AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1010530

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1010530 MtrunA17_Chr7g0221761 80.392 51 10 0 1 51 1 51 2.57e-22 85.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 41 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAAATTGCTTTAACGTAAT+TGG 0.106249 7_1:+13702929 None:intergenic
CATGATATTTGTAACTTCTT+TGG 0.215077 7_1:-13702700 Msa1010530:three_prime_UTR
ATGGAACCAGATATGGAAAT+AGG 0.262567 7_1:-13703064 Msa1010530:three_prime_UTR
GGATACCCTATTTCCATATC+TGG 0.279714 7_1:+13703058 None:intergenic
AAACGTTGAAATAGCTTTAG+AGG 0.304799 7_1:+13704962 None:intergenic
TCCAATTCAAGTGTGGAATT+AGG 0.315174 7_1:-13705041 Msa1010530:CDS
ACCTAATTCCACACTTGAAT+TGG 0.317381 7_1:+13705040 None:intergenic
TACGTTAAAGCAATTTGAAT+TGG 0.328292 7_1:-13702924 Msa1010530:three_prime_UTR
GAAGCACACCTGAAAGAAAA+AGG 0.345967 7_1:+13705062 None:intergenic
GGAGATAAAGAAAGTAATTC+AGG 0.354220 7_1:+13702950 None:intergenic
CCAATCTTTAACATTATTTG+TGG 0.386735 7_1:+13702988 None:intergenic
CTTGTGGGACTTATTATTGT+TGG 0.387779 7_1:-13702837 Msa1010530:three_prime_UTR
CCACAAATAATGTTAAAGAT+TGG 0.389223 7_1:-13702988 Msa1010530:three_prime_UTR
GTGAAGCATGTAACACATAT+TGG 0.392648 7_1:-13703028 Msa1010530:three_prime_UTR
AACTATTATTGTTAATTTGA+GGG 0.395391 7_1:+13705162 None:intergenic
TGAGGAGATGGAACCAGATA+TGG 0.397227 7_1:-13703071 Msa1010530:three_prime_UTR
GTAACACATATTGGACTTGA+TGG 0.403212 7_1:-13703019 Msa1010530:three_prime_UTR
CCTGCAGCTACATTAGGCTT+TGG 0.406315 7_1:+13704806 None:intergenic
CAACTATTATTGTTAATTTG+AGG 0.414083 7_1:+13705161 None:intergenic
CAATGAGTGGTTGGTGAGCT+TGG 0.421221 7_1:+13702891 None:intergenic
CACAAATAATGTTAAAGATT+GGG 0.428541 7_1:-13702987 Msa1010530:three_prime_UTR
AGAAGAAATGAGAAATCATA+TGG 0.448869 7_1:-13705102 Msa1010530:exon
TGGAACCAGATATGGAAATA+GGG 0.449151 7_1:-13703063 Msa1010530:three_prime_UTR
TAAAGATTGGGACAATTTGA+AGG 0.461704 7_1:-13702975 Msa1010530:three_prime_UTR
CAAAGAGCATATTGAGGAGA+TGG 0.473749 7_1:-13703083 Msa1010530:three_prime_UTR
TGTATGCCTGCAGCTACATT+AGG 0.488754 7_1:+13704800 None:intergenic
AAGAGTTATCAATGAGTGGT+TGG 0.512846 7_1:+13702882 None:intergenic
AATGAGTGGTTGGTGAGCTT+GGG 0.519534 7_1:+13702892 None:intergenic
ATTTGAAATATTTGTTTGCA+AGG 0.525428 7_1:-13704896 Msa1010530:CDS
TGTTTGCAAGGAAGACAAGA+AGG 0.535313 7_1:-13704884 Msa1010530:CDS
CCAAAGCCTAATGTAGCTGC+AGG 0.535602 7_1:-13704806 Msa1010530:exon
CAGGCATACAGAGATTGATC+AGG 0.545062 7_1:-13704787 Msa1010530:three_prime_UTR
AAAGCAATTTGAATTGGCCA+TGG 0.548884 7_1:-13702918 Msa1010530:three_prime_UTR
TAACACATATTGGACTTGAT+GGG 0.552869 7_1:-13703018 Msa1010530:three_prime_UTR
AGTTTACAAAGAGCATATTG+AGG 0.553012 7_1:-13703089 Msa1010530:three_prime_UTR
TTGGTGAGCTTGGGTAGCCA+TGG 0.554788 7_1:+13702901 None:intergenic
GGAGAAGAGTTATCAATGAG+TGG 0.571021 7_1:+13702878 None:intergenic
GTTACATGCTTCACATCCGT+TGG 0.572507 7_1:+13703037 None:intergenic
TATTATTGTTAATTTGAGGG+AGG 0.623153 7_1:+13705165 None:intergenic
GTGTGCTTCCAATTCAAGTG+TGG 0.660727 7_1:-13705048 Msa1010530:CDS
TATGGAAATAGGGTATCCAA+CGG 0.670674 7_1:-13703053 Msa1010530:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAAATATAAATGCTTTTAA+AGG - chr7_1:13704462-13704481 Msa1010530:intron 10.0%
!! TTATTCATATATTTGTATTA+TGG - chr7_1:13704638-13704657 Msa1010530:intron 10.0%
!!! AAGTATTTTTAATTACATTT+TGG + chr7_1:13704991-13705010 None:intergenic 10.0%
!!! AACTATTATTGTTAATTTGA+GGG + chr7_1:13702686-13702705 None:intergenic 15.0%
!!! ATTTTTCTTTCTTTAGTTAT+TGG - chr7_1:13702918-13702937 Msa1010530:three_prime_UTR 15.0%
!!! TACTTAATTTGATTATATGT+CGG + chr7_1:13703222-13703241 None:intergenic 15.0%
!! AATATAACATATATTGTGTA+TGG - chr7_1:13703899-13703918 Msa1010530:intron 15.0%
!! AGTAATATTCTAAATTTGAA+TGG + chr7_1:13704168-13704187 None:intergenic 15.0%
!!! GTTTTTTTTTTTTTGAAGAA+AGG - chr7_1:13704488-13704507 Msa1010530:intron 15.0%
!! ATACAAATATATGAATAAGT+GGG + chr7_1:13704636-13704655 None:intergenic 15.0%
!! AATACAAATATATGAATAAG+TGG + chr7_1:13704637-13704656 None:intergenic 15.0%
!! AATGTAATTAAAAATACTTG+TGG - chr7_1:13704992-13705011 Msa1010530:CDS 15.0%
!! ATGTAATTAAAAATACTTGT+GGG - chr7_1:13704993-13705012 Msa1010530:CDS 15.0%
!!! TATCATGAATTTTAATTGTA+TGG + chr7_1:13705132-13705151 None:intergenic 15.0%
!!! CAACTATTATTGTTAATTTG+AGG + chr7_1:13702687-13702706 None:intergenic 20.0%
!! TATATACACCAACAAAAAAT+TGG - chr7_1:13702716-13702735 Msa1010530:three_prime_UTR 20.0%
!! ATATACACCAACAAAAAATT+GGG - chr7_1:13702717-13702736 Msa1010530:three_prime_UTR 20.0%
!!! ATTTGAAATATTTGTTTGCA+AGG - chr7_1:13702949-13702968 Msa1010530:three_prime_UTR 20.0%
!!! TCTTTACATCTTTTTATTGT+TGG - chr7_1:13703141-13703160 Msa1010530:intron 20.0%
!!! AATTTGTTTTTGTTTGTACA+TGG - chr7_1:13703175-13703194 Msa1010530:intron 20.0%
!!! ACTTAATTTGATTATATGTC+GGG + chr7_1:13703221-13703240 None:intergenic 20.0%
!! TTTGATTAGCAATAATAGTT+TGG - chr7_1:13703327-13703346 Msa1010530:intron 20.0%
!!! AATAATAGTTTGGAACAATT+GGG - chr7_1:13703337-13703356 Msa1010530:intron 20.0%
!! TAGCTAAGTTTATAACTTTA+TGG - chr7_1:13704346-13704365 Msa1010530:intron 20.0%
!!! ATCGTTTTAATTTTTTAGCT+CGG + chr7_1:13704376-13704395 None:intergenic 20.0%
!! CACAAATAATGTTAAAGATT+GGG - chr7_1:13704858-13704877 Msa1010530:CDS 20.0%
!!! TTCTAAACCCAATTTTTTGT+TGG + chr7_1:13702727-13702746 None:intergenic 25.0%
! AGAAGAAATGAGAAATCATA+TGG - chr7_1:13702743-13702762 Msa1010530:three_prime_UTR 25.0%
! CAACCAAAATCAAGAAAAAA+AGG - chr7_1:13702995-13703014 Msa1010530:three_prime_UTR 25.0%
!!! AGACCTTTTTTTCTTGATTT+TGG + chr7_1:13703001-13703020 None:intergenic 25.0%
!! CAATAATAGTTTGGAACAAT+TGG - chr7_1:13703336-13703355 Msa1010530:intron 25.0%
!!! TTTTTTTTTTCAACTGTCGT+CGG - chr7_1:13704209-13704228 Msa1010530:intron 25.0%
!!! TCGTTTTAATTTTTTAGCTC+GGG + chr7_1:13704375-13704394 None:intergenic 25.0%
! TAAGTGGGATTGAAATAAAT+GGG + chr7_1:13704621-13704640 None:intergenic 25.0%
! ATAAGTGGGATTGAAATAAA+TGG + chr7_1:13704622-13704641 None:intergenic 25.0%
! CCAATCTTTAACATTATTTG+TGG + chr7_1:13704860-13704879 None:intergenic 25.0%
! CCACAAATAATGTTAAAGAT+TGG - chr7_1:13704857-13704876 Msa1010530:CDS 25.0%
! TCAAATTGCTTTAACGTAAT+TGG + chr7_1:13704919-13704938 None:intergenic 25.0%
! TACGTTAAAGCAATTTGAAT+TGG - chr7_1:13704921-13704940 Msa1010530:CDS 25.0%
!!! GTTGATGATGATGTTTTTAT+AGG - chr7_1:13705094-13705113 Msa1010530:CDS 25.0%
! CATGATATTTGTAACTTCTT+TGG - chr7_1:13705145-13705164 Msa1010530:five_prime_UTR 25.0%
! TAGTTCTTCCTTTTTCTTTC+AGG - chr7_1:13702775-13702794 Msa1010530:three_prime_UTR 30.0%
!! AAACGTTGAAATAGCTTTAG+AGG + chr7_1:13702886-13702905 None:intergenic 30.0%
ATCAAGAAAAAAAGGTCTTC+TGG - chr7_1:13703003-13703022 Msa1010530:three_prime_UTR 30.0%
AGTAGCCAAAGAGTTAATAA+GGG - chr7_1:13703936-13703955 Msa1010530:intron 30.0%
CTTATCCCTTATTAACTCTT+TGG + chr7_1:13703944-13703963 None:intergenic 30.0%
! AGAGCAAACATTTTATCACA+TGG - chr7_1:13704131-13704150 Msa1010530:intron 30.0%
AATAAATGGGAAAATCATCC+AGG + chr7_1:13704608-13704627 None:intergenic 30.0%
! AGTTTACAAAGAGCATATTG+AGG - chr7_1:13704756-13704775 Msa1010530:intron 30.0%
TAACACATATTGGACTTGAT+GGG - chr7_1:13704827-13704846 Msa1010530:CDS 30.0%
TAAAGATTGGGACAATTTGA+AGG - chr7_1:13704870-13704889 Msa1010530:CDS 30.0%
GGAGATAAAGAAAGTAATTC+AGG + chr7_1:13704898-13704917 None:intergenic 30.0%
TCCAATTCAAGTGTGGAATT+AGG - chr7_1:13702804-13702823 Msa1010530:three_prime_UTR 35.0%
ACCTAATTCCACACTTGAAT+TGG + chr7_1:13702808-13702827 None:intergenic 35.0%
TGGGCATATCAATGAACAAA+TGG - chr7_1:13703356-13703375 Msa1010530:intron 35.0%
GGAAATTAGATAGAGAGATG+TGG - chr7_1:13703377-13703396 Msa1010530:intron 35.0%
! ACTCGTTGGTTGAGTTTATT+AGG + chr7_1:13703430-13703449 None:intergenic 35.0%
AACCAACGAGTTTGTGAAAA+AGG - chr7_1:13703439-13703458 Msa1010530:intron 35.0%
TTCAACCATCTGATAGCAAA+CGG - chr7_1:13703593-13703612 Msa1010530:intron 35.0%
ATGTGTATTAGAGACGATGA+AGG + chr7_1:13703692-13703711 None:intergenic 35.0%
CACTTCTAACTCTCTATGTT+CGG - chr7_1:13703761-13703780 Msa1010530:intron 35.0%
GTTAGAATCTACTCTTGAGT+TGG + chr7_1:13703856-13703875 None:intergenic 35.0%
GAGTAGCCAAAGAGTTAATA+AGG - chr7_1:13703935-13703954 Msa1010530:intron 35.0%
AAAAAAATAATGCACGTGCC+TGG - chr7_1:13704587-13704606 Msa1010530:intron 35.0%
ATGGAACCAGATATGGAAAT+AGG - chr7_1:13704781-13704800 Msa1010530:three_prime_UTR 35.0%
TGGAACCAGATATGGAAATA+GGG - chr7_1:13704782-13704801 Msa1010530:three_prime_UTR 35.0%
! TATGGAAATAGGGTATCCAA+CGG - chr7_1:13704792-13704811 Msa1010530:three_prime_UTR 35.0%
GTGAAGCATGTAACACATAT+TGG - chr7_1:13704817-13704836 Msa1010530:exon 35.0%
GTAACACATATTGGACTTGA+TGG - chr7_1:13704826-13704845 Msa1010530:CDS 35.0%
AAAGCAATTTGAATTGGCCA+TGG - chr7_1:13704927-13704946 Msa1010530:CDS 35.0%
AAGAGTTATCAATGAGTGGT+TGG + chr7_1:13704966-13704985 None:intergenic 35.0%
CTTGTGGGACTTATTATTGT+TGG - chr7_1:13705008-13705027 Msa1010530:CDS 35.0%
! GATGATGATGATGATGATGA+TGG - chr7_1:13705072-13705091 Msa1010530:CDS 35.0%
GAAGCACACCTGAAAGAAAA+AGG + chr7_1:13702786-13702805 None:intergenic 40.0%
TGTTTGCAAGGAAGACAAGA+AGG - chr7_1:13702961-13702980 Msa1010530:three_prime_UTR 40.0%
!! GTCCTTTTTCACAAACTCGT+TGG + chr7_1:13703444-13703463 None:intergenic 40.0%
CGTAGAGATGAATCTGAACT+TGG + chr7_1:13703503-13703522 None:intergenic 40.0%
!! GTTTGCTATCAGATGGTTGA+AGG + chr7_1:13703594-13703613 None:intergenic 40.0%
!! TCCTTCATCAGCTTTTAGGA+TGG - chr7_1:13703631-13703650 Msa1010530:intron 40.0%
!!! CCTTCATCAGCTTTTAGGAT+GGG - chr7_1:13703632-13703651 Msa1010530:intron 40.0%
ATATTGATGCAGCTTTCTCC+TGG + chr7_1:13703739-13703758 None:intergenic 40.0%
! CAAAGAGCATATTGAGGAGA+TGG - chr7_1:13704762-13704781 Msa1010530:three_prime_UTR 40.0%
GGATACCCTATTTCCATATC+TGG + chr7_1:13704790-13704809 None:intergenic 40.0%
GGAGAAGAGTTATCAATGAG+TGG + chr7_1:13704970-13704989 None:intergenic 40.0%
GTGTGCTTCCAATTCAAGTG+TGG - chr7_1:13702797-13702816 Msa1010530:three_prime_UTR 45.0%
TGTATGCCTGCAGCTACATT+AGG + chr7_1:13703048-13703067 None:intergenic 45.0%
CAGGCATACAGAGATTGATC+AGG - chr7_1:13703058-13703077 Msa1010530:three_prime_UTR 45.0%
! GATTGCTCATAGCCTTGCTA+GGG + chr7_1:13703406-13703425 None:intergenic 45.0%
! AGATTGCTCATAGCCTTGCT+AGG + chr7_1:13703407-13703426 None:intergenic 45.0%
CGAGTTTGTGAAAAAGGACG+AGG - chr7_1:13703445-13703464 Msa1010530:intron 45.0%
ACCATCTGATAGCAAACGGT+AGG - chr7_1:13703597-13703616 Msa1010530:intron 45.0%
CCTAAAAGCTGATGAAGGAG+AGG + chr7_1:13703630-13703649 None:intergenic 45.0%
! CCTCTCCTTCATCAGCTTTT+AGG - chr7_1:13703627-13703646 Msa1010530:intron 45.0%
CCCATCCTAAAAGCTGATGA+AGG + chr7_1:13703635-13703654 None:intergenic 45.0%
TCAAGTAGTAGAGTGGGGAT+TGG + chr7_1:13703716-13703735 None:intergenic 45.0%
TCCTGGTCAAGTAGTAGAGT+GGG + chr7_1:13703722-13703741 None:intergenic 45.0%
!! GATGTGTTGCCGCTTTATTG+CGG - chr7_1:13703813-13703832 Msa1010530:intron 45.0%
CGAACAACAATATGCGAGAG+GGG + chr7_1:13703878-13703897 None:intergenic 45.0%
GCGAACAACAATATGCGAGA+GGG + chr7_1:13703879-13703898 None:intergenic 45.0%
TGCGAACAACAATATGCGAG+AGG + chr7_1:13703880-13703899 None:intergenic 45.0%
TGAGGAGATGGAACCAGATA+TGG - chr7_1:13704774-13704793 Msa1010530:three_prime_UTR 45.0%
GTTACATGCTTCACATCCGT+TGG + chr7_1:13704811-13704830 None:intergenic 45.0%
!! AATGAGTGGTTGGTGAGCTT+GGG + chr7_1:13704956-13704975 None:intergenic 45.0%
!! TTTATTCAATTAAAATAATA+AGG - chr7_1:13704008-13704027 Msa1010530:intron 5.0%
CCTGCAGCTACATTAGGCTT+TGG + chr7_1:13703042-13703061 None:intergenic 50.0%
CCAAAGCCTAATGTAGCTGC+AGG - chr7_1:13703039-13703058 Msa1010530:three_prime_UTR 50.0%
!! GCCTACCGTTTGCTATCAGA+TGG + chr7_1:13703601-13703620 None:intergenic 50.0%
GCTGATGAAGGAGAGGCTTT+AGG + chr7_1:13703623-13703642 None:intergenic 50.0%
CCTGGTCAAGTAGTAGAGTG+GGG + chr7_1:13703721-13703740 None:intergenic 50.0%
CTCCTGGTCAAGTAGTAGAG+TGG + chr7_1:13703723-13703742 None:intergenic 50.0%
GCAGACATGCCGCAATAAAG+CGG + chr7_1:13703825-13703844 None:intergenic 50.0%
!! CAATGAGTGGTTGGTGAGCT+TGG + chr7_1:13704957-13704976 None:intergenic 50.0%
! TGCTCATAGCCTTGCTAGGG+CGG + chr7_1:13703403-13703422 None:intergenic 55.0%
CCCCACTCTACTACTTGACC+AGG - chr7_1:13703718-13703737 Msa1010530:intron 55.0%
TTGGTGAGCTTGGGTAGCCA+TGG + chr7_1:13704947-13704966 None:intergenic 55.0%
GAGATGTGGCCGCCCTAGCA+AGG - chr7_1:13703391-13703410 Msa1010530:intron 65.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 13702683 13705184 13702683 ID=Msa1010530;Name=Msa1010530
chr7_1 mRNA 13702683 13705184 13702683 ID=Msa1010530-mRNA-1;Parent=Msa1010530;Name=Msa1010530-mRNA-1;_AED=0.14;_eAED=0.14;_QI=67|1|1|1|0|0|2|486|99
chr7_1 exon 13702683 13703109 13702683 ID=Msa1010530-mRNA-1:exon:3500;Parent=Msa1010530-mRNA-1
chr7_1 exon 13704759 13705184 13704759 ID=Msa1010530-mRNA-1:exon:3499;Parent=Msa1010530-mRNA-1
chr7_1 five_prime_UTR 13705118 13705184 13705118 ID=Msa1010530-mRNA-1:five_prime_utr;Parent=Msa1010530-mRNA-1
chr7_1 CDS 13704818 13705117 13704818 ID=Msa1010530-mRNA-1:cds;Parent=Msa1010530-mRNA-1
chr7_1 three_prime_UTR 13704759 13704817 13704759 ID=Msa1010530-mRNA-1:three_prime_utr;Parent=Msa1010530-mRNA-1
chr7_1 three_prime_UTR 13702683 13703109 13702683 ID=Msa1010530-mRNA-1:three_prime_utr;Parent=Msa1010530-mRNA-1
Gene Sequence

>Msa1010530

ATGAGAAATCATATGGAGAGATTAGTAGTTCTTCCTTTTTCTTTCAGGTGTGCTTCCAATTCAAGTGTGGAATTAGGTGAACAAAAAGTGCAAAAACTAGATTCAAAAGACTCAATTGATTCAAGTAGTTTCTCCTCTAAAGCTATTTCAACGTTTCTATATTCATTCATTTTTCTTTCTTTAGTTATTGGAGTTCGTAATTTGAAATATTTGTTTGCAAGGAAGACAAGAAGGACAAGTCATCACAACCAAAATCAAGAAAAAAAGGTCTTCTGGATTTTTTGTTCTACCAAAGCCTAA
Protein sequence

>Msa1010530

MRNHMERLVVLPFSFRCASNSSVELGEQKVQKLDSKDSIDSSSFSSKAISTFLYSFIFLSLVIGVRNLKYLFARKTRRTSHHNQNQEKKVFWIFCSTKA*