AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24258


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24258.t1 MTR_1g022395 89.510 143 13 1 1 141 1 143 3.27e-91 261
MS.gene24258.t1 MTR_3g111970 62.238 143 45 5 1 140 1 137 2.78e-54 167
MS.gene24258.t1 MTR_3g111970 63.636 121 35 5 1 118 1 115 8.78e-45 142
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24258.t1 AT1G19530 41.860 129 56 3 1 128 1 111 2.92e-18 75.5
MS.gene24258.t1 AT1G19530 41.860 129 56 3 1 128 1 111 2.92e-18 75.5

Find 34 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGATGAAATTGATGCTTAT+TGG 0.156482 1.1:-1891441 MS.gene24258:CDS
AATCATATGGTACCTGATTT+AGG 0.175839 1.1:+1891619 None:intergenic
CTGAATAGTCTTTGACAAAT+TGG 0.206876 1.1:+1891375 None:intergenic
GAACGTACTTGACACAAATT+TGG 0.215908 1.1:-1890310 MS.gene24258:CDS
GTCAAGTACGTTCATATTAA+AGG 0.224800 1.1:+1890320 None:intergenic
CTGTTTCAGCCATACTTAAA+AGG 0.239435 1.1:-1891480 MS.gene24258:intron
CAATTTGTCAAAGACTATTC+AGG 0.285232 1.1:-1891374 MS.gene24258:intron
GCAGGTGGACTAAGAGTAAC+TGG 0.334701 1.1:-1890117 MS.gene24258:intron
TCAAGTACGTTCATATTAAA+GGG 0.359264 1.1:+1890321 None:intergenic
TCTTCAATTGATCCTAAATC+AGG 0.362673 1.1:-1891631 MS.gene24258:intron
TTGGATGCAGCTTCCATCAT+TGG 0.363993 1.1:+1890076 None:intergenic
ACAGTTTCACGTTGCCAGTT+TGG 0.389711 1.1:-1890041 MS.gene24258:CDS
GGGTTCTCTTATGGCAGGAT+GGG 0.445491 1.1:-1891659 MS.gene24258:CDS
TCTGAATGAGCCACCAATGA+TGG 0.467236 1.1:-1890089 MS.gene24258:CDS
CCATGCCCGTGGCCCACGTA+AGG 0.471373 1.1:-1890347 MS.gene24258:CDS
GGGTCCCTTACGTGGGCCAC+GGG 0.472849 1.1:+1890342 None:intergenic
GGGGTCCCTTACGTGGGCCA+CGG 0.474803 1.1:+1890341 None:intergenic
CCTTACGTGGGCCACGGGCA+TGG 0.492032 1.1:+1890347 None:intergenic
GGTTCTCTTATGGCAGGATG+GGG 0.492223 1.1:-1891658 MS.gene24258:CDS
CAATCACTAACTTCATCTAC+GGG 0.495529 1.1:+1890001 None:intergenic
GAAATCAAAGAAGAAGATAG+AGG 0.499005 1.1:-1891419 MS.gene24258:CDS
GATGCAGCTTCCATCATTGG+TGG 0.505474 1.1:+1890079 None:intergenic
TGGGTTCTCTTATGGCAGGA+TGG 0.507870 1.1:-1891660 MS.gene24258:CDS
ACAAATTGGAAATTGCTGTA+AGG 0.512610 1.1:+1891389 None:intergenic
TCAATCACTAACTTCATCTA+CGG 0.513170 1.1:+1890000 None:intergenic
AAACTGTGCTGCATACTTGT+TGG 0.515262 1.1:+1890057 None:intergenic
TATTAAAGGGGTCCCTTACG+TGG 0.530982 1.1:+1890334 None:intergenic
AAAATGGGTTCTCTTATGGC+AGG 0.548408 1.1:-1891664 MS.gene24258:CDS
CATGCCCGTGGCCCACGTAA+GGG 0.568293 1.1:-1890346 MS.gene24258:CDS
GAAGTCAATGACCATGCCCG+TGG 0.649977 1.1:-1890358 MS.gene24258:CDS
CAAGTACGTTCATATTAAAG+GGG 0.651488 1.1:+1890322 None:intergenic
ATTAAAGGGGTCCCTTACGT+GGG 0.678500 1.1:+1890335 None:intergenic
CAGGTGGACTAAGAGTAACT+GGG 0.688506 1.1:-1890116 MS.gene24258:CDS
AATCACTAACTTCATCTACG+GGG 0.796732 1.1:+1890002 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAAATAAAAACATTAAAAT+TGG + chr1.1:1891204-1891223 None:intergenic 10.0%
!!! TACAAAATCATATATATTTT+CGG + chr1.1:1891062-1891081 None:intergenic 10.0%
!!! TTATTTTTTTTGGAAAAATT+TGG + chr1.1:1890390-1890409 None:intergenic 10.0%
!! AATAAATAAAATACATACGA+AGG - chr1.1:1890405-1890424 MS.gene24258:intron 15.0%
!! TATAGTATTATATATAGTGT+TGG + chr1.1:1890749-1890768 None:intergenic 15.0%
!! TTTACACACAATATTAAAAT+TGG + chr1.1:1891173-1891192 None:intergenic 15.0%
!!! AAATACATCTTTAATTTCAT+TGG - chr1.1:1890563-1890582 MS.gene24258:intron 15.0%
!!! TTAATGTTTTTATTTCATGA+TGG - chr1.1:1891207-1891226 MS.gene24258:intron 15.0%
!! CATATGCATAATTCATATAT+AGG + chr1.1:1891499-1891518 None:intergenic 20.0%
!! CTAAACATTAATTTCAAACT+TGG + chr1.1:1891247-1891266 None:intergenic 20.0%
!! CTATATATGAATTATGCATA+TGG - chr1.1:1891497-1891516 MS.gene24258:intron 20.0%
!! TAATCATATTAGAACTTAGA+CGG - chr1.1:1890129-1890148 MS.gene24258:intron 20.0%
!!! AAGTATCGTTATTAATCATA+TGG + chr1.1:1890058-1890077 None:intergenic 20.0%
!!! CAAGTTTGAAATTAATGTTT+AGG - chr1.1:1891245-1891264 MS.gene24258:intron 20.0%
!!! CTACTATTTTCTTTTTCTTT+TGG + chr1.1:1890717-1890736 None:intergenic 20.0%
!!! TATTAATTTAATTTGAGTGC+AGG - chr1.1:1891526-1891545 MS.gene24258:intron 20.0%
! AAGATGAAATTGATGCTTAT+TGG - chr1.1:1890220-1890239 MS.gene24258:intron 25.0%
! AATGAAATGTTAGAGAAAGT+TGG - chr1.1:1890439-1890458 MS.gene24258:intron 25.0%
! ACACTTGAAAAAATCAACAA+GGG - chr1.1:1890685-1890704 MS.gene24258:intron 25.0%
! ACTATAATAATTGGAAGAGT+AGG + chr1.1:1891411-1891430 None:intergenic 25.0%
! GAACCCTAATAATTGTTAAT+TGG + chr1.1:1890479-1890498 None:intergenic 25.0%
! GCTCCAATTAACAATTATTA+GGG - chr1.1:1890473-1890492 MS.gene24258:intron 25.0%
! TACACTTGAAAAAATCAACA+AGG - chr1.1:1890684-1890703 MS.gene24258:intron 25.0%
! TCAAGTACGTTCATATTAAA+GGG + chr1.1:1891343-1891362 None:intergenic 25.0%
! TGCTCCAATTAACAATTATT+AGG - chr1.1:1890472-1890491 MS.gene24258:intron 25.0%
!! AGTATTATATATAGTGTTGG+TGG + chr1.1:1890746-1890765 None:intergenic 25.0%
!! TAGTTTTCTAATATGCAAGA+AGG + chr1.1:1891001-1891020 None:intergenic 25.0%
!! TATATTTTCGGATTTCACTT+AGG + chr1.1:1891050-1891069 None:intergenic 25.0%
!!! GTATTATATATAGTGTTGGT+GGG + chr1.1:1890745-1890764 None:intergenic 25.0%
!!! TATTATATATAGTGTTGGTG+GGG + chr1.1:1890744-1890763 None:intergenic 25.0%
!!! TTTTTTGGAAAAATTTGGTG+TGG + chr1.1:1890385-1890404 None:intergenic 25.0%
AACTTATCAACAAAAATGGC+TGG - chr1.1:1891377-1891396 MS.gene24258:CDS 30.0%
AATATGCAAGAAGGACTAAA+AGG + chr1.1:1890992-1891011 None:intergenic 30.0%
AATCATATGGTACCTGATTT+AGG + chr1.1:1890045-1890064 None:intergenic 30.0%
ACAAATTGGAAATTGCTGTA+AGG + chr1.1:1890275-1890294 None:intergenic 30.0%
ACGCGACAAACATTAATTAT+TGG - chr1.1:1890902-1890921 MS.gene24258:intron 30.0%
ACTCAAACACACAAGAAAAA+TGG + chr1.1:1890622-1890641 None:intergenic 30.0%
AGACGGTACTTATATTTATG+AGG - chr1.1:1890146-1890165 MS.gene24258:intron 30.0%
CAAGTACGTTCATATTAAAG+GGG + chr1.1:1891342-1891361 None:intergenic 30.0%
CAATTTGTCAAAGACTATTC+AGG - chr1.1:1890287-1890306 MS.gene24258:CDS 30.0%
CTGAATAGTCTTTGACAAAT+TGG + chr1.1:1890289-1890308 None:intergenic 30.0%
GAAATCAAAGAAGAAGATAG+AGG - chr1.1:1890242-1890261 MS.gene24258:intron 30.0%
GACGGTACTTATATTTATGA+GGG - chr1.1:1890147-1890166 MS.gene24258:intron 30.0%
GAGCAACTTATCAACAAAAA+TGG - chr1.1:1891373-1891392 MS.gene24258:intron 30.0%
GTCAAGTACGTTCATATTAA+AGG + chr1.1:1891344-1891363 None:intergenic 30.0%
TCAATCACTAACTTCATCTA+CGG + chr1.1:1891664-1891683 None:intergenic 30.0%
TCTTCAATTGATCCTAAATC+AGG - chr1.1:1890030-1890049 MS.gene24258:CDS 30.0%
TTACTCTAGTAGAAGAATAC+TGG + chr1.1:1890871-1890890 None:intergenic 30.0%
TTTCTTGTGTGTTTGAGTAA+TGG - chr1.1:1890624-1890643 MS.gene24258:intron 30.0%
! GTGCTTAGTATTTTATGTTG+CGG - chr1.1:1890100-1890119 MS.gene24258:CDS 30.0%
! TTTCATCTTTTGTAAGTGAC+TGG + chr1.1:1890209-1890228 None:intergenic 30.0%
!! TAATTTAATTTGAGTGCAGG+TGG - chr1.1:1891529-1891548 MS.gene24258:intron 30.0%
AATCACTAACTTCATCTACG+GGG + chr1.1:1891662-1891681 None:intergenic 35.0%
CAATCACTAACTTCATCTAC+GGG + chr1.1:1891663-1891682 None:intergenic 35.0%
CTGTTTCAGCCATACTTAAA+AGG - chr1.1:1890181-1890200 MS.gene24258:intron 35.0%
GAACGTACTTGACACAAATT+TGG - chr1.1:1891351-1891370 MS.gene24258:intron 35.0%
! ATTTTCGGATTTCACTTAGG+TGG + chr1.1:1891047-1891066 None:intergenic 35.0%
!! TGAAACTTCTTTTCAGGATC+AGG + chr1.1:1891283-1891302 None:intergenic 35.0%
!! TGACTAAGAGCACTACAATT+TGG - chr1.1:1890772-1890791 MS.gene24258:intron 35.0%
!! TGACTGGTTCCTTTTAAGTA+TGG + chr1.1:1890193-1890212 None:intergenic 35.0%
!! TTTGGAAAAATTTGGTGTGG+CGG + chr1.1:1890382-1890401 None:intergenic 35.0%
!!! CAATTTTGTCGATTCCAAAC+TGG + chr1.1:1891637-1891656 None:intergenic 35.0%
!!! GACTTCTGAAACTTCTTTTC+AGG + chr1.1:1891289-1891308 None:intergenic 35.0%
AAACTGTGCTGCATACTTGT+TGG + chr1.1:1891607-1891626 None:intergenic 40.0%
AAAGAAGAAGCAGACAGAGT+TGG + chr1.1:1890597-1890616 None:intergenic 40.0%
ATGTTTGTCGCGTCTCAAAT+AGG + chr1.1:1890895-1890914 None:intergenic 40.0%
!! ATCCAACTTATGGTTTGGTG+CGG - chr1.1:1890353-1890372 MS.gene24258:CDS 40.0%
ACAGTTTCACGTTGCCAGTT+TGG - chr1.1:1891620-1891639 MS.gene24258:intron 45.0%
ATTAAAGGGGTCCCTTACGT+GGG + chr1.1:1891329-1891348 None:intergenic 45.0%
TATTAAAGGGGTCCCTTACG+TGG + chr1.1:1891330-1891349 None:intergenic 45.0%
TCTGAATGAGCCACCAATGA+TGG - chr1.1:1891572-1891591 MS.gene24258:intron 45.0%
TTGGATGCAGCTTCCATCAT+TGG + chr1.1:1891588-1891607 None:intergenic 45.0%
! AAGAAGCAGACAGAGTTGGT+GGG + chr1.1:1890593-1890612 None:intergenic 45.0%
!! CAGGTGGACTAAGAGTAACT+GGG - chr1.1:1891545-1891564 MS.gene24258:intron 45.0%
!! TACTTGCCACTTTCCAGCAT+GGG - chr1.1:1890327-1890346 MS.gene24258:CDS 45.0%
!! TATTATAGTTATATAATAAT+TGG - chr1.1:1891422-1891441 MS.gene24258:CDS 5.0%
!! TATTATATAACTATAATAAT+TGG + chr1.1:1891420-1891439 None:intergenic 5.0%
!!! TGTATTTTATTTATTTTTTT+TGG + chr1.1:1890400-1890419 None:intergenic 5.0%
AGCCGCACCAAACCATAAGT+TGG + chr1.1:1890358-1890377 None:intergenic 50.0%
GAAGAAGCAGACAGAGTTGG+TGG + chr1.1:1890594-1890613 None:intergenic 50.0%
GATGCAGCTTCCATCATTGG+TGG + chr1.1:1891585-1891604 None:intergenic 50.0%
GGCGGATCCAACTTATGGTT+TGG - chr1.1:1890348-1890367 MS.gene24258:CDS 50.0%
GGGTTCTCTTATGGCAGGAT+GGG - chr1.1:1890002-1890021 MS.gene24258:CDS 50.0%
GGTTCTCTTATGGCAGGATG+GGG - chr1.1:1890003-1890022 MS.gene24258:CDS 50.0%
TGCTGGAAAGTGGCAAGTAG+AGG + chr1.1:1890326-1890345 None:intergenic 50.0%
TGGGTTCTCTTATGGCAGGA+TGG - chr1.1:1890001-1890020 MS.gene24258:CDS 50.0%
!! AGAAGCAGACAGAGTTGGTG+GGG + chr1.1:1890592-1890611 None:intergenic 50.0%
!! CTACTTGCCACTTTCCAGCA+TGG - chr1.1:1890326-1890345 MS.gene24258:CDS 50.0%
!! GCAGGTGGACTAAGAGTAAC+TGG - chr1.1:1891544-1891563 MS.gene24258:intron 50.0%
GAAGTCAATGACCATGCCCG+TGG - chr1.1:1891303-1891322 MS.gene24258:intron 55.0%
GCATGGGCGGATCCAACTTA+TGG - chr1.1:1890343-1890362 MS.gene24258:CDS 55.0%
! TAAGTTGGATCCGCCCATGC+TGG + chr1.1:1890343-1890362 None:intergenic 55.0%
!! TTGCCACTTTCCAGCATGGG+CGG - chr1.1:1890330-1890349 MS.gene24258:CDS 55.0%
GATCCGCCCATGCTGGAAAG+TGG + chr1.1:1890336-1890355 None:intergenic 60.0%
CATGCCCGTGGCCCACGTAA+GGG - chr1.1:1891315-1891334 MS.gene24258:intron 65.0%
CCATGCCCGTGGCCCACGTA+AGG - chr1.1:1891314-1891333 MS.gene24258:intron 70.0%
CCTTACGTGGGCCACGGGCA+TGG + chr1.1:1891317-1891336 None:intergenic 70.0%
GGGGTCCCTTACGTGGGCCA+CGG + chr1.1:1891323-1891342 None:intergenic 70.0%
GGGTCCCTTACGTGGGCCAC+GGG + chr1.1:1891322-1891341 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 1890000 1891683 1890000 ID=MS.gene24258
chr1.1 mRNA 1890000 1891683 1890000 ID=MS.gene24258.t1;Parent=MS.gene24258
chr1.1 exon 1891632 1891683 1891632 ID=MS.gene24258.t1.exon1;Parent=MS.gene24258.t1
chr1.1 CDS 1891632 1891683 1891632 ID=cds.MS.gene24258.t1;Parent=MS.gene24258.t1
chr1.1 exon 1891375 1891493 1891375 ID=MS.gene24258.t1.exon2;Parent=MS.gene24258.t1
chr1.1 CDS 1891375 1891493 1891375 ID=cds.MS.gene24258.t1;Parent=MS.gene24258.t1
chr1.1 exon 1890285 1890403 1890285 ID=MS.gene24258.t1.exon3;Parent=MS.gene24258.t1
chr1.1 CDS 1890285 1890403 1890285 ID=cds.MS.gene24258.t1;Parent=MS.gene24258.t1
chr1.1 exon 1890000 1890135 1890000 ID=MS.gene24258.t1.exon4;Parent=MS.gene24258.t1
chr1.1 CDS 1890000 1890135 1890000 ID=cds.MS.gene24258.t1;Parent=MS.gene24258.t1
Gene Sequence

>MS.gene24258

ATGGGTTCTCTTATGGCAGGATGGGGCTCTTCTTCAATTGATCCTAAATCAGGTACCATATGATTAATAACGATACTTATATTATACACATATATGCTTTGTGCTTAGTATTTTATGTTGCGGAGCAATTAATCATATTAGAACTTAGACGGTACTTATATTTATGAGGGAACTTTTTTCACTGTTTCAGCCATACTTAAAAGGAACCAGTCACTTACAAAAGATGAAATTGATGCTTATTGGAAATCAAAGAAGAAGATAGAGGAAGAACACCTTACAGCAATTTCCAATTTGTCAAAGACTATTCAGGTTTGATATTCAAACCTCTACTTGCCACTTTCCAGCATGGGCGGATCCAACTTATGGTTTGGTGCGGCTACCGCCACACCAAATTTTTCCAAAAAAAATAAATAAAATACATACGAAGGATTTCTATAAAAATGAAATGTTAGAGAAAGTTGGCAAATCATTTTGCTCCAATTAACAATTATTAGGGTTCAAATGCATTTGAGCTAATAAAACTAAAAAAAAAAAACTATAAAAATTGTTATTTTAAGTGAAATAAATACATCTTTAATTTCATTGGACACCCCACCAACTCTGTCTGCTTCTTCTTTTACCATTTTTCTTGTGTGTTTGAGTAATGGTCACTACTAAATTATTGAAATGAATTAAAGATTTTTTTACACTTGAAAAAATCAACAAGGGATAAGACCAAAAGAAAAAGAAAATAGTAGCACACCCCACCAACACTATATATAATACTATAATATGACTAAGAGCACTACAATTTGGATCGTGATTGTGAATTTTTAATCTCTATTTTTTTTTATTATAAGTCTTTGTATCAATTTTTTTCTTCATTTTTCCAGTATTCTTCTACTAGAGTAATCCTATTTGAGACGCGACAAACATTAATTATTGGTTTGATTGATTGTGAAATTACAACTTCTTTTACTAGATTCAATCTCTATTAATTTCTATATCAACCTTTTAGTCCTTCTTGCATATTAGAAAACTAAGTGACTATAAAATATAGTTATGCCACCTAAGTGAAATCCGAAAATATATATGATTTTGTAATTTCTAGTAATTAAAAGATGAATACAAGACTAAAAAACAAATTCAATATATCTATAAAGATAAAAAATATATTTAACTCATTAATTTCCAATTTTAATATTGTGTGTAAAAAAAAAAACCAATTTTAATGTTTTTATTTCATGATGGAGTAACAGACAATTCCAAGTTTGAAATTAATGTTTAGGATGATGATGCAGCCTGATCCTGAAAAGAAGTTTCAGAAGTCAATGACCATGCCCGTGGCCCACGTAAGGGACCCCTTTAATATGAACGTACTTGACACAAATTTGGAGCAACTTATCAACAAAAATGGCTGGTAAATTAACCTACTCTTCCAATTATTATAGTTATATAATAATTGGTTAGTTTAATATTTTTATACTTTTATTGCTATTTTTGCTAGAGAAAGTACTCCTATATATGAATTATGCATATGGATCATATATTAATTTAATTTGAGTGCAGGTGGACTAAGAGTAACTGGGCATTTCTGAATGAGCCACCAATGATGGAAGCTGCATCCAACAAGTATGCAGCACAGTTTCACGTTGCCAGTTTGGAATCGACAAAATTGAACCCCGTAGATGAAGTTAGTGATTGA

Protein sequence

>MS.gene24258.t1

MGSLMAGWGSSSIDPKSAILKRNQSLTKDEIDAYWKSKKKIEEEHLTAISNLSKTIQPDPEKKFQKSMTMPVAHVRDPFNMNVLDTNLEQLINKNGWWTKSNWAFLNEPPMMEAASNKYAAQFHVASLESTKLNPVDEVSD