATGCTCCTGACTCTTCCATCTGATATCCCTCTAGCTAAGGCTTTTTCAGGGTTGCAGTTTTTACTTCACAAGGCTCAAGTTATGCAAGAAAATCATTCAAAGTTCACCTTCTCAAATCAGTTGAAATCTGTTTTTGATCTGATGTCATCATGGCAAAAGATGGAACTGGGTTCTTGGCCCGTGTTGCTTGATGAGGTGATGGATCAGTATGAGAACAATGCTAAAAAATTGTGGTTTCCTTTGTACTCTCTTCTTCTATCCACTACTTCCGATCAATCAATTTTCCAAAGCCTGGAGGACTTTATTCAGACTTCCAGCTTTGGGGAATTCAGGAAACGGCTTCAGCTTCTTTATGCTTTCCTTGGTCAAAATCATACAAGTGCATGCCTGAAAATTAATTCCAGCTGTTGTCGGACGGAGCAGTCAACATTCTTGTACAATATGTTTGGATTTTATGTGCAGTTCTTACCAACTGTATCGAAGCACATTGATGCTAGTAGGAAAGAAATTTCGACTGAACTGAAAGATTTGGTGAAACTATGTCGGTGGGAGCAGGATAAGAGTTATTCATCAATTGAAAATTTGAAAAAGAGTCGACAGAAGCTGAAAAAGCTTATAAAGAAGCATACTGTAAGTAGCATTACTCTGCCTGCCTGTGGTTTAGTTTTATATGTAAATATAATTGGCTATTGA

Protein sequence

>Msa1275940

MTCVSFCSLWIQDSNAHEIEQMLKVLAPLRQQIISLLNEWEEQNDLQRFLDVIDMLLTLPSDIPLAKAFSGLQFLLHKAQVMQENHSKFTFSNQLKSVFDLMSSWQKMELGSWPVLLDEVMDQYENNAKKLWFPLYSLLLSTTSDQSIFQSLEDFIQTSSFGEFRKRLQLLYAFLGQNHTSACLKINSSCCRTEQSTFLYNMFGFYVQFLPTVSKHIDASRKEISTELKDLVKLCRWEQDKSYSSIENLKKSRQKLKKLIKKHTVSSITLPACGLVLYVNIIGY*