AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene37633


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene37633.t1 MTR_5g087960 94.545 165 8 1 1 165 1 164 1.06e-112 317
MS.gene37633.t1 MTR_5g087980 49.383 81 36 2 34 109 18 98 7.88e-15 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene37633.t1 AT5G60335 61.806 144 52 2 19 159 15 158 9.75e-60 183
MS.gene37633.t1 AT5G60335 61.806 144 52 2 19 159 15 158 9.75e-60 183
MS.gene37633.t1 AT5G60335 61.806 144 52 2 19 159 15 158 9.75e-60 183

Find 28 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATTGCAAGAATGCTCTTC+AGG 0.355119 5.3:+70748902 None:intergenic
GACTGGTAACTTAAAATTCA+AGG 0.371883 5.3:-70750928 None:intergenic
TATAGAGCTGTGGAAGTATA+AGG 0.373462 5.3:+70751189 MS.gene37633:CDS
TTTAAGTTACCAGTCTATAT+CGG 0.383846 5.3:+70750936 MS.gene37633:CDS
TAATCCTTTGCATACCGATT+CGG 0.416395 5.3:+70749077 MS.gene37633:CDS
TCGGCTGCTGCTCGAAGTGT+TGG 0.445083 5.3:+70749096 MS.gene37633:CDS
AAGACAAAGTGCTTCAAGAA+TGG 0.452510 5.3:+70751114 MS.gene37633:CDS
GGAGACATTCTTGTCATTGA+AGG 0.464999 5.3:+70751135 MS.gene37633:CDS
ATTAGAATCATGGCTCACTT+TGG 0.488635 5.3:-70749058 None:intergenic
ACTTCGAGCAGCAGCCGAAT+CGG 0.492615 5.3:-70749091 None:intergenic
GCTCGAAGTGTTGGATTTGA+CGG 0.493664 5.3:+70749105 MS.gene37633:CDS
TGTCATTGAAGGTGAAGCAT+TGG 0.511579 5.3:+70751146 MS.gene37633:CDS
TGTTGGATTTGACGGTCCAT+TGG 0.517875 5.3:+70749113 MS.gene37633:CDS
TATGCAAAGGATTAGAATCA+TGG 0.523318 5.3:-70749068 None:intergenic
TATATCGGAGATCTGATTGT+TGG 0.535277 5.3:+70750951 MS.gene37633:CDS
ATCAGATCTCCGATATAGAC+TGG 0.547920 5.3:-70750945 None:intergenic
CTTCCACAGCTCTATAGTCA+AGG 0.549215 5.3:-70751182 None:intergenic
TGAGATACATACACAGCTGC+AGG 0.568759 5.3:-70750903 None:intergenic
ACAAGCATTCCGTGTACCAA+TGG 0.578578 5.3:-70749129 None:intergenic
ACAACTCATGTGCTTAAACC+TGG 0.583457 5.3:+70748982 MS.gene37633:CDS
TTCCACAGCTCTATAGTCAA+GGG 0.621924 5.3:-70751181 None:intergenic
AACTTCAGTATCTGAGTCCG+AGG 0.623783 5.3:+70748947 MS.gene37633:CDS
TTTGACGGTCCATTGGTACA+CGG 0.626095 5.3:+70749120 MS.gene37633:CDS
GTACTGAAGAACATCTTCCT+CGG 0.633973 5.3:-70749034 None:intergenic
AACCCTTGACTATAGAGCTG+TGG 0.641884 5.3:+70751179 MS.gene37633:CDS
ACAGCTCTATAGTCAAGGGT+TGG 0.646507 5.3:-70751177 None:intergenic
GCAGCCGAATCGGTATGCAA+AGG 0.665902 5.3:-70749081 None:intergenic
AAATGTGATGAGATGATATG+CGG 0.720781 5.3:-70749165 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGATCAAATATAATATAT+AGG + chr5.3:70749516-70749535 MS.gene37633:intron 10.0%
!! AAGATCAAATATAATATATA+GGG + chr5.3:70749517-70749536 MS.gene37633:intron 10.0%
!! ATATAATAGATATGATATTA+TGG + chr5.3:70750530-70750549 MS.gene37633:intron 10.0%
!! ATTTAATACATGTAAATAAT+TGG + chr5.3:70750748-70750767 MS.gene37633:intron 10.0%
!! TTTAATACATGTAAATAATT+GGG + chr5.3:70750749-70750768 MS.gene37633:intron 10.0%
!! TACATGTATTAAATAGAATA+AGG - chr5.3:70750742-70750761 None:intergenic 15.0%
!!! AAGATGTTATAGAAATTTTA+AGG + chr5.3:70749974-70749993 MS.gene37633:intron 15.0%
!!! AATAAAGATTTTAGAAGAAT+GGG + chr5.3:70749336-70749355 MS.gene37633:intron 15.0%
!!! ATTCGTTTTTTTTTTTATGT+TGG - chr5.3:70750703-70750722 None:intergenic 15.0%
!!! GTTTATTAGATATACATTTT+TGG + chr5.3:70750015-70750034 MS.gene37633:intron 15.0%
!!! TTTTTTTTTTTATGTTGGTT+TGG - chr5.3:70750698-70750717 None:intergenic 15.0%
!! AGAATTTATGAAAATAGCTT+AGG + chr5.3:70749602-70749621 MS.gene37633:intron 20.0%
!! ATAATTCACAATGAGAAAAT+TGG - chr5.3:70750196-70750215 None:intergenic 20.0%
!! ATCTTAATCTTTCTAATAAG+AGG - chr5.3:70749959-70749978 None:intergenic 20.0%
!! TAATTCACAATGAGAAAATT+GGG - chr5.3:70750195-70750214 None:intergenic 20.0%
!! TATAATTAACTGACAAGTAT+AGG + chr5.3:70749468-70749487 MS.gene37633:intron 20.0%
!! TGAAAATAACCACAAAATAT+TGG + chr5.3:70750113-70750132 MS.gene37633:intron 20.0%
!! TTGAATAATAATGTGAATTG+AGG + chr5.3:70750477-70750496 MS.gene37633:intron 20.0%
!! TTGTCAGTTAATTATATTAG+AGG - chr5.3:70749464-70749483 None:intergenic 20.0%
!!! AGAACAAATTGATTCTTTTT+TGG + chr5.3:70749281-70749300 MS.gene37633:intron 20.0%
!!! GAATAAAGATTTTAGAAGAA+TGG + chr5.3:70749335-70749354 MS.gene37633:intron 20.0%
!!! TTTTCAGTGTTATTAAATAG+CGG + chr5.3:70750231-70750250 MS.gene37633:intron 20.0%
! AATGAAACAAATCCATTTCA+GGG + chr5.3:70749364-70749383 MS.gene37633:intron 25.0%
! ACAAAATATTGGATTCTCAT+TGG + chr5.3:70750124-70750143 MS.gene37633:intron 25.0%
! ACAAGTATAGGAAAGAAATT+TGG + chr5.3:70749480-70749499 MS.gene37633:intron 25.0%
! ATTATATCCAACAATACCAT+GGG + chr5.3:70750571-70750590 MS.gene37633:intron 25.0%
! TATAATATATAGGGTCTGTT+TGG + chr5.3:70749526-70749545 MS.gene37633:intron 25.0%
! TATTATATCCAACAATACCA+TGG + chr5.3:70750570-70750589 MS.gene37633:intron 25.0%
! TTGTAAAACAGTTAGGAAAA+TGG + chr5.3:70749693-70749712 MS.gene37633:intron 25.0%
!! AATGAGAATCCAATATTTTG+TGG - chr5.3:70750125-70750144 None:intergenic 25.0%
!! ATTAAGTTGTTTATCCAAAC+AGG + chr5.3:70749664-70749683 MS.gene37633:intron 25.0%
!! CAGTAACTATTTTCATAATG+CGG + chr5.3:70750389-70750408 MS.gene37633:intron 25.0%
!! TTAAGTTGTTTATCCAAACA+GGG + chr5.3:70749665-70749684 MS.gene37633:intron 25.0%
!! TTCCTAACTGTTTTACAATA+TGG - chr5.3:70749691-70749710 None:intergenic 25.0%
!! TTTAAGTTACCAGTCTATAT+CGG + chr5.3:70750936-70750955 MS.gene37633:CDS 25.0%
!!! AATTTCTAGTAGAGATATCA+AGG - chr5.3:70749228-70749247 None:intergenic 25.0%
!!! CTTCACTTTTCTAATGTTAT+GGG + chr5.3:70750869-70750888 MS.gene37633:intron 25.0%
!!! GTGATGTTTTGAAAAAAACA+CGG + chr5.3:70749004-70749023 MS.gene37633:CDS 25.0%
!!! TCTTCACTTTTCTAATGTTA+TGG + chr5.3:70750868-70750887 MS.gene37633:intron 25.0%
!!! TCTTGTGCATTTTTTTGAAT+TGG + chr5.3:70751038-70751057 MS.gene37633:intron 25.0%
!!! TGACTGAAAGAAGTTTTAAA+GGG - chr5.3:70749811-70749830 None:intergenic 25.0%
!!! TGATGTTTTGAAAAAAACAC+GGG + chr5.3:70749005-70749024 MS.gene37633:CDS 25.0%
!!! TTGACTGAAAGAAGTTTTAA+AGG - chr5.3:70749812-70749831 None:intergenic 25.0%
!!! TTTTTTATGTTGGTTTGGTT+GGG - chr5.3:70750693-70750712 None:intergenic 25.0%
!!! TTTTTTTATGTTGGTTTGGT+TGG - chr5.3:70750694-70750713 None:intergenic 25.0%
AAATGTGATGAGATGATATG+CGG - chr5.3:70749168-70749187 None:intergenic 30.0%
CAATGAAACAAATCCATTTC+AGG + chr5.3:70749363-70749382 MS.gene37633:intron 30.0%
GACTGGTAACTTAAAATTCA+AGG - chr5.3:70750931-70750950 None:intergenic 30.0%
TAGCATAAACACTTACCATA+TGG - chr5.3:70749634-70749653 None:intergenic 30.0%
TATGCAAAGGATTAGAATCA+TGG - chr5.3:70749071-70749090 None:intergenic 30.0%
TATTGAAGGATGAAGTGAAA+AGG + chr5.3:70749873-70749892 MS.gene37633:intron 30.0%
TGAATCTCAGAATCAAATCT+AGG - chr5.3:70749778-70749797 None:intergenic 30.0%
TTATTAAATAGCGGCTATAG+TGG + chr5.3:70750240-70750259 MS.gene37633:intron 30.0%
TTCAAAAAAATGCACAAGAC+AGG - chr5.3:70751037-70751056 None:intergenic 30.0%
! AATTAGAAAGTACACTTACG+TGG - chr5.3:70750087-70750106 None:intergenic 30.0%
! ACTGTATTTTCTCTCTGTTT+TGG - chr5.3:70750621-70750640 None:intergenic 30.0%
! GTAATATCACGAGTTTTCAT+GGG - chr5.3:70750065-70750084 None:intergenic 30.0%
!! AAACTGACGAAAAGTATTGA+AGG + chr5.3:70749859-70749878 MS.gene37633:intron 30.0%
!! TCATAACAGATGTTAGCTTT+AGG + chr5.3:70749749-70749768 MS.gene37633:intron 30.0%
!! TTGTACTAATCAGAGTATTG+CGG - chr5.3:70750284-70750303 None:intergenic 30.0%
!! TTTAAAGAGAGCATTAGCAT+GGG - chr5.3:70749198-70749217 None:intergenic 30.0%
!!! GTTTTTTTCAAAACATCACC+AGG - chr5.3:70749003-70749022 None:intergenic 30.0%
!!! TTTTAAAGAGAGCATTAGCA+TGG - chr5.3:70749199-70749218 None:intergenic 30.0%
AGACTAATAGACATTTGCTC+AGG - chr5.3:70749390-70749409 None:intergenic 35.0%
AGTTATTCCCATGGTATTGT+TGG - chr5.3:70750581-70750600 None:intergenic 35.0%
ATTAGAAAAGTGAAGAAGCC+AGG - chr5.3:70750864-70750883 None:intergenic 35.0%
ATTAGAATCATGGCTCACTT+TGG - chr5.3:70749061-70749080 None:intergenic 35.0%
GGCCATATTGTAAAACAGTT+AGG + chr5.3:70749686-70749705 MS.gene37633:intron 35.0%
TAGTGACTTATGCAACTTAG+AGG + chr5.3:70750647-70750666 MS.gene37633:intron 35.0%
TATATCGGAGATCTGATTGT+TGG + chr5.3:70750951-70750970 MS.gene37633:CDS 35.0%
! AAGACAAAGTGCTTCAAGAA+TGG + chr5.3:70751114-70751133 MS.gene37633:CDS 35.0%
! AATAATTGGGCCTTGTCTAT+TGG + chr5.3:70750762-70750781 MS.gene37633:intron 35.0%
! AGTTTCTTCGTTTTCATTCC+TGG + chr5.3:70750843-70750862 MS.gene37633:intron 35.0%
! GGTAATATCACGAGTTTTCA+TGG - chr5.3:70750066-70750085 None:intergenic 35.0%
! TAATCCTTTGCATACCGATT+CGG + chr5.3:70749077-70749096 MS.gene37633:CDS 35.0%
! TTTTACAATATGGCCCTGTT+TGG - chr5.3:70749681-70749700 None:intergenic 35.0%
!! ATAGAGGTTTGTTCTAGTTC+TGG - chr5.3:70750349-70750368 None:intergenic 35.0%
!!! AAAGAAGTTTTAAAGGGCAG+CGG - chr5.3:70749805-70749824 None:intergenic 35.0%
AAGCACTTGAGTAGAAGTCT+TGG - chr5.3:70750459-70750478 None:intergenic 40.0%
ACAACTCATGTGCTTAAACC+TGG + chr5.3:70748982-70749001 MS.gene37633:CDS 40.0%
ACCTTCGTGTTATGTTAGCA+GGG - chr5.3:70750788-70750807 None:intergenic 40.0%
ATCAGATCTCCGATATAGAC+TGG - chr5.3:70750948-70750967 None:intergenic 40.0%
GCGGTGAAATTATACATGCA+TGG + chr5.3:70750408-70750427 MS.gene37633:intron 40.0%
GGAGACATTCTTGTCATTGA+AGG + chr5.3:70751135-70751154 MS.gene37633:CDS 40.0%
GTACTGAAGAACATCTTCCT+CGG - chr5.3:70749037-70749056 None:intergenic 40.0%
GTTGTCGATGAAAAACACCT+CGG - chr5.3:70748967-70748986 None:intergenic 40.0%
TAATAGCAGCCATAGTACTG+TGG + chr5.3:70750313-70750332 MS.gene37633:intron 40.0%
TAGCTTAGGACATGTCCATA+TGG + chr5.3:70749616-70749635 MS.gene37633:intron 40.0%
TCATGAAAGAACTAGAGCGA+AGG - chr5.3:70750811-70750830 None:intergenic 40.0%
TGTCATTGAAGGTGAAGCAT+TGG + chr5.3:70751146-70751165 MS.gene37633:CDS 40.0%
TTCCACAGCTCTATAGTCAA+GGG - chr5.3:70751184-70751203 None:intergenic 40.0%
! AAAAACACGGGTTTTTACCG+AGG + chr5.3:70749017-70749036 MS.gene37633:CDS 40.0%
!!! AAGAAGTTTTAAAGGGCAGC+GGG - chr5.3:70749804-70749823 None:intergenic 40.0%
AACCCTTGACTATAGAGCTG+TGG + chr5.3:70751179-70751198 MS.gene37633:CDS 45.0%
AACTTCAGTATCTGAGTCCG+AGG + chr5.3:70748947-70748966 MS.gene37633:CDS 45.0%
ACAAGCATTCCGTGTACCAA+TGG - chr5.3:70749132-70749151 None:intergenic 45.0%
ACAGCTCTATAGTCAAGGGT+TGG - chr5.3:70751180-70751199 None:intergenic 45.0%
CTTCCACAGCTCTATAGTCA+AGG - chr5.3:70751185-70751204 None:intergenic 45.0%
GACCTTCGTGTTATGTTAGC+AGG - chr5.3:70750789-70750808 None:intergenic 45.0%
GGAATAACTCTCTGCAGAGT+TGG + chr5.3:70750592-70750611 MS.gene37633:intron 45.0%
TCTGCAGAGAGTTATTCCCA+TGG - chr5.3:70750590-70750609 None:intergenic 45.0%
TCTGCTATGCCACAGTACTA+TGG - chr5.3:70750325-70750344 None:intergenic 45.0%
TGAGATACATACACAGCTGC+AGG - chr5.3:70750906-70750925 None:intergenic 45.0%
TGTTGGATTTGACGGTCCAT+TGG + chr5.3:70749113-70749132 MS.gene37633:CDS 45.0%
TTTGACGGTCCATTGGTACA+CGG + chr5.3:70749120-70749139 MS.gene37633:CDS 45.0%
! CACGAGTTTTCATGGGATGT+TGG - chr5.3:70750058-70750077 None:intergenic 45.0%
!! GCTCGAAGTGTTGGATTTGA+CGG + chr5.3:70749105-70749124 MS.gene37633:CDS 45.0%
CATTTGCTCAGGCCCTGAAA+TGG - chr5.3:70749379-70749398 None:intergenic 50.0%
GCCCTGCTAACATAACACGA+AGG + chr5.3:70750784-70750803 MS.gene37633:intron 50.0%
GTTAGCAGGGCCAATAGACA+AGG - chr5.3:70750775-70750794 None:intergenic 50.0%
TCGCAGATCGCAGCAAATAG+AGG - chr5.3:70750365-70750384 None:intergenic 50.0%
ACTTCGAGCAGCAGCCGAAT+CGG - chr5.3:70749094-70749113 None:intergenic 55.0%
GCAGCCGAATCGGTATGCAA+AGG - chr5.3:70749084-70749103 None:intergenic 55.0%
TCGGCTGCTGCTCGAAGTGT+TGG + chr5.3:70749096-70749115 MS.gene37633:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 70748913 70751209 70748913 ID=MS.gene37633
chr5.3 mRNA 70748913 70751209 70748913 ID=MS.gene37633.t1;Parent=MS.gene37633
chr5.3 exon 70748913 70749188 70748913 ID=MS.gene37633.t1.exon1;Parent=MS.gene37633.t1
chr5.3 CDS 70748913 70749188 70748913 ID=cds.MS.gene37633.t1;Parent=MS.gene37633.t1
chr5.3 exon 70750903 70751018 70750903 ID=MS.gene37633.t1.exon2;Parent=MS.gene37633.t1
chr5.3 CDS 70750903 70751018 70750903 ID=cds.MS.gene37633.t1;Parent=MS.gene37633.t1
chr5.3 exon 70751104 70751209 70751104 ID=MS.gene37633.t1.exon3;Parent=MS.gene37633.t1
chr5.3 CDS 70751104 70751209 70751104 ID=cds.MS.gene37633.t1;Parent=MS.gene37633.t1
Gene Sequence

>MS.gene37633

ATGCTCTTCAGGTGTTTATTATATTCTAGTAGCAAACTTCAGTATCTGAGTCCGAGGTGTTTTTCATCGACAACTCATGTGCTTAAACCTGGTGATGTTTTGAAAAAAACACGGGTTTTTACCGAGGAAGATGTTCTTCAGTACTCCAAAGTGAGCCATGATTCTAATCCTTTGCATACCGATTCGGCTGCTGCTCGAAGTGTTGGATTTGACGGTCCATTGGTACACGGAATGCTTGTTGCTTCGCTTTTTCCGCATATCATCTCATCACATTTTGTAAGTCCCATGCTAATGCTCTCTTTAAAATTTAAACCTTGATATCTCTACTAGAAATTATATGATCAACAATTCAACAAACTCATTTAGAAAGAACAAATTGATTCTTTTTTGGTAAGCACTAAACGAATAGATTATTCATGATAGAATAAAGATTTTAGAAGAATGGGATGTCAATGAAACAAATCCATTTCAGGGCCTGAGCAAATGTCTATTAGTCTCATACTTAAAGAGTTTGAGCTATATGATACACTATTTTTTGAAAGAATCATCCTCTAATATAATTAACTGACAAGTATAGGAAAGAAATTTGGAAACTTTTTACTGAAAGATCAAATATAATATATAGGGTCTGTTTGGATTGACTTATTTGAAATTATATATTCGCATAAGCACTTGTGATACTCTTTAAGAGAATTTATGAAAATAGCTTAGGACATGTCCATATGGTAAGTGTTTATGCTATAACTATTTAATTAAGTTGTTTATCCAAACAGGGCCATATTGTAAAACAGTTAGGAAAATGGTCACTTTTTTGTGCTTTATGCAAGTGAAATTTCTCATAACAGATGTTAGCTTTAGGAAACCTAGATTTGATTCTGAGATTCAAAACCCGCTGCCCTTTAAAACTTCTTTCAGTCAACTAGAGAATTAGACGCATGTTTGTAGAAAACTGACGAAAAGTATTGAAGGATGAAGTGAAAAGGATAAAATGTGAAATAGTAATTTGCACTATTAGTAATGTTCAATTAAGTGTCTAAGTTGTTCCTCTTATTAGAAAGATTAAGATGTTATAGAAATTTTAAGGATCATGTAATGTAGACGAGTTTATTAGATATACATTTTTGGCATAATATAGTTTTACACCAACATCCCATGAAAACTCGTGATATTACCACGTAAGTGTACTTTCTAATTACAATTTGAAAATAACCACAAAATATTGGATTCTCATTGGACATCAGCGTAAAGCTAGTTTATCGTTTACACTGACAATGCATATCCCAATTTTCTCATTGTGAATTATCATAATTTTGACTATTTTTCAGTGTTATTAAATAGCGGCTATAGTGGCAGTATAGTATTATTGTTCCGCAATACTCTGATTAGTACAAAGTGTTGTTTAATAGCAGCCATAGTACTGTGGCATAGCAGAACCAGAACTAGAACAAACCTCTATTTGCTGCGATCTGCGATTGACAGTAACTATTTTCATAATGCGGTGAAATTATACATGCATGGATAAAAGAGTTATACTCAACAACAACCAAGACTTCTACTCAAGTGCTTGAATAATAATGTGAATTGAGGCAATAACATGAAAGATCTTGTATATACAGTATATAATAGATATGATATTATGGAACAATACTTGTTGTATTATTATATCCAACAATACCATGGGAATAACTCTCTGCAGAGTTGGTTACCAAAACAGAGAGAAAATACAGTAACTGCTAGTGACTTATGCAACTTAGAGGAATTAGAGAGTCTAGTCTCTCCCAACCAAACCAACATAAAAAAAAAAACGAATGACAGTAAATGTTCATCCTTATTCTATTTAATACATGTAAATAATTGGGCCTTGTCTATTGGCCCTGCTAACATAACACGAAGGTCCTTCGCTCTAGTTCTTTCATGATAACTTTCATAAAGTTTCTTCGTTTTCATTCCTGGCTTCTTCACTTTTCTAATGTTATGGGTAATTGTGTAGCCTGCAGCTGTGTATGTATCTCAAACCTTGAATTTTAAGTTACCAGTCTATATCGGAGATCTGATTGTTGGTGAAGTACAAGCAACTAATCTACGAGAAAACAAAAATCGATATTTGTAAGTTTTGACATTCCTGTCTTGTGCATTTTTTTGAATTGGTAATGATTTTGTTTCTACTGAAGTGTTTGTCAATGTTATTCAGTGCGAAGTTTAAGACAAAGTGCTTCAAGAATGGAGACATTCTTGTCATTGAAGGTGAAGCATTGGCTTTGTTACCAACCCTTGACTATAGAGCTGTGGAAGTATAA

Protein sequence

>MS.gene37633.t1

MLFRCLLYSSSKLQYLSPRCFSSTTHVLKPGDVLKKTRVFTEEDVLQYSKVSHDSNPLHTDSAAARSVGFDGPLVHGMLVASLFPHIISSHFPAAVYVSQTLNFKLPVYIGDLIVGEVQATNLRENKNRYFAKFKTKCFKNGDILVIEGEALALLPTLDYRAVEV