AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0696640


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0696640 MtrunA17_Chr4g0049371 93.694 111 7 0 1 111 418 528 1.81e-70 219
Msa0696640 MtrunA17_Chr5g0411431 66.038 106 27 2 1 101 387 488 1.61e-41 142
Msa0696640 MtrunA17_Chr2g0280091 84.722 72 11 0 1 72 390 461 4.37e-40 138
Msa0696640 MtrunA17_Chr2g0280111 60.256 78 20 2 39 111 144 215 5.81e-24 91.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0696640 AT5G64500.1 69.608 102 30 1 1 102 383 483 1.31e-47 159
Msa0696640 AT2G22730.6 81.928 83 15 0 1 83 408 490 2.67e-45 153
Msa0696640 AT2G22730.3 81.928 83 15 0 1 83 434 516 4.04e-45 153
Msa0696640 AT2G22730.7 84.507 71 11 0 1 71 323 393 1.70e-39 136
Msa0696640 AT2G22730.1 84.507 71 11 0 1 71 408 478 5.21e-39 136
Msa0696640 AT2G22730.2 84.507 71 11 0 1 71 434 504 1.05e-38 135
Msa0696640 AT5G65687.1 66.667 81 27 0 1 81 389 469 3.45e-35 125

Find 33 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAGCTGCAATATGGTTTAT+TGG 0.232883 4_4:-66592464 Msa0696640:intron
GTTCCTTCCGCGCCTCTTGT+TGG 0.325321 4_4:-66592654 Msa0696640:CDS
ATGTTTATGTTTCACCATCT+TGG 0.336990 4_4:-66591762 Msa0696640:three_prime_UTR
TGCTTGAAGATATTACAAAA+AGG 0.368513 4_4:+66592172 None:intergenic
CATCAAAAGATATTACAAAA+AGG 0.379177 4_4:+66591939 None:intergenic
TGTTTATGTTTCACCATCTT+GGG 0.390266 4_4:-66591761 Msa0696640:three_prime_UTR
GCCTCTTGTTGGAGTTGTCC+AGG 0.411072 4_4:-66592643 Msa0696640:intron
GGTTAACCTTCTTGGGATTG+AGG 0.418224 4_4:+66592193 None:intergenic
CATCATGTATCAAATGTAGA+AGG 0.434075 4_4:-66592256 Msa0696640:CDS
ATTGATAGTGGCCTCAAACT+TGG 0.439716 4_4:+66592714 None:intergenic
CACAGGATCATATTAACAAC+TGG 0.443858 4_4:-66592526 Msa0696640:intron
TATATGTTTGTATATGCAAT+CGG 0.472667 4_4:-66592080 Msa0696640:three_prime_UTR
AAAGTGCTGGACACACGTTT+AGG 0.477991 4_4:-66592057 Msa0696640:three_prime_UTR
AAGTTTGAGGCCACTATCAA+TGG 0.484428 4_4:-66592712 Msa0696640:CDS
CATGTCTTCTCTTCAAGCAA+TGG 0.487785 4_4:+66592140 None:intergenic
GTAGACATAGCCATTGATAG+TGG 0.500369 4_4:+66592702 None:intergenic
CTCTTCAAGCAATGGTGCTG+TGG 0.501555 4_4:+66592148 None:intergenic
CTCTTCAAGCAACGGCGCAG+TGG 0.528433 4_4:+66592228 None:intergenic
ATGGAGACATACATAATTCA+CGG 0.540315 4_4:+66592746 None:intergenic
TTCTTGGGATTGAGGTTCTG+CGG 0.555513 4_4:+66592201 None:intergenic
ACTCCAACAAGAGGCGCGGA+AGG 0.560727 4_4:+66592651 None:intergenic
TTTACATGATGTGCCCAAGA+TGG 0.580075 4_4:+66591748 None:intergenic
ATAAACCATATTGCAGCTGT+AGG 0.595782 4_4:+66592467 None:intergenic
GCGGTCTTCTCTTCAAGCAA+CGG 0.597251 4_4:+66592220 None:intergenic
TATATGCAATCGGAAAGTGC+TGG 0.605386 4_4:-66592070 Msa0696640:three_prime_UTR
ATTGTGTTAAGCCAAGTTTG+AGG 0.607042 4_4:-66592725 Msa0696640:CDS
TGGAGACATACATAATTCAC+GGG 0.613940 4_4:+66592747 None:intergenic
ACCTGGACAACTCCAACAAG+AGG 0.626399 4_4:+66592642 None:intergenic
TCAAACTTGGCTTAACACAA+TGG 0.635878 4_4:+66592727 None:intergenic
GCAGAACCTCAATCCCAAGA+AGG 0.639701 4_4:-66592199 Msa0696640:CDS
GACAACTCCAACAAGAGGCG+CGG 0.651802 4_4:+66592647 None:intergenic
AATGTACGAAACAAACTACG+TGG 0.765297 4_4:+66591911 None:intergenic
TATTGTTGTTAGAATCAACG+CGG 0.775609 4_4:+66592496 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATATGTTTGTATATGCAAT+CGG - chr4_4:66592390-66592409 Msa0696640:intron 20.0%
!! AAAAAGGTTAATAGTATGTT+TGG + chr4_4:66592518-66592537 None:intergenic 20.0%
!! CATCAAAAGATATTACAAAA+AGG + chr4_4:66592534-66592553 None:intergenic 20.0%
!!! CTTTTTGTAATATCTTTTGA+TGG - chr4_4:66592532-66592551 Msa0696640:intron 20.0%
!! TATATGTTTGTATATGCAAT+CGG - chr4_4:66592390-66592409 Msa0696640:intron 20.0%
!! AAAAAGGTTAATAGTATGTT+TGG + chr4_4:66592518-66592537 None:intergenic 20.0%
!! CATCAAAAGATATTACAAAA+AGG + chr4_4:66592534-66592553 None:intergenic 20.0%
!!! CTTTTTGTAATATCTTTTGA+TGG - chr4_4:66592532-66592551 Msa0696640:intron 20.0%
!! ACTGTAGCTATTCATATTTT+CGG - chr4_4:66591789-66591808 Msa0696640:three_prime_UTR 25.0%
! TGCTTGAAGATATTACAAAA+AGG + chr4_4:66592301-66592320 None:intergenic 25.0%
!!! ATATTTTTGCTTTTGCTTAG+TGG - chr4_4:66592644-66592663 Msa0696640:CDS 25.0%
!! ACTGTAGCTATTCATATTTT+CGG - chr4_4:66591789-66591808 Msa0696640:three_prime_UTR 25.0%
! TGCTTGAAGATATTACAAAA+AGG + chr4_4:66592301-66592320 None:intergenic 25.0%
!!! ATATTTTTGCTTTTGCTTAG+TGG - chr4_4:66592644-66592663 Msa0696640:CDS 25.0%
ATGGAGACATACATAATTCA+CGG + chr4_4:66591727-66591746 None:intergenic 30.0%
CATACAGTACAATATTCTGA+TGG - chr4_4:66591909-66591928 Msa0696640:three_prime_UTR 30.0%
! TATTGTTGTTAGAATCAACG+CGG + chr4_4:66591977-66591996 None:intergenic 30.0%
TGTAGCATCATATAATAGCA+TGG - chr4_4:66592091-66592110 Msa0696640:three_prime_UTR 30.0%
ACTATGCAAAAATATTCCTG+TGG + chr4_4:66592167-66592186 None:intergenic 30.0%
!! AGGAATATTTTTGCATAGTG+TGG - chr4_4:66592168-66592187 Msa0696640:three_prime_UTR 30.0%
CATCATGTATCAAATGTAGA+AGG - chr4_4:66592214-66592233 Msa0696640:CDS 30.0%
ACAAAAAGGTTAACCTTCTT+GGG + chr4_4:66592287-66592306 None:intergenic 30.0%
TACAAAAAGGTTAACCTTCT+TGG + chr4_4:66592288-66592307 None:intergenic 30.0%
TCAGAAAAAACACGTCAAAA+AGG - chr4_4:66592457-66592476 Msa0696640:intron 30.0%
! AAAACACGTCAAAAAGGTTT+TGG - chr4_4:66592463-66592482 Msa0696640:intron 30.0%
! AAACACGTCAAAAAGGTTTT+GGG - chr4_4:66592464-66592483 Msa0696640:intron 30.0%
ATGTTTATGTTTCACCATCT+TGG - chr4_4:66592708-66592727 Msa0696640:CDS 30.0%
TGTTTATGTTTCACCATCTT+GGG - chr4_4:66592709-66592728 Msa0696640:CDS 30.0%
ATGGAGACATACATAATTCA+CGG + chr4_4:66591727-66591746 None:intergenic 30.0%
CATACAGTACAATATTCTGA+TGG - chr4_4:66591909-66591928 Msa0696640:three_prime_UTR 30.0%
! TATTGTTGTTAGAATCAACG+CGG + chr4_4:66591977-66591996 None:intergenic 30.0%
TGTAGCATCATATAATAGCA+TGG - chr4_4:66592091-66592110 Msa0696640:three_prime_UTR 30.0%
ACTATGCAAAAATATTCCTG+TGG + chr4_4:66592167-66592186 None:intergenic 30.0%
!! AGGAATATTTTTGCATAGTG+TGG - chr4_4:66592168-66592187 Msa0696640:three_prime_UTR 30.0%
CATCATGTATCAAATGTAGA+AGG - chr4_4:66592214-66592233 Msa0696640:CDS 30.0%
ACAAAAAGGTTAACCTTCTT+GGG + chr4_4:66592287-66592306 None:intergenic 30.0%
TACAAAAAGGTTAACCTTCT+TGG + chr4_4:66592288-66592307 None:intergenic 30.0%
TCAGAAAAAACACGTCAAAA+AGG - chr4_4:66592457-66592476 Msa0696640:intron 30.0%
! AAAACACGTCAAAAAGGTTT+TGG - chr4_4:66592463-66592482 Msa0696640:intron 30.0%
! AAACACGTCAAAAAGGTTTT+GGG - chr4_4:66592464-66592483 Msa0696640:intron 30.0%
ATGTTTATGTTTCACCATCT+TGG - chr4_4:66592708-66592727 Msa0696640:CDS 30.0%
TGTTTATGTTTCACCATCTT+GGG - chr4_4:66592709-66592728 Msa0696640:CDS 30.0%
TGGAGACATACATAATTCAC+GGG + chr4_4:66591726-66591745 None:intergenic 35.0%
TCAAACTTGGCTTAACACAA+TGG + chr4_4:66591746-66591765 None:intergenic 35.0%
ATTGTGTTAAGCCAAGTTTG+AGG - chr4_4:66591745-66591764 Msa0696640:three_prime_UTR 35.0%
! TTGTCCAGGTTAGCATTTTT+AGG - chr4_4:66591841-66591860 Msa0696640:three_prime_UTR 35.0%
TACACCTAAAAATGCTAACC+TGG + chr4_4:66591848-66591867 None:intergenic 35.0%
ACAGTACAATATTCTGATGG+CGG - chr4_4:66591912-66591931 Msa0696640:three_prime_UTR 35.0%
CACAGGATCATATTAACAAC+TGG - chr4_4:66591944-66591963 Msa0696640:three_prime_UTR 35.0%
! TTTTTCCTACAGCTGCAATA+TGG - chr4_4:66591998-66592017 Msa0696640:three_prime_UTR 35.0%
ATAAACCATATTGCAGCTGT+AGG + chr4_4:66592006-66592025 None:intergenic 35.0%
ACAGCTGCAATATGGTTTAT+TGG - chr4_4:66592006-66592025 Msa0696640:three_prime_UTR 35.0%
GGTTTATTGGTAAGTCATCA+TGG - chr4_4:66592019-66592038 Msa0696640:three_prime_UTR 35.0%
AATGTACGAAACAAACTACG+TGG + chr4_4:66592562-66592581 None:intergenic 35.0%
!! TTGCTTTTGCTTAGTGGAAA+TGG - chr4_4:66592650-66592669 Msa0696640:CDS 35.0%
TGGAGACATACATAATTCAC+GGG + chr4_4:66591726-66591745 None:intergenic 35.0%
TCAAACTTGGCTTAACACAA+TGG + chr4_4:66591746-66591765 None:intergenic 35.0%
ATTGTGTTAAGCCAAGTTTG+AGG - chr4_4:66591745-66591764 Msa0696640:three_prime_UTR 35.0%
! TTGTCCAGGTTAGCATTTTT+AGG - chr4_4:66591841-66591860 Msa0696640:three_prime_UTR 35.0%
TACACCTAAAAATGCTAACC+TGG + chr4_4:66591848-66591867 None:intergenic 35.0%
ACAGTACAATATTCTGATGG+CGG - chr4_4:66591912-66591931 Msa0696640:three_prime_UTR 35.0%
CACAGGATCATATTAACAAC+TGG - chr4_4:66591944-66591963 Msa0696640:three_prime_UTR 35.0%
! TTTTTCCTACAGCTGCAATA+TGG - chr4_4:66591998-66592017 Msa0696640:three_prime_UTR 35.0%
ATAAACCATATTGCAGCTGT+AGG + chr4_4:66592006-66592025 None:intergenic 35.0%
ACAGCTGCAATATGGTTTAT+TGG - chr4_4:66592006-66592025 Msa0696640:three_prime_UTR 35.0%
GGTTTATTGGTAAGTCATCA+TGG - chr4_4:66592019-66592038 Msa0696640:three_prime_UTR 35.0%
AATGTACGAAACAAACTACG+TGG + chr4_4:66592562-66592581 None:intergenic 35.0%
!! TTGCTTTTGCTTAGTGGAAA+TGG - chr4_4:66592650-66592669 Msa0696640:CDS 35.0%
!! ATTGATAGTGGCCTCAAACT+TGG + chr4_4:66591759-66591778 None:intergenic 40.0%
! AAGTTTGAGGCCACTATCAA+TGG - chr4_4:66591758-66591777 Msa0696640:three_prime_UTR 40.0%
GTAGACATAGCCATTGATAG+TGG + chr4_4:66591771-66591790 None:intergenic 40.0%
TCATGATACTTTGTTGCCAC+AGG - chr4_4:66592148-66592167 Msa0696640:three_prime_UTR 40.0%
CATGTCTTCTCTTCAAGCAA+TGG + chr4_4:66592333-66592352 None:intergenic 40.0%
! TATATGCAATCGGAAAGTGC+TGG - chr4_4:66592400-66592419 Msa0696640:intron 40.0%
TTTACATGATGTGCCCAAGA+TGG + chr4_4:66592725-66592744 None:intergenic 40.0%
!! ATTGATAGTGGCCTCAAACT+TGG + chr4_4:66591759-66591778 None:intergenic 40.0%
! AAGTTTGAGGCCACTATCAA+TGG - chr4_4:66591758-66591777 Msa0696640:three_prime_UTR 40.0%
GTAGACATAGCCATTGATAG+TGG + chr4_4:66591771-66591790 None:intergenic 40.0%
TCATGATACTTTGTTGCCAC+AGG - chr4_4:66592148-66592167 Msa0696640:three_prime_UTR 40.0%
CATGTCTTCTCTTCAAGCAA+TGG + chr4_4:66592333-66592352 None:intergenic 40.0%
! TATATGCAATCGGAAAGTGC+TGG - chr4_4:66592400-66592419 Msa0696640:intron 40.0%
TTTACATGATGTGCCCAAGA+TGG + chr4_4:66592725-66592744 None:intergenic 40.0%
TTCTTGGGATTGAGGTTCTG+CGG + chr4_4:66592272-66592291 None:intergenic 45.0%
GGTTAACCTTCTTGGGATTG+AGG + chr4_4:66592280-66592299 None:intergenic 45.0%
!! AAAGTGCTGGACACACGTTT+AGG - chr4_4:66592413-66592432 Msa0696640:intron 45.0%
TACATAATTCACGGGACCCT+GGG + chr4_4:66591718-66591737 None:intergenic 45.0%
ATACATAATTCACGGGACCC+TGG + chr4_4:66591719-66591738 None:intergenic 45.0%
TTCTTGGGATTGAGGTTCTG+CGG + chr4_4:66592272-66592291 None:intergenic 45.0%
GGTTAACCTTCTTGGGATTG+AGG + chr4_4:66592280-66592299 None:intergenic 45.0%
!! AAAGTGCTGGACACACGTTT+AGG - chr4_4:66592413-66592432 Msa0696640:intron 45.0%
ACCTGGACAACTCCAACAAG+AGG + chr4_4:66591831-66591850 None:intergenic 50.0%
GCGGTCTTCTCTTCAAGCAA+CGG + chr4_4:66592253-66592272 None:intergenic 50.0%
GCAGAACCTCAATCCCAAGA+AGG - chr4_4:66592271-66592290 Msa0696640:CDS 50.0%
! CTCTTCAAGCAATGGTGCTG+TGG + chr4_4:66592325-66592344 None:intergenic 50.0%
ACCTGGACAACTCCAACAAG+AGG + chr4_4:66591831-66591850 None:intergenic 50.0%
GCGGTCTTCTCTTCAAGCAA+CGG + chr4_4:66592253-66592272 None:intergenic 50.0%
GCAGAACCTCAATCCCAAGA+AGG - chr4_4:66592271-66592290 Msa0696640:CDS 50.0%
! CTCTTCAAGCAATGGTGCTG+TGG + chr4_4:66592325-66592344 None:intergenic 50.0%
GACAACTCCAACAAGAGGCG+CGG + chr4_4:66591826-66591845 None:intergenic 55.0%
GCCTCTTGTTGGAGTTGTCC+AGG - chr4_4:66591827-66591846 Msa0696640:three_prime_UTR 55.0%
GACAACTCCAACAAGAGGCG+CGG + chr4_4:66591826-66591845 None:intergenic 55.0%
GCCTCTTGTTGGAGTTGTCC+AGG - chr4_4:66591827-66591846 Msa0696640:three_prime_UTR 55.0%
GTTCCTTCCGCGCCTCTTGT+TGG - chr4_4:66591816-66591835 Msa0696640:three_prime_UTR 60.0%
! ACTCCAACAAGAGGCGCGGA+AGG + chr4_4:66591822-66591841 None:intergenic 60.0%
! GATGGCGGCTCTATGCACAC+AGG - chr4_4:66591927-66591946 Msa0696640:three_prime_UTR 60.0%
CTCTTCAAGCAACGGCGCAG+TGG + chr4_4:66592245-66592264 None:intergenic 60.0%
GTTCCTTCCGCGCCTCTTGT+TGG - chr4_4:66591816-66591835 Msa0696640:three_prime_UTR 60.0%
! ACTCCAACAAGAGGCGCGGA+AGG + chr4_4:66591822-66591841 None:intergenic 60.0%
! GATGGCGGCTCTATGCACAC+AGG - chr4_4:66591927-66591946 Msa0696640:three_prime_UTR 60.0%
CTCTTCAAGCAACGGCGCAG+TGG + chr4_4:66592245-66592264 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 66591717 66592775 66591717 ID=Msa0696640;Name=Msa0696640
chr4_4 mRNA 66591717 66592775 66591717 ID=Msa0696640-mRNA-1;Parent=Msa0696640;Name=Msa0696640-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|1|0.66|1|1|1|3|478|112
chr4_4 exon 66591717 66592322 66591717 ID=Msa0696640-mRNA-1:exon:19401;Parent=Msa0696640-mRNA-1
chr4_4 exon 66592465 66592543 66592465 ID=Msa0696640-mRNA-1:exon:19400;Parent=Msa0696640-mRNA-1
chr4_4 exon 66592644 66592775 66592644 ID=Msa0696640-mRNA-1:exon:19399;Parent=Msa0696640-mRNA-1
chr4_4 CDS 66592644 66592775 66592644 ID=Msa0696640-mRNA-1:cds;Parent=Msa0696640-mRNA-1
chr4_4 CDS 66592465 66592543 66592465 ID=Msa0696640-mRNA-1:cds;Parent=Msa0696640-mRNA-1
chr4_4 CDS 66592195 66592322 66592195 ID=Msa0696640-mRNA-1:cds;Parent=Msa0696640-mRNA-1
chr4_4 three_prime_UTR 66591717 66592194 66591717 ID=Msa0696640-mRNA-1:three_prime_utr;Parent=Msa0696640-mRNA-1
Gene Sequence

>Msa0696640

CAGGGTCCCGTGAATTATGTATGTCTCCATTGTGTTAAGCCAAGTTTGAGGCCACTATCAATGGCTATGTCTACTGTAGCTATTCATATTTTCGGAGATGTTCCTTCCGCGCCTCTTGTTGGAGTTGTCCAGGATCATATTAACAACTGGAGAACTACCGCGTTGATTCTAACAACAATATTTTTTCCTACAGCTGCAATATGGTTTATTGGAATATTTTTGCATAGTGTGGATAAATTTAATGAAGAGAGTGAGCATCATGTATCAAATGTAGAAGGAACAACCACTGCGCCGTTGCTTGAAGAGAAGACCGCAGAACCTCAATCCCAAGAAGGTTAA

Protein sequence

>Msa0696640

QGPVNYVCLHCVKPSLRPLSMAMSTVAIHIFGDVPSAPLVGVVQDHINNWRTTALILTTIFFPTAAIWFIGIFLHSVDKFNEESEHHVSNVEGTTTAPLLEEKTAEPQSQEG*