AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0833690

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0833690 MtrunA17_Chr4g0056141 100.000 62 0 0 1 62 1 62 2.23e-39 123
Msa0833690 MtrunA17_Chr5g0399231 100.000 62 0 0 1 62 1 62 2.23e-39 123
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0833690 AT2G19750.1 95.161 62 3 0 1 62 1 62 6.52e-30 100
Msa0833690 AT5G56670.1 95.161 62 3 0 1 62 1 62 6.52e-30 100
Msa0833690 AT4G29390.1 95.161 62 3 0 1 62 1 62 6.52e-30 100

Find 38 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAACTAAAGCCTAATTTCTT+AGG 0.142531 5_4:-6790951 None:intergenic
TTGTATTGTGGACTTGGGTT+AGG 0.260795 5_4:-6790220 None:intergenic
GTCTTATTCCCTAAGAAATT+AGG 0.272965 5_4:+6790942 Msa0833690:three_prime_UTR
TGCTATTTGTATTGTGGACT+TGG 0.309964 5_4:-6790226 None:intergenic
AAGCTTTAACGAAAATAGTT+TGG 0.328213 5_4:-6790253 None:intergenic
GCTTTGCTACCTTTGGTGTT+TGG 0.335294 5_4:-6790510 None:intergenic
TTTCGTTAAAGCTTCGATTC+TGG 0.348037 5_4:+6790262 Msa0833690:five_prime_UTR
TTGTCTTGCTTTGCTACCTT+TGG 0.348505 5_4:-6790517 None:intergenic
TGTTTGGCCTCTAACCTTAC+CGG 0.358772 5_4:-6790494 None:intergenic
TCTTACTTCTCAGATGAGTT+TGG 0.367396 5_4:-6790731 None:intergenic
TGTATTGTGGACTTGGGTTA+GGG 0.369532 5_4:-6790219 None:intergenic
GTTATTGTAGTTGTTGGATT+CGG 0.405984 5_4:+6790695 Msa0833690:intron
GCCTCTAACCTTACCGGCAC+GGG 0.419662 5_4:-6790488 None:intergenic
AACTAAAGCCTAATTTCTTA+GGG 0.428130 5_4:-6790950 None:intergenic
ATCGTTGGCCCGTGCCGGTA+AGG 0.433030 5_4:+6790480 Msa0833690:CDS
TTAACATATTTCAAAAGCTA+AGG 0.439992 5_4:-6790781 None:intergenic
GCCCGTGCCGGTAAGGTTAG+AGG 0.445776 5_4:+6790487 Msa0833690:CDS
ACGCTTGTGAGCACGGCCAC+GGG 0.451262 5_4:-6790551 None:intergenic
CACGGATCGTTGGCCCGTGC+CGG 0.457604 5_4:+6790475 Msa0833690:CDS
TACGCTTGTGAGCACGGCCA+CGG 0.461093 5_4:-6790552 None:intergenic
CTCTCTCTCTTTAGCTTCTG+CGG 0.475217 5_4:-6790297 None:intergenic
TAACATATTTCAAAAGCTAA+GGG 0.489070 5_4:-6790780 None:intergenic
GGCCTCTAACCTTACCGGCA+CGG 0.499402 5_4:-6790489 None:intergenic
GCTATTTGTATTGTGGACTT+GGG 0.524204 5_4:-6790225 None:intergenic
TCTTTAGCTTCTGCGGCTTG+AGG 0.529758 5_4:-6790290 None:intergenic
TTATATCTGCTGAATAATTG+TGG 0.561819 5_4:+6790992 Msa0833690:three_prime_UTR
ACTGCATACGCTTGTGAGCA+CGG 0.575185 5_4:-6790558 None:intergenic
CGCTTGTGAGCACGGCCACG+GGG 0.579942 5_4:-6790550 None:intergenic
AGGAAAGGTTCACGGATCGT+TGG 0.583409 5_4:+6790465 Msa0833690:intron
TACCGGCAGTGACGAATCTG+CGG 0.585546 5_4:-6790585 None:intergenic
AACCGCAGATTCGTCACTGC+CGG 0.593013 5_4:+6790583 Msa0833690:CDS
GTTGGATTCGGTAAGAAGAG+AGG 0.609691 5_4:+6790707 Msa0833690:CDS
TAATTGTGGTGCGAATTGTA+TGG 0.622953 5_4:+6791006 Msa0833690:three_prime_UTR
AACATATTTCAAAAGCTAAG+GGG 0.626402 5_4:-6790779 None:intergenic
TGCGAATTGTATGGTAGAAG+TGG 0.641711 5_4:+6791015 Msa0833690:three_prime_UTR
GGTTAGAGGCCAAACACCAA+AGG 0.645954 5_4:+6790501 Msa0833690:CDS
TCATCTGAGAAGTAAGATCG+TGG 0.647924 5_4:+6790737 Msa0833690:exon
GACAAGAAGAAGCAGCCCCG+TGG 0.665991 5_4:+6790535 Msa0833690:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAATAAATCTAAAAAATTA+GGG - chr5_4:6790622-6790641 None:intergenic 10.0%
!! ATGAATAAATCTAAAAAATT+AGG - chr5_4:6790623-6790642 None:intergenic 10.0%
!! AAAAAAAAAAAAAAAAAAGG+AGG - chr5_4:6790831-6790850 None:intergenic 10.0%
!! CCAAAAAAAAAAAAAAAAAA+AGG - chr5_4:6790834-6790853 None:intergenic 10.0%
!!! CCTTTTTTTTTTTTTTTTTT+TGG + chr5_4:6790831-6790850 Msa0833690:three_prime_UTR 10.0%
!! TGAATAAATCTAAAAAATTA+GGG - chr5_4:6790622-6790641 None:intergenic 10.0%
!! ATGAATAAATCTAAAAAATT+AGG - chr5_4:6790623-6790642 None:intergenic 10.0%
!! AAAAAAAAAAAAAAAAAAGG+AGG - chr5_4:6790831-6790850 None:intergenic 10.0%
!! CCAAAAAAAAAAAAAAAAAA+AGG - chr5_4:6790834-6790853 None:intergenic 10.0%
!!! CCTTTTTTTTTTTTTTTTTT+TGG + chr5_4:6790831-6790850 Msa0833690:three_prime_UTR 10.0%
!!! ATCTTTTTTTTTTCAATCAT+GGG + chr5_4:6790348-6790367 Msa0833690:exon 15.0%
!!! ATCTTTTTTTTTTCAATCAT+GGG + chr5_4:6790348-6790367 Msa0833690:exon 15.0%
!!! CATCTTTTTTTTTTCAATCA+TGG + chr5_4:6790347-6790366 Msa0833690:exon 20.0%
!! TAACATATTTCAAAAGCTAA+GGG - chr5_4:6790783-6790802 None:intergenic 20.0%
!! TTAACATATTTCAAAAGCTA+AGG - chr5_4:6790784-6790803 None:intergenic 20.0%
!! ATATTTAACTAGCACAAAAA+AGG - chr5_4:6790886-6790905 None:intergenic 20.0%
!!! CATCTTTTTTTTTTCAATCA+TGG + chr5_4:6790347-6790366 Msa0833690:exon 20.0%
!! TAACATATTTCAAAAGCTAA+GGG - chr5_4:6790783-6790802 None:intergenic 20.0%
!! TTAACATATTTCAAAAGCTA+AGG - chr5_4:6790784-6790803 None:intergenic 20.0%
!! ATATTTAACTAGCACAAAAA+AGG - chr5_4:6790886-6790905 None:intergenic 20.0%
!! AAGCTTTAACGAAAATAGTT+TGG - chr5_4:6790256-6790275 None:intergenic 25.0%
!!! ATTCTTGTTATTGTAGTTGT+TGG + chr5_4:6790689-6790708 Msa0833690:intron 25.0%
! AACATATTTCAAAAGCTAAG+GGG - chr5_4:6790782-6790801 None:intergenic 25.0%
! AACTAAAGCCTAATTTCTTA+GGG - chr5_4:6790953-6790972 None:intergenic 25.0%
! TAACTAAAGCCTAATTTCTT+AGG - chr5_4:6790954-6790973 None:intergenic 25.0%
! TTATATCTGCTGAATAATTG+TGG + chr5_4:6790992-6791011 Msa0833690:three_prime_UTR 25.0%
!! AAGCTTTAACGAAAATAGTT+TGG - chr5_4:6790256-6790275 None:intergenic 25.0%
!!! ATTCTTGTTATTGTAGTTGT+TGG + chr5_4:6790689-6790708 Msa0833690:intron 25.0%
! AACATATTTCAAAAGCTAAG+GGG - chr5_4:6790782-6790801 None:intergenic 25.0%
! AACTAAAGCCTAATTTCTTA+GGG - chr5_4:6790953-6790972 None:intergenic 25.0%
! TAACTAAAGCCTAATTTCTT+AGG - chr5_4:6790954-6790973 None:intergenic 25.0%
! TTATATCTGCTGAATAATTG+TGG + chr5_4:6790992-6791011 Msa0833690:three_prime_UTR 25.0%
!!! GGTTTTTGCTATTTGTATTG+TGG - chr5_4:6790235-6790254 None:intergenic 30.0%
!! AACAATGAAATCGATTTTGC+AGG + chr5_4:6790445-6790464 Msa0833690:intron 30.0%
TCTAAAAAATTAGGGTTTCG+AGG - chr5_4:6790614-6790633 None:intergenic 30.0%
GTTATTGTAGTTGTTGGATT+CGG + chr5_4:6790695-6790714 Msa0833690:intron 30.0%
! GTCTTATTCCCTAAGAAATT+AGG + chr5_4:6790942-6790961 Msa0833690:three_prime_UTR 30.0%
!!! GGTTTTTGCTATTTGTATTG+TGG - chr5_4:6790235-6790254 None:intergenic 30.0%
!! AACAATGAAATCGATTTTGC+AGG + chr5_4:6790445-6790464 Msa0833690:intron 30.0%
TCTAAAAAATTAGGGTTTCG+AGG - chr5_4:6790614-6790633 None:intergenic 30.0%
GTTATTGTAGTTGTTGGATT+CGG + chr5_4:6790695-6790714 Msa0833690:intron 30.0%
! GTCTTATTCCCTAAGAAATT+AGG + chr5_4:6790942-6790961 Msa0833690:three_prime_UTR 30.0%
GCTATTTGTATTGTGGACTT+GGG - chr5_4:6790228-6790247 None:intergenic 35.0%
! TGCTATTTGTATTGTGGACT+TGG - chr5_4:6790229-6790248 None:intergenic 35.0%
TTTCGTTAAAGCTTCGATTC+TGG + chr5_4:6790262-6790281 Msa0833690:five_prime_UTR 35.0%
!! TGAAATCGATTTTGCAGGAA+AGG + chr5_4:6790450-6790469 Msa0833690:intron 35.0%
TCTTACTTCTCAGATGAGTT+TGG - chr5_4:6790734-6790753 None:intergenic 35.0%
TAATTGTGGTGCGAATTGTA+TGG + chr5_4:6791006-6791025 Msa0833690:three_prime_UTR 35.0%
GCTATTTGTATTGTGGACTT+GGG - chr5_4:6790228-6790247 None:intergenic 35.0%
! TGCTATTTGTATTGTGGACT+TGG - chr5_4:6790229-6790248 None:intergenic 35.0%
TTTCGTTAAAGCTTCGATTC+TGG + chr5_4:6790262-6790281 Msa0833690:five_prime_UTR 35.0%
!! TGAAATCGATTTTGCAGGAA+AGG + chr5_4:6790450-6790469 Msa0833690:intron 35.0%
TCTTACTTCTCAGATGAGTT+TGG - chr5_4:6790734-6790753 None:intergenic 35.0%
TAATTGTGGTGCGAATTGTA+TGG + chr5_4:6791006-6791025 Msa0833690:three_prime_UTR 35.0%
TGTATTGTGGACTTGGGTTA+GGG - chr5_4:6790222-6790241 None:intergenic 40.0%
TTGTATTGTGGACTTGGGTT+AGG - chr5_4:6790223-6790242 None:intergenic 40.0%
! GATTTTGCAGGAAAGGTTCA+CGG + chr5_4:6790457-6790476 Msa0833690:intron 40.0%
TTGTCTTGCTTTGCTACCTT+TGG - chr5_4:6790520-6790539 None:intergenic 40.0%
! TTAGGGTTTCGAGGTATTAC+CGG - chr5_4:6790605-6790624 None:intergenic 40.0%
TCATCTGAGAAGTAAGATCG+TGG + chr5_4:6790737-6790756 Msa0833690:exon 40.0%
TGCGAATTGTATGGTAGAAG+TGG + chr5_4:6791015-6791034 Msa0833690:three_prime_UTR 40.0%
TGTATTGTGGACTTGGGTTA+GGG - chr5_4:6790222-6790241 None:intergenic 40.0%
TTGTATTGTGGACTTGGGTT+AGG - chr5_4:6790223-6790242 None:intergenic 40.0%
! GATTTTGCAGGAAAGGTTCA+CGG + chr5_4:6790457-6790476 Msa0833690:intron 40.0%
TTGTCTTGCTTTGCTACCTT+TGG - chr5_4:6790520-6790539 None:intergenic 40.0%
! TTAGGGTTTCGAGGTATTAC+CGG - chr5_4:6790605-6790624 None:intergenic 40.0%
TCATCTGAGAAGTAAGATCG+TGG + chr5_4:6790737-6790756 Msa0833690:exon 40.0%
TGCGAATTGTATGGTAGAAG+TGG + chr5_4:6791015-6791034 Msa0833690:three_prime_UTR 40.0%
! CTCTCTCTCTTTAGCTTCTG+CGG - chr5_4:6790300-6790319 None:intergenic 45.0%
TGTTTGGCCTCTAACCTTAC+CGG - chr5_4:6790497-6790516 None:intergenic 45.0%
!! GCTTTGCTACCTTTGGTGTT+TGG - chr5_4:6790513-6790532 None:intergenic 45.0%
! GTTGGATTCGGTAAGAAGAG+AGG + chr5_4:6790707-6790726 Msa0833690:CDS 45.0%
! CTCTCTCTCTTTAGCTTCTG+CGG - chr5_4:6790300-6790319 None:intergenic 45.0%
TGTTTGGCCTCTAACCTTAC+CGG - chr5_4:6790497-6790516 None:intergenic 45.0%
!! GCTTTGCTACCTTTGGTGTT+TGG - chr5_4:6790513-6790532 None:intergenic 45.0%
! GTTGGATTCGGTAAGAAGAG+AGG + chr5_4:6790707-6790726 Msa0833690:CDS 45.0%
!!! CTTTTTTTTTTTTTTTTTTT+GGG + chr5_4:6790832-6790851 Msa0833690:three_prime_UTR 5.0%
!!! CTTTTTTTTTTTTTTTTTTT+GGG + chr5_4:6790832-6790851 Msa0833690:three_prime_UTR 5.0%
! TCTTTAGCTTCTGCGGCTTG+AGG - chr5_4:6790293-6790312 None:intergenic 50.0%
AGGAAAGGTTCACGGATCGT+TGG + chr5_4:6790465-6790484 Msa0833690:intron 50.0%
GGTTAGAGGCCAAACACCAA+AGG + chr5_4:6790501-6790520 Msa0833690:CDS 50.0%
ACTGCATACGCTTGTGAGCA+CGG - chr5_4:6790561-6790580 None:intergenic 50.0%
! TCTTTAGCTTCTGCGGCTTG+AGG - chr5_4:6790293-6790312 None:intergenic 50.0%
AGGAAAGGTTCACGGATCGT+TGG + chr5_4:6790465-6790484 Msa0833690:intron 50.0%
GGTTAGAGGCCAAACACCAA+AGG + chr5_4:6790501-6790520 Msa0833690:CDS 50.0%
ACTGCATACGCTTGTGAGCA+CGG - chr5_4:6790561-6790580 None:intergenic 50.0%
AACCGCAGATTCGTCACTGC+CGG + chr5_4:6790583-6790602 Msa0833690:CDS 55.0%
TACCGGCAGTGACGAATCTG+CGG - chr5_4:6790588-6790607 None:intergenic 55.0%
AACCGCAGATTCGTCACTGC+CGG + chr5_4:6790583-6790602 Msa0833690:CDS 55.0%
TACCGGCAGTGACGAATCTG+CGG - chr5_4:6790588-6790607 None:intergenic 55.0%
GCCTCTAACCTTACCGGCAC+GGG - chr5_4:6790491-6790510 None:intergenic 60.0%
GGCCTCTAACCTTACCGGCA+CGG - chr5_4:6790492-6790511 None:intergenic 60.0%
GACAAGAAGAAGCAGCCCCG+TGG + chr5_4:6790535-6790554 Msa0833690:CDS 60.0%
TACGCTTGTGAGCACGGCCA+CGG - chr5_4:6790555-6790574 None:intergenic 60.0%
GCCTCTAACCTTACCGGCAC+GGG - chr5_4:6790491-6790510 None:intergenic 60.0%
GGCCTCTAACCTTACCGGCA+CGG - chr5_4:6790492-6790511 None:intergenic 60.0%
GACAAGAAGAAGCAGCCCCG+TGG + chr5_4:6790535-6790554 Msa0833690:CDS 60.0%
TACGCTTGTGAGCACGGCCA+CGG - chr5_4:6790555-6790574 None:intergenic 60.0%
! ATCGTTGGCCCGTGCCGGTA+AGG + chr5_4:6790480-6790499 Msa0833690:CDS 65.0%
! GCCCGTGCCGGTAAGGTTAG+AGG + chr5_4:6790487-6790506 Msa0833690:CDS 65.0%
ACGCTTGTGAGCACGGCCAC+GGG - chr5_4:6790554-6790573 None:intergenic 65.0%
! ATCGTTGGCCCGTGCCGGTA+AGG + chr5_4:6790480-6790499 Msa0833690:CDS 65.0%
! GCCCGTGCCGGTAAGGTTAG+AGG + chr5_4:6790487-6790506 Msa0833690:CDS 65.0%
ACGCTTGTGAGCACGGCCAC+GGG - chr5_4:6790554-6790573 None:intergenic 65.0%
CACGGATCGTTGGCCCGTGC+CGG + chr5_4:6790475-6790494 Msa0833690:CDS 70.0%
CGCTTGTGAGCACGGCCACG+GGG - chr5_4:6790553-6790572 None:intergenic 70.0%
CACGGATCGTTGGCCCGTGC+CGG + chr5_4:6790475-6790494 Msa0833690:CDS 70.0%
CGCTTGTGAGCACGGCCACG+GGG - chr5_4:6790553-6790572 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 6790213 6791043 6790213 ID=Msa0833690;Name=Msa0833690
chr5_4 mRNA 6790213 6791043 6790213 ID=Msa0833690-mRNA-1;Parent=Msa0833690;Name=Msa0833690-mRNA-1;_AED=0.01;_eAED=0.01;_QI=153|1|1|1|1|1|3|292|62
chr5_4 exon 6790213 6790369 6790213 ID=Msa0833690-mRNA-1:exon:2991;Parent=Msa0833690-mRNA-1
chr5_4 exon 6790467 6790604 6790467 ID=Msa0833690-mRNA-1:exon:2992;Parent=Msa0833690-mRNA-1
chr5_4 exon 6790705 6791043 6790705 ID=Msa0833690-mRNA-1:exon:2993;Parent=Msa0833690-mRNA-1
chr5_4 five_prime_UTR 6790213 6790365 6790213 ID=Msa0833690-mRNA-1:five_prime_utr;Parent=Msa0833690-mRNA-1
chr5_4 CDS 6790366 6790369 6790366 ID=Msa0833690-mRNA-1:cds;Parent=Msa0833690-mRNA-1
chr5_4 CDS 6790467 6790604 6790467 ID=Msa0833690-mRNA-1:cds;Parent=Msa0833690-mRNA-1
chr5_4 CDS 6790705 6790751 6790705 ID=Msa0833690-mRNA-1:cds;Parent=Msa0833690-mRNA-1
chr5_4 three_prime_UTR 6790752 6791043 6790752 ID=Msa0833690-mRNA-1:three_prime_utr;Parent=Msa0833690-mRNA-1
Gene Sequence

>Msa0833690

ATGGGAAAGGTTCACGGATCGTTGGCCCGTGCCGGTAAGGTTAGAGGCCAAACACCAAAGGTAGCAAAGCAAGACAAGAAGAAGCAGCCCCGTGGCCGTGCTCACAAGCGTATGCAGTACAACCGCAGATTCGTCACTGCCGTTGTTGGATTCGGTAAGAAGAGAGGACCAAACTCATCTGAGAAGTAA
Protein sequence

>Msa0833690

MGKVHGSLARAGKVRGQTPKVAKQDKKKQPRGRAHKRMQYNRRFVTAVVGFGKKRGPNSSEK*