AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0141670


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0141670 MtrunA17_Chr5g0448421 81.967 61 11 0 1 61 1 61 6.36e-25 93.6
Msa0141670 MtrunA17_Chr5g0448411 91.304 46 4 0 1 46 1 46 4.93e-20 80.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 136 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATATCTTCCTGATCCATT+TGG 0.346145 1_4:-278295 Msa0141670:five_prime_UTR
TGCATCCACATGGCTACATT+TGG 0.361353 1_4:-278329 Msa0141670:five_prime_UTR
AGATCACTCCCATCTTCAAT+AGG 0.372428 1_4:-278097 Msa0141670:CDS
TTCTTCAAGAATGTAGTAGA+TGG 0.375775 1_4:+278235 None:intergenic
ATACACGTAATATGATGAAT+TGG 0.425683 1_4:+278433 None:intergenic
GTAATATGATGAATTGGATA+AGG 0.430261 1_4:+278439 None:intergenic
AACTATAAGCCAAATGGATC+AGG 0.432629 1_4:+278286 None:intergenic
CTAGAAGACCCTATTGAAGA+TGG 0.437182 1_4:+278088 None:intergenic
AAAGATGAGGGCTCATGGCC+TGG 0.443254 1_4:-275901 Msa0141670:intron
TCAATAGGGTCTTCTAGAAA+AGG 0.446420 1_4:-278082 Msa0141670:CDS
AAGGCATGAGCCCTCGTCTC+TGG 0.449170 1_4:+275840 None:intergenic
GAGACGAGGGCTCATGCCTT+AGG 0.457094 1_4:-275837 Msa0141670:CDS
TAATATGATGAATTGGATAA+GGG 0.458916 1_4:+278440 None:intergenic
GAAGTAAACTATAAGCCAAA+TGG 0.459137 1_4:+278280 None:intergenic
AGTGAGAGATAGACCTTGGC+AGG 0.481039 1_4:+278028 None:intergenic
AGCTTCTTCTCCTCCTGCCA+AGG 0.490862 1_4:-278041 Msa0141670:intron
TTCCCTCCTTTGTTACCTCT+AGG 0.504632 1_4:+278199 None:intergenic
GATCACTCCCATCTTCAATA+GGG 0.512694 1_4:-278096 Msa0141670:CDS
CTATTGAGCAAAAGCTCCTA+AGG 0.512964 1_4:+275821 None:intergenic
CATTTAAAGATGAGGGCTCA+TGG 0.514115 1_4:-275906 Msa0141670:intron
GAGGCTGTGAGACAGAGTCT+TGG 0.514771 1_4:-278124 Msa0141670:CDS
AAAAGGTTCCTTTGTTGTCA+AGG 0.526175 1_4:-278065 Msa0141670:CDS
CGTGGTTGAGCAAAAGCTCC+AGG 0.533143 1_4:+275883 None:intergenic
TAGAAGACCCTATTGAAGAT+GGG 0.548284 1_4:+278089 None:intergenic
TTCCTAGAGGTAACAAAGGA+GGG 0.554204 1_4:-278201 Msa0141670:five_prime_UTR
ATTACGTGTATAAACATGGT+TGG 0.565397 1_4:-278421 Msa0141670:five_prime_UTR
TCATATTACGTGTATAAACA+TGG 0.603916 1_4:-278425 Msa0141670:five_prime_UTR
CTTGTTCCTAGAGGTAACAA+AGG 0.604243 1_4:-278205 Msa0141670:five_prime_UTR
GAGAGATAGACCTTGGCAGG+AGG 0.606963 1_4:+278031 None:intergenic
GTTCCTAGAGGTAACAAAGG+AGG 0.614577 1_4:-278202 Msa0141670:five_prime_UTR
AGAAGCTGCCTTGACAACAA+AGG 0.615553 1_4:+278057 None:intergenic
TTCTTGTGGTAGATATTGCA+TGG 0.626511 1_4:+278361 None:intergenic
ACGTCCACGTTGCATCCACA+TGG 0.626539 1_4:-278339 Msa0141670:five_prime_UTR
ATGCAACGTGGACGTTCTTG+TGG 0.631074 1_4:+278347 None:intergenic
CTAAGCCAAATGTAGCCATG+TGG 0.681870 1_4:+278324 None:intergenic
TAACAAAGGAGGGAAGAACA+TGG 0.683240 1_4:-278191 Msa0141670:exon
GAGCAAAAGCTCCATCGTCG+TGG 0.685079 1_4:+275865 None:intergenic
GTAGCCATGTGGATGCAACG+TGG 0.793429 1_4:+278335 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAAAAAAAAAATAAGTTA+TGG - chr1_4:276921-276940 Msa0141670:intron 10.0%
!! GAAAAAAAAAAATAAGTTAT+GGG - chr1_4:276922-276941 Msa0141670:intron 10.0%
!! AATGATTAGTATTATAAATA+AGG - chr1_4:276964-276983 Msa0141670:intron 10.0%
!!! TATTTATTTATTTTGAAGTT+AGG - chr1_4:277906-277925 Msa0141670:intron 10.0%
!! AACAATATTCAAATAGAATA+TGG - chr1_4:277778-277797 Msa0141670:intron 15.0%
!! TATATGAAAACAAAATCAAA+AGG + chr1_4:277835-277854 None:intergenic 15.0%
!! TAATAGATAAATTAGGATAT+AGG + chr1_4:277950-277969 None:intergenic 15.0%
!! TCAAAGATAATAGATAAATT+AGG + chr1_4:277957-277976 None:intergenic 15.0%
!! TAATATGATGAATTGGATAA+GGG + chr1_4:275877-275896 None:intergenic 20.0%
!!! ATAACTTTCTTTTCTCTTTT+TGG - chr1_4:276489-276508 Msa0141670:intron 20.0%
!! TTGAACAAAAAACTATTGTA+AGG - chr1_4:276600-276619 Msa0141670:intron 20.0%
!! TATTATAAATAAGGAAGCTT+AGG - chr1_4:276973-276992 Msa0141670:intron 20.0%
!! TTTGTAAGATTATGAGAATT+AGG - chr1_4:277188-277207 Msa0141670:intron 20.0%
!! TTGTAAGATTATGAGAATTA+GGG - chr1_4:277189-277208 Msa0141670:intron 20.0%
!!! ATTTTTTCTAATTGTTGACA+TGG - chr1_4:277635-277654 Msa0141670:intron 20.0%
!!! TGATCTTATTTTGTAAATGT+CGG - chr1_4:278259-278278 Msa0141670:five_prime_UTR 20.0%
! GTAATATGATGAATTGGATA+AGG + chr1_4:275878-275897 None:intergenic 25.0%
! ATACACGTAATATGATGAAT+TGG + chr1_4:275884-275903 None:intergenic 25.0%
! TCATATTACGTGTATAAACA+TGG - chr1_4:275889-275908 Msa0141670:CDS 25.0%
!!! AGTTTTTTGTTCAACTACTA+AGG + chr1_4:276594-276613 None:intergenic 25.0%
! AACAAAAAACTATTGTAAGG+TGG - chr1_4:276603-276622 Msa0141670:intron 25.0%
! CTTGATTAAACTGTTTACTT+AGG + chr1_4:276665-276684 None:intergenic 25.0%
! NNNNTAAATATGCGATGTGT+TGG - chr1_4:276818-276837 Msa0141670:intron 25.0%
!! GATGTGTTGGTATTATATAT+AGG - chr1_4:276831-276850 Msa0141670:intron 25.0%
! CTTATTAGTGTAAGTAGAAT+TGG - chr1_4:276887-276906 Msa0141670:intron 25.0%
! CATTCTTCCTAAATCTATTT+AGG + chr1_4:276948-276967 None:intergenic 25.0%
! GATTTCAGAAAAACAATCTA+AGG - chr1_4:277090-277109 Msa0141670:intron 25.0%
!! AGAAAAACAATCTAAGGTAA+GGG - chr1_4:277096-277115 Msa0141670:intron 25.0%
!!! AAACCGTTGAATTGTTTTAA+AGG - chr1_4:277242-277261 Msa0141670:intron 25.0%
!!! AACCGTTGAATTGTTTTAAA+GGG - chr1_4:277243-277262 Msa0141670:intron 25.0%
!! GGAGTTTTTATTCATCATAA+GGG - chr1_4:277267-277286 Msa0141670:intron 25.0%
! TGATGTTTCATGTTGAATTA+GGG - chr1_4:277422-277441 Msa0141670:intron 25.0%
! ATCGTAAAACATATTCACAT+TGG + chr1_4:277517-277536 None:intergenic 25.0%
!!! TAATCTCGTCTTATTTGAAT+TGG - chr1_4:277668-277687 Msa0141670:intron 25.0%
! TTTACTAGAAGCTAATATCA+TGG + chr1_4:277806-277825 None:intergenic 25.0%
! TAAATTAGGATATAGGTGTT+TGG + chr1_4:277943-277962 None:intergenic 25.0%
!!! GTTATATAAAGAAGTGCTAT+TGG - chr1_4:278105-278124 Msa0141670:CDS 25.0%
ATTACGTGTATAAACATGGT+TGG - chr1_4:275893-275912 Msa0141670:CDS 30.0%
GAAGTAAACTATAAGCCAAA+TGG + chr1_4:276037-276056 None:intergenic 30.0%
TTCTTCAAGAATGTAGTAGA+TGG + chr1_4:276082-276101 None:intergenic 30.0%
! AAGAAAAAACTTGTTCCTAG+AGG - chr1_4:276100-276119 Msa0141670:intron 30.0%
ATATTACAACTGTCTCATGT+GGG - chr1_4:276365-276384 Msa0141670:intron 30.0%
AAAGCAAAGTCTTTCTTACT+TGG - chr1_4:276554-276573 Msa0141670:intron 30.0%
! GTGTTGGTATTATATATAGG+TGG - chr1_4:276834-276853 Msa0141670:intron 30.0%
ATTAGTGTAAGTAGAATTGG+AGG - chr1_4:276890-276909 Msa0141670:intron 30.0%
TTATGGGCCTAAATAGATTT+AGG - chr1_4:276938-276957 Msa0141670:intron 30.0%
!! TTTTACGTTAAACCGCTTTT+TGG - chr1_4:277010-277029 Msa0141670:intron 30.0%
! CAGAAAAACAATCTAAGGTA+AGG - chr1_4:277095-277114 Msa0141670:intron 30.0%
! TTGAGTGAGAATTGATGATT+AGG - chr1_4:277212-277231 Msa0141670:intron 30.0%
!!! ACCGTTGAATTGTTTTAAAG+GGG - chr1_4:277244-277263 Msa0141670:intron 30.0%
! GGGAGTTTTTATTCATCATA+AGG - chr1_4:277266-277285 Msa0141670:intron 30.0%
GTGATGTTTCATGTTGAATT+AGG - chr1_4:277421-277440 Msa0141670:intron 30.0%
GATGTTTCATGTTGAATTAG+GGG - chr1_4:277423-277442 Msa0141670:intron 30.0%
!! TTGAATTAGGGGTTGATATT+TGG - chr1_4:277434-277453 Msa0141670:intron 30.0%
!! TAATGGCATCGATTCTAATA+CGG + chr1_4:277486-277505 None:intergenic 30.0%
TCATGAACCTATAAGGAATA+AGG + chr1_4:277596-277615 None:intergenic 30.0%
TCCAGAATATGTTAAGAGAT+TGG - chr1_4:277725-277744 Msa0141670:intron 30.0%
CCAGAATATGTTAAGAGATT+GGG - chr1_4:277726-277745 Msa0141670:intron 30.0%
AGATTGGGATTAATGAAGTA+AGG - chr1_4:277741-277760 Msa0141670:intron 30.0%
TATACCACTTGTACTTATTC+TGG - chr1_4:277853-277872 Msa0141670:intron 30.0%
CATCTTTAAATGAGTATGCA+TGG + chr1_4:278400-278419 None:intergenic 30.0%
TGCATACTCATTTAAAGATG+AGG - chr1_4:278400-278419 Msa0141670:five_prime_UTR 30.0%
GCATACTCATTTAAAGATGA+GGG - chr1_4:278401-278420 Msa0141670:five_prime_UTR 30.0%
AGCAAAAACGTAATAGCAGT+GGG - chr1_4:275837-275856 Msa0141670:CDS 35.0%
TTCTTGTGGTAGATATTGCA+TGG + chr1_4:275956-275975 None:intergenic 35.0%
TCATATCTTCCTGATCCATT+TGG - chr1_4:276019-276038 Msa0141670:intron 35.0%
AACTATAAGCCAAATGGATC+AGG + chr1_4:276031-276050 None:intergenic 35.0%
TAGAAGACCCTATTGAAGAT+GGG + chr1_4:276228-276247 None:intergenic 35.0%
! TCAATAGGGTCTTCTAGAAA+AGG - chr1_4:276232-276251 Msa0141670:intron 35.0%
! AAAAGGTTCCTTTGTTGTCA+AGG - chr1_4:276249-276268 Msa0141670:intron 35.0%
CACATGAGACAGTTGTAATA+TGG + chr1_4:276366-276385 None:intergenic 35.0%
CATATTACAACTGTCTCATG+TGG - chr1_4:276364-276383 Msa0141670:intron 35.0%
CACTTGTATATTTGTCCAAG+AGG + chr1_4:276445-276464 None:intergenic 35.0%
!!! CTTTTTGGTGTTCAGCAAAA+TGG - chr1_4:276504-276523 Msa0141670:intron 35.0%
ATGGAGCAAATAGACAATTG+TGG - chr1_4:276523-276542 Msa0141670:intron 35.0%
CAAAGTCTTTCTTACTTGGA+TGG - chr1_4:276558-276577 Msa0141670:intron 35.0%
TGTTTACTTAGGCATACTCT+AGG + chr1_4:276654-276673 None:intergenic 35.0%
! GATTGCATCTAACGTGTTTT+AGG - chr1_4:277159-277178 Msa0141670:intron 35.0%
!! CCCCCTTTAAAACAATTCAA+CGG + chr1_4:277248-277267 None:intergenic 35.0%
!!! CCGTTGAATTGTTTTAAAGG+GGG - chr1_4:277245-277264 Msa0141670:intron 35.0%
!!! CGTTGAATTGTTTTAAAGGG+GGG - chr1_4:277246-277265 Msa0141670:intron 35.0%
ATAAGGGATGTGTATTCATG+TGG - chr1_4:277283-277302 Msa0141670:intron 35.0%
!! AATGGCATCGATTCTAATAC+GGG + chr1_4:277485-277504 None:intergenic 35.0%
TAGAATCGATGCCATTATCT+AGG - chr1_4:277489-277508 Msa0141670:intron 35.0%
!! TCACATTGGTTCCTAGATAA+TGG + chr1_4:277503-277522 None:intergenic 35.0%
TGCGATTCCTTATTCCTTAT+AGG - chr1_4:277586-277605 Msa0141670:intron 35.0%
CTTCAGTTCATGAACCTATA+AGG + chr1_4:277603-277622 None:intergenic 35.0%
CCCAATCTCTTAACATATTC+TGG + chr1_4:277729-277748 None:intergenic 35.0%
!!! TTTTGAAGTTAGGCATGACA+CGG - chr1_4:277916-277935 Msa0141670:intron 35.0%
! ATCTCTTTGTTTCACATCAG+AGG + chr1_4:278030-278049 None:intergenic 35.0%
CAGCAAAAACGTAATAGCAG+TGG - chr1_4:275836-275855 Msa0141670:CDS 40.0%
CTTGTTCCTAGAGGTAACAA+AGG - chr1_4:276109-276128 Msa0141670:intron 40.0%
TTCCTAGAGGTAACAAAGGA+GGG - chr1_4:276113-276132 Msa0141670:intron 40.0%
TAACAAAGGAGGGAAGAACA+TGG - chr1_4:276123-276142 Msa0141670:intron 40.0%
!! ATCTCTTACTTTTGCAGCTG+AGG - chr1_4:276171-276190 Msa0141670:intron 40.0%
AGATCACTCCCATCTTCAAT+AGG - chr1_4:276217-276236 Msa0141670:intron 40.0%
GATCACTCCCATCTTCAATA+GGG - chr1_4:276218-276237 Msa0141670:intron 40.0%
CTAGAAGACCCTATTGAAGA+TGG + chr1_4:276229-276248 None:intergenic 40.0%
TTTGAGTGAGAGATAGACCT+TGG + chr1_4:276293-276312 None:intergenic 40.0%
GTCTTTCTTACTTGGATGGA+AGG - chr1_4:276562-276581 Msa0141670:intron 40.0%
!!! TAAACCGCTTTTTGGAGAAG+AGG - chr1_4:277018-277037 Msa0141670:intron 40.0%
TTCTCCTCTTCTCCAAAAAG+CGG + chr1_4:277025-277044 None:intergenic 40.0%
!! TTTTTGGAGAAGAGGAGAAG+AGG - chr1_4:277026-277045 Msa0141670:intron 40.0%
TGTATTCATGTGGCTAGTGA+AGG - chr1_4:277293-277312 Msa0141670:intron 40.0%
!! ATGGCATCGATTCTAATACG+GGG + chr1_4:277484-277503 None:intergenic 40.0%
CGTACCAGAATAAGTACAAG+TGG + chr1_4:277860-277879 None:intergenic 40.0%
TACTTATTCTGGTACGCTAG+TGG - chr1_4:277864-277883 Msa0141670:intron 40.0%
CATACGGTAGAGACATGTAT+GGG + chr1_4:278006-278025 None:intergenic 40.0%
CATTTAAAGATGAGGGCTCA+TGG - chr1_4:278408-278427 Msa0141670:five_prime_UTR 40.0%
CTATTGAGCAAAAGCTCCTA+AGG + chr1_4:278496-278515 None:intergenic 40.0%
TGCATCCACATGGCTACATT+TGG - chr1_4:275985-276004 Msa0141670:intron 45.0%
CTAAGCCAAATGTAGCCATG+TGG + chr1_4:275993-276012 None:intergenic 45.0%
GTTCCTAGAGGTAACAAAGG+AGG - chr1_4:276112-276131 Msa0141670:intron 45.0%
TTCCCTCCTTTGTTACCTCT+AGG + chr1_4:276118-276137 None:intergenic 45.0%
AGAAGCTGCCTTGACAACAA+AGG + chr1_4:276260-276279 None:intergenic 45.0%
CCATACGGTAGAGACATGTA+TGG + chr1_4:278007-278026 None:intergenic 45.0%
CCATACATGTCTCTACCGTA+TGG - chr1_4:278004-278023 Msa0141670:intron 45.0%
GTTTCACATCAGAGGCCATA+CGG + chr1_4:278022-278041 None:intergenic 45.0%
! TTTTGCTCAACCAGAGACGA+GGG - chr1_4:278464-278483 Msa0141670:five_prime_UTR 45.0%
ATGCAACGTGGACGTTCTTG+TGG + chr1_4:275970-275989 None:intergenic 50.0%
AGTGAGAGATAGACCTTGGC+AGG + chr1_4:276289-276308 None:intergenic 50.0%
ACCACTGAACTGACACCTCT+TGG - chr1_4:276427-276446 Msa0141670:intron 50.0%
!! TCCAAGAGGTGTCAGTTCAG+TGG + chr1_4:276431-276450 None:intergenic 50.0%
GAGAACTCAGAGAGAGAGCT+AGG - chr1_4:277048-277067 Msa0141670:intron 50.0%
! CTTTTGCTCAACCACGACGA+TGG - chr1_4:278438-278457 Msa0141670:five_prime_UTR 50.0%
! CTTTTGCTCAACCAGAGACG+AGG - chr1_4:278463-278482 Msa0141670:five_prime_UTR 50.0%
ACGTCCACGTTGCATCCACA+TGG - chr1_4:275975-275994 Msa0141670:intron 55.0%
GTAGCCATGTGGATGCAACG+TGG + chr1_4:275982-276001 None:intergenic 55.0%
GAGGCTGTGAGACAGAGTCT+TGG - chr1_4:276190-276209 Msa0141670:intron 55.0%
AGCTTCTTCTCCTCCTGCCA+AGG - chr1_4:276273-276292 Msa0141670:intron 55.0%
GAGAGATAGACCTTGGCAGG+AGG + chr1_4:276286-276305 None:intergenic 55.0%
AAAGATGAGGGCTCATGGCC+TGG - chr1_4:278413-278432 Msa0141670:five_prime_UTR 55.0%
CGTGGTTGAGCAAAAGCTCC+AGG + chr1_4:278434-278453 None:intergenic 55.0%
GAGCAAAAGCTCCATCGTCG+TGG + chr1_4:278452-278471 None:intergenic 55.0%
AAGGCATGAGCCCTCGTCTC+TGG + chr1_4:278477-278496 None:intergenic 60.0%
GAGACGAGGGCTCATGCCTT+AGG - chr1_4:278477-278496 Msa0141670:five_prime_UTR 60.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 275821 278515 275821 ID=Msa0141670;Name=Msa0141670
chr1_4 mRNA 275821 278515 275821 ID=Msa0141670-mRNA-1;Parent=Msa0141670;Name=Msa0141670-mRNA-1;_AED=0.20;_eAED=0.20;_QI=321|0|0.5|0.5|1|1|2|0|83
chr1_4 exon 275821 275919 275821 ID=Msa0141670-mRNA-1:exon:36;Parent=Msa0141670-mRNA-1
chr1_4 exon 278042 278515 278042 ID=Msa0141670-mRNA-1:exon:35;Parent=Msa0141670-mRNA-1
chr1_4 five_prime_UTR 278195 278515 278195 ID=Msa0141670-mRNA-1:five_prime_utr;Parent=Msa0141670-mRNA-1
chr1_4 CDS 278042 278194 278042 ID=Msa0141670-mRNA-1:cds;Parent=Msa0141670-mRNA-1
chr1_4 CDS 275821 275919 275821 ID=Msa0141670-mRNA-1:cds;Parent=Msa0141670-mRNA-1
Gene Sequence

>Msa0141670

ATGGCTACACAAGCTCTAGTGTCGTCATCATCTCTTACTTTTGCAGCTGAGGCTGTGAGACAGAGTCTTGGAGCAAGATCACTCCCATCTTCAATAGGGTCTTCTAGAAAAGGTTCCTTTGTTGTCAAGGCAGCTTCTTCTCCTCCTGCCAAGATGAGGGCTCATGGCCTGGAGCTTTTGCTCAACCACGACGATGGAGCTTTTGCTCAACCAGAGACGAGGGCTCATGCCTTAGGAGCTTTTGCTCAATAG

Protein sequence

>Msa0141670

MATQALVSSSSLTFAAEAVRQSLGARSLPSSIGSSRKGSFVVKAASSPPAKMRAHGLELLLNHDDGAFAQPETRAHALGAFAQ*