AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene78251


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78251.t1 MTR_4g120040 94.118 102 6 0 1 102 1 102 4.00e-69 202
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78251.t1 AT4G15910 41.379 87 48 1 15 101 20 103 2.86e-15 65.9
MS.gene78251.t1 AT1G02820 43.421 76 27 3 23 95 25 87 6.38e-11 54.3

Find 38 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTCTGTAGTATCCGGTTTC+TGG 0.094835 8.4:+11954980 None:intergenic
TAGACATGGGCTTCTCTTCA+AGG 0.339449 8.4:+11955041 None:intergenic
GTCTGGCGCCCATGCCGAAC+AGG 0.356618 8.4:+11955003 None:intergenic
GTCTGTAGTATCCGGTTTCT+GGG 0.391156 8.4:+11954981 None:intergenic
TAGTATCCGGTTTCTGGGTC+TGG 0.400740 8.4:+11954986 None:intergenic
AGCCCATGGCTACGGAAAGC+TGG 0.420672 8.4:-11955068 MS.gene78251:CDS
TGCTTCAGCTAGAGTTGGAT+TGG 0.428759 8.4:-11955098 MS.gene78251:CDS
CTGACCGTTGAAGATGAAAC+AGG 0.428944 8.4:+11955969 None:intergenic
TTCCCAGCTTTCCGTAGCCA+TGG 0.438449 8.4:+11955065 None:intergenic
CTAGCTCTATTAGGATGATC+TGG 0.442792 8.4:+11954895 None:intergenic
CCCATGCCGAACAGGCCTCT+TGG 0.447286 8.4:+11955011 None:intergenic
TGGGCGCCAGACCCAGAAAC+CGG 0.464783 8.4:-11954992 MS.gene78251:CDS
CTCTTGGCCATCTCTAGACA+TGG 0.474198 8.4:+11955027 None:intergenic
AGATGGCCAAGAGGCCTGTT+CGG 0.475265 8.4:-11955017 MS.gene78251:CDS
GCCAAGAGGCCTGTTCGGCA+TGG 0.485879 8.4:-11955012 MS.gene78251:CDS
CCAAGAGGCCTGTTCGGCAT+GGG 0.486297 8.4:-11955011 MS.gene78251:CDS
AGCATCTGTCGGAGCTCCAC+CGG 0.490620 8.4:+11954932 None:intergenic
ATTGATGGGTCTGTAGTATC+CGG 0.491419 8.4:+11954973 None:intergenic
GCTTCAGCTAGAGTTGGATT+GGG 0.505486 8.4:-11955097 MS.gene78251:CDS
TCCCAGCTTTCCGTAGCCAT+GGG 0.510770 8.4:+11955066 None:intergenic
TCTGATGCTTCAGCTAGAGT+TGG 0.513043 8.4:-11955103 MS.gene78251:CDS
GCCCATGGCTACGGAAAGCT+GGG 0.533179 8.4:-11955067 MS.gene78251:CDS
TGCGTTTGAGTAGCATCTGT+CGG 0.543834 8.4:+11954921 None:intergenic
GTTAGCTTGTGAGAGAGAGC+AGG 0.562013 8.4:+11956015 None:intergenic
AACTCTAGCTGAAGCATCAG+AGG 0.572077 8.4:+11955105 None:intergenic
GGTAGTATAGCCCATGGCTA+CGG 0.583121 8.4:-11955076 MS.gene78251:CDS
GCATCTGTCGGAGCTCCACC+GGG 0.595147 8.4:+11954933 None:intergenic
TCTTGGCCATCTCTAGACAT+GGG 0.599128 8.4:+11955028 None:intergenic
GAGAAGCCCATGTCTAGAGA+TGG 0.605275 8.4:-11955034 MS.gene78251:CDS
TGACCGTTGAAGATGAAACA+GGG 0.659345 8.4:+11955970 None:intergenic
GGAGAGATTGAGCAACAAGA+CGG 0.667162 8.4:+11955993 None:intergenic
GGATTGGGTAGTATAGCCCA+TGG 0.667307 8.4:-11955082 MS.gene78251:CDS
TCTAGCTGAAGCATCAGAGG+CGG 0.672860 8.4:+11955108 None:intergenic
CACTCCTAAAATTGACCCGG+TGG 0.689227 8.4:-11954948 MS.gene78251:CDS
TTACACTCCTAAAATTGACC+CGG 0.690275 8.4:-11954951 MS.gene78251:CDS
CATGTCTAGAGATGGCCAAG+AGG 0.705730 8.4:-11955026 MS.gene78251:CDS
ACCGTTGAAGATGAAACAGG+GGG 0.706818 8.4:+11955972 None:intergenic
GACCGTTGAAGATGAAACAG+GGG 0.712207 8.4:+11955971 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTATATGTAAAATTTAGTT+TGG + chr8.4:11955562-11955581 None:intergenic 10.0%
!! ATAATATTATGAATCAAAGT+TGG + chr8.4:11954982-11955001 None:intergenic 15.0%
!! CAAATTATACTTTAAACTAA+GGG - chr8.4:11955646-11955665 MS.gene78251:intron 15.0%
!!! AAATTTTACATATAAACCAA+TGG - chr8.4:11955566-11955585 MS.gene78251:intron 15.0%
!!! ATCTTACACAAATTTAATTT+AGG - chr8.4:11955180-11955199 MS.gene78251:intron 15.0%
!!! GAATTTTTAAAACAATGTAA+GGG - chr8.4:11955729-11955748 MS.gene78251:intron 15.0%
!!! TATTTTAAAAGCCTTAAAAT+CGG - chr8.4:11955221-11955240 MS.gene78251:intron 15.0%
!!! TGAATTTTTAAAACAATGTA+AGG - chr8.4:11955728-11955747 MS.gene78251:intron 15.0%
!!! TTTCATTTTACAATTGTTTT+AGG - chr8.4:11955513-11955532 MS.gene78251:intron 15.0%
!! AACTATGTAAGTATTATTTG+CGG - chr8.4:11955318-11955337 MS.gene78251:intron 20.0%
!! CAAATAATACTTACATAGTT+TGG + chr8.4:11955318-11955337 None:intergenic 20.0%
!! CCAAATTATACTTTAAACTA+AGG - chr8.4:11955645-11955664 MS.gene78251:intron 20.0%
!! CTAAACTTTATACATAGATT+AGG - chr8.4:11955614-11955633 MS.gene78251:intron 20.0%
!! CTGTGATTATATATGAATTA+GGG - chr8.4:11955029-11955048 MS.gene78251:CDS 20.0%
!! TAAATGTTCAAATAAATCTC+TGG + chr8.4:11955756-11955775 None:intergenic 20.0%
!! TCTATGTATAAAGTTTAGTT+TGG + chr8.4:11955612-11955631 None:intergenic 20.0%
!! TCTGTGATTATATATGAATT+AGG - chr8.4:11955028-11955047 MS.gene78251:CDS 20.0%
!!! CAAGATAGTTTTATTATGTT+TGG - chr8.4:11955443-11955462 MS.gene78251:intron 20.0%
!!! CCTTAGTTTAAAGTATAATT+TGG + chr8.4:11955648-11955667 None:intergenic 20.0%
!!! TCTTATATGAACTTTAGTTT+TGG - chr8.4:11955111-11955130 MS.gene78251:CDS 20.0%
! AAATCAAACCTATAGTTGAA+AGG + chr8.4:11955280-11955299 None:intergenic 25.0%
! AATCAAACCTATAGTTGAAA+GGG + chr8.4:11955279-11955298 None:intergenic 25.0%
! ATATAGTTAACCTCATAAGA+GGG + chr8.4:11955417-11955436 None:intergenic 25.0%
! CTATGGTAAATTGTTAAATC+TGG + chr8.4:11955693-11955712 None:intergenic 25.0%
! GGTTATTTAACAGATATTCA+GGG - chr8.4:11955464-11955483 MS.gene78251:intron 25.0%
! TATATAGTTAACCTCATAAG+AGG + chr8.4:11955418-11955437 None:intergenic 25.0%
! TGGTTATTTAACAGATATTC+AGG - chr8.4:11955463-11955482 MS.gene78251:intron 25.0%
! TTATACATAGATTAGGATCT+AGG - chr8.4:11955621-11955640 MS.gene78251:intron 25.0%
!!! AAAGTTTTAATTTGGTCCAT+TGG + chr8.4:11955585-11955604 None:intergenic 25.0%
!!! AATTTTAGGAGTGTAATTGA+TGG + chr8.4:11955968-11955987 None:intergenic 25.0%
!!! ATTGTTTTAGGTTTAACTGT+AGG - chr8.4:11955525-11955544 MS.gene78251:intron 25.0%
!!! ATTTTAGGAGTGTAATTGAT+GGG + chr8.4:11955967-11955986 None:intergenic 25.0%
!!! TTGGTCAGAAAGTTTTAATT+TGG + chr8.4:11955593-11955612 None:intergenic 25.0%
!!! TTGTTTTAGGTTTAACTGTA+GGG - chr8.4:11955526-11955545 MS.gene78251:intron 25.0%
! CAGTTTGATCATTTTCTCTA+TGG + chr8.4:11955710-11955729 None:intergenic 30.0%
!! GACTAACTTAACCGATTTTA+AGG + chr8.4:11955235-11955254 None:intergenic 30.0%
!! TATCACTTATTTTTCCCTGT+AGG - chr8.4:11955779-11955798 MS.gene78251:intron 30.0%
!!! AACTTTAGTTTTGGTGAAGT+GGG - chr8.4:11955120-11955139 MS.gene78251:CDS 30.0%
GTCTCTTAGCTTATCTATGT+TGG - chr8.4:11955252-11955271 MS.gene78251:intron 35.0%
TAACAGATATTCAGGGAACT+TGG - chr8.4:11955471-11955490 MS.gene78251:intron 35.0%
TACTCCTAACAAGTGTCTTA+GGG + chr8.4:11955359-11955378 None:intergenic 35.0%
TTACACTCCTAAAATTGACC+CGG - chr8.4:11955972-11955991 MS.gene78251:intron 35.0%
TTACTCCTAACAAGTGTCTT+AGG + chr8.4:11955360-11955379 None:intergenic 35.0%
!!! GAACTTTAGTTTTGGTGAAG+TGG - chr8.4:11955119-11955138 MS.gene78251:CDS 35.0%
ACTCCTAACAAGTGTCTTAG+GGG + chr8.4:11955358-11955377 None:intergenic 40.0%
CATCTGTTTACCCTCTTATG+AGG - chr8.4:11955404-11955423 MS.gene78251:intron 40.0%
TGACCGTTGAAGATGAAACA+GGG + chr8.4:11954956-11954975 None:intergenic 40.0%
TGTTGGTCCCTTTCAACTAT+AGG - chr8.4:11955269-11955288 MS.gene78251:intron 40.0%
! ATTGATGGGTCTGTAGTATC+CGG + chr8.4:11955953-11955972 None:intergenic 40.0%
ACCGTTGAAGATGAAACAGG+GGG + chr8.4:11954954-11954973 None:intergenic 45.0%
AGTCCCCTAAGACACTTGTT+AGG - chr8.4:11955352-11955371 MS.gene78251:intron 45.0%
CTGACCGTTGAAGATGAAAC+AGG + chr8.4:11954957-11954976 None:intergenic 45.0%
GACCGTTGAAGATGAAACAG+GGG + chr8.4:11954955-11954974 None:intergenic 45.0%
GCTTCAGCTAGAGTTGGATT+GGG - chr8.4:11955826-11955845 MS.gene78251:intron 45.0%
GGAGAGATTGAGCAACAAGA+CGG + chr8.4:11954933-11954952 None:intergenic 45.0%
GTCTGTAGTATCCGGTTTCT+GGG + chr8.4:11955945-11955964 None:intergenic 45.0%
TAGACATGGGCTTCTCTTCA+AGG + chr8.4:11955885-11955904 None:intergenic 45.0%
TCCCCCTGTTTCATCTTCAA+CGG - chr8.4:11954950-11954969 MS.gene78251:CDS 45.0%
TCTGATGCTTCAGCTAGAGT+TGG - chr8.4:11955820-11955839 MS.gene78251:intron 45.0%
TCTTGGCCATCTCTAGACAT+GGG + chr8.4:11955898-11955917 None:intergenic 45.0%
TGCGTTTGAGTAGCATCTGT+CGG + chr8.4:11956005-11956024 None:intergenic 45.0%
TGCTTCAGCTAGAGTTGGAT+TGG - chr8.4:11955825-11955844 MS.gene78251:intron 45.0%
! AACTCTAGCTGAAGCATCAG+AGG + chr8.4:11955821-11955840 None:intergenic 45.0%
!! CTTATTTTTCCCTGTAGGCG+AGG - chr8.4:11955784-11955803 MS.gene78251:intron 45.0%
CACTCCTAAAATTGACCCGG+TGG - chr8.4:11955975-11955994 MS.gene78251:CDS 50.0%
CATGTCTAGAGATGGCCAAG+AGG - chr8.4:11955897-11955916 MS.gene78251:intron 50.0%
CTCTTGGCCATCTCTAGACA+TGG + chr8.4:11955899-11955918 None:intergenic 50.0%
GAGAAGCCCATGTCTAGAGA+TGG - chr8.4:11955889-11955908 MS.gene78251:intron 50.0%
GGATTGGGTAGTATAGCCCA+TGG - chr8.4:11955841-11955860 MS.gene78251:intron 50.0%
GGTAGTATAGCCCATGGCTA+CGG - chr8.4:11955847-11955866 MS.gene78251:intron 50.0%
GGTCTGTAGTATCCGGTTTC+TGG + chr8.4:11955946-11955965 None:intergenic 50.0%
! AGCTCCACCGGGTCAATTTT+AGG + chr8.4:11955982-11956001 None:intergenic 50.0%
! TAGTATCCGGTTTCTGGGTC+TGG + chr8.4:11955940-11955959 None:intergenic 50.0%
! TCTAGCTGAAGCATCAGAGG+CGG + chr8.4:11955818-11955837 None:intergenic 50.0%
!! GTTAGCTTGTGAGAGAGAGC+AGG + chr8.4:11954911-11954930 None:intergenic 50.0%
AGATGGCCAAGAGGCCTGTT+CGG - chr8.4:11955906-11955925 MS.gene78251:intron 55.0%
GCTGCAAAACCTCGCCTACA+GGG + chr8.4:11955796-11955815 None:intergenic 55.0%
TCCCAGCTTTCCGTAGCCAT+GGG + chr8.4:11955860-11955879 None:intergenic 55.0%
TTCCCAGCTTTCCGTAGCCA+TGG + chr8.4:11955861-11955880 None:intergenic 55.0%
AGCATCTGTCGGAGCTCCAC+CGG + chr8.4:11955994-11956013 None:intergenic 60.0%
AGCCCATGGCTACGGAAAGC+TGG - chr8.4:11955855-11955874 MS.gene78251:intron 60.0%
CCAAGAGGCCTGTTCGGCAT+GGG - chr8.4:11955912-11955931 MS.gene78251:intron 60.0%
GCCCATGGCTACGGAAAGCT+GGG - chr8.4:11955856-11955875 MS.gene78251:intron 60.0%
GGCTGCAAAACCTCGCCTAC+AGG + chr8.4:11955797-11955816 None:intergenic 60.0%
CCCATGCCGAACAGGCCTCT+TGG + chr8.4:11955915-11955934 None:intergenic 65.0%
GCATCTGTCGGAGCTCCACC+GGG + chr8.4:11955993-11956012 None:intergenic 65.0%
GCCAAGAGGCCTGTTCGGCA+TGG - chr8.4:11955911-11955930 MS.gene78251:intron 65.0%
TGGGCGCCAGACCCAGAAAC+CGG - chr8.4:11955931-11955950 MS.gene78251:intron 65.0%
GTCTGGCGCCCATGCCGAAC+AGG + chr8.4:11955923-11955942 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 11954904 11956041 11954904 ID=MS.gene78251
chr8.4 mRNA 11954904 11956041 11954904 ID=MS.gene78251.t1;Parent=MS.gene78251
chr8.4 exon 11955974 11956041 11955974 ID=MS.gene78251.t1.exon1;Parent=MS.gene78251.t1
chr8.4 CDS 11955974 11956041 11955974 ID=cds.MS.gene78251.t1;Parent=MS.gene78251.t1
chr8.4 exon 11954904 11955144 11954904 ID=MS.gene78251.t1.exon2;Parent=MS.gene78251.t1
chr8.4 CDS 11954904 11955144 11954904 ID=cds.MS.gene78251.t1;Parent=MS.gene78251.t1
Gene Sequence

>MS.gene78251

ATGGCCTGCTCTCTCTCACAAGCTAACCGTCTTGTTGCTCAATCTCTCCCCCTGTTTCATCTTCAACGGTCAGTTCCAACTTTGATTCATAATATTATATTATTTCATTTAGTAATCATTATTTTCTGTGATTATATATGAATTAGGGATATGTGTATACAGATTCAACATTTCTTTTATAAAACGATTATGAATATTTGTTTCAGTTCTTATATGAACTTTAGTTTTGGTGAAGTGGGTGTCAATATATTTTCTTTTTACATAAATAAAAATCTAATCTTACACAAATTTAATTTAGGCTTAAATGCATCTTTATCTATTTTAAAAGCCTTAAAATCGGTTAAGTTAGTCTCTTAGCTTATCTATGTTGGTCCCTTTCAACTATAGGTTTGATTTTAGAGACTAAACTGACCAAACTATGTAAGTATTATTTGCGGCATACTAAACTAGTCCCCTAAGACACTTGTTAGGAGTAAAAAATTGTATTTGAAAATAAATCACATCTGTTTACCCTCTTATGAGGTTAACTATATAAATTTCAAGATAGTTTTATTATGTTTGGTTATTTAACAGATATTCAGGGAACTTGGTAGCTTTTTTTTCATATTGTTTCATTTTACAATTGTTTTAGGTTTAACTGTAGGGATCAATTTGACCAAACTAAATTTTACATATAAACCAATGGACCAAATTAAAACTTTCTGACCAAACTAAACTTTATACATAGATTAGGATCTAGGACCAAATTATACTTTAAACTAAGGGACTAAACTGAATTTTTCGAAACCAGATTTAACAATTTACCATAGAGAAAATGATCAAACTGAATTTTTAAAACAATGTAAGGGACCAGAGATTTATTTGAACATTTAATTTATCACTTATTTTTCCCTGTAGGCGAGGTTTTGCAGCCGCCTCTGATGCTTCAGCTAGAGTTGGATTGGGTAGTATAGCCCATGGCTACGGAAAGCTGGGAAGCCTTGAAGAGAAGCCCATGTCTAGAGATGGCCAAGAGGCCTGTTCGGCATGGGCGCCAGACCCAGAAACCGGATACTACAGACCCATCAATTACACTCCTAAAATTGACCCGGTGGAGCTCCGACAGATGCTACTCAAACGCAATACCAGATCATCCTAA

Protein sequence

>MS.gene78251.t1

MACSLSQANRLVAQSLPLFHLQRRGFAAASDASARVGLGSIAHGYGKLGSLEEKPMSRDGQEACSAWAPDPETGYYRPINYTPKIDPVELRQMLLKRNTRSS