AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1409410


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1409410 MtrunA17_Chr4g0070481 97.596 208 5 0 1 208 1 208 2.95e-149 412
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1409410 AT3G42725.1 47.525 202 99 2 7 207 6 201 4.40e-57 179

Find 43 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCAATAGTTTAGCTTCTTT+TGG 0.129943 tig0023524:+3493 None:intergenic
GAGAAAATGAAAAGCAAATA+TGG 0.232910 tig0023524:-3250 Msa1409410:CDS
TTTGGTAAACAAAGCAAATA+TGG 0.284232 tig0023524:+3555 None:intergenic
TTGGAGGCTTGCATTCTCTT+TGG 0.331209 tig0023524:+3537 None:intergenic
CTTACACTAGCCTCTTTGAT+AGG 0.334310 tig0023524:-3589 Msa1409410:CDS
CCCTTGATGACTTTAACATT+TGG 0.375463 tig0023524:+3518 None:intergenic
TTGCAAGAAAGAGGAGTAGA+AGG 0.398153 tig0023524:-3345 Msa1409410:CDS
AAAATGCCACCAACTTCATT+TGG 0.415049 tig0023524:-3709 Msa1409410:CDS
TTGATGACTTTAACATTTGG+AGG 0.415123 tig0023524:+3521 None:intergenic
TATGTTGCAGTTTGTTGTGT+TGG 0.427873 tig0023524:-3437 Msa1409410:CDS
TGAAATTCAAAGAGCAAAGA+AGG 0.444128 tig0023524:+3779 None:intergenic
TGAAAAGCAAATATGGGCAG+TGG 0.445200 tig0023524:-3243 Msa1409410:CDS
CCCAAAAGAAGCTAAACTAT+TGG 0.454597 tig0023524:-3494 Msa1409410:CDS
CTATCAAAGAGGCTAGTGTA+AGG 0.458593 tig0023524:+3590 None:intergenic
ATTTGGCATGGCATTCCTCA+TGG 0.474932 tig0023524:-3692 Msa1409410:CDS
AGAAAATGAAAAGCAAATAT+GGG 0.492982 tig0023524:-3249 Msa1409410:CDS
TCCAAATGTTAAAGTCATCA+AGG 0.501062 tig0023524:-3519 Msa1409410:CDS
GATTGACGAAATTAAAGATA+AGG 0.504450 tig0023524:-3281 Msa1409410:CDS
AGAACTTGAAGCTGAGAAAG+AGG 0.510711 tig0023524:-3371 Msa1409410:CDS
TATTGGTAAGGCTTGAATGT+GGG 0.529499 tig0023524:-3477 Msa1409410:CDS
AAGAAGCTAAACTATTGGTA+AGG 0.535909 tig0023524:-3489 Msa1409410:CDS
AAGAGGCTATTGCAAGAAAG+AGG 0.537999 tig0023524:-3354 Msa1409410:CDS
GCCACCAACTTCATTTGGCA+TGG 0.540473 tig0023524:-3704 Msa1409410:CDS
ATTGGTAAGGCTTGAATGTG+GGG 0.545428 tig0023524:-3476 Msa1409410:CDS
GCAAAGAAGGAGGACGGTGA+AGG 0.548740 tig0023524:+3792 None:intergenic
AATCTTAGCTACATTTGCAG+TGG 0.558481 tig0023524:+3300 None:intergenic
GAAAAGCAAATATGGGCAGT+GGG 0.567953 tig0023524:-3242 Msa1409410:CDS
AAGGATTTCTAAAGTGCAAG+AGG 0.585321 tig0023524:-3326 Msa1409410:CDS
GAAAATTTGTCCTATCAAAG+AGG 0.589405 tig0023524:+3579 None:intergenic
GAGAATGGTTGGTGCAAATG+AGG 0.594224 tig0023524:+3735 None:intergenic
AATGCCATGCCAAATGAAGT+TGG 0.603497 tig0023524:+3700 None:intergenic
TATCAAAGAGGCTAGTGTAA+GGG 0.605138 tig0023524:+3591 None:intergenic
AGACGAGAAAAGTGAGATGG+TGG 0.612626 tig0023524:+3666 None:intergenic
CCAAATGTTAAAGTCATCAA+GGG 0.626958 tig0023524:-3518 Msa1409410:CDS
CAAAGAGCAAAGAAGGAGGA+CGG 0.630557 tig0023524:+3786 None:intergenic
CTATTGGTAAGGCTTGAATG+TGG 0.636368 tig0023524:-3478 Msa1409410:CDS
TTGTGTAGTGCATAGTTGTG+TGG 0.646229 tig0023524:-3407 Msa1409410:CDS
GAAAGACGAGAAAAGTGAGA+TGG 0.658650 tig0023524:+3663 None:intergenic
TGAGAAAACACAAGTGTGTG+AGG 0.679362 tig0023524:+3623 None:intergenic
AATTCAAAGAGCAAAGAAGG+AGG 0.681520 tig0023524:+3782 None:intergenic
GTGAGATGGTGGAAACCATG+AGG 0.690704 tig0023524:+3677 None:intergenic
GCCATGCCAAATGAAGTTGG+TGG 0.694987 tig0023524:+3703 None:intergenic
GTGCAAATGAGGTAGCACAA+AGG 0.723598 tig0023524:+3746 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAAATGAAAAGCAAATAT+GGG - tig0023524:3793-3812 Msa1409410:CDS 20.0%
! TTTGGTAAACAAAGCAAATA+TGG + tig0023524:3490-3509 None:intergenic 25.0%
! GATTGACGAAATTAAAGATA+AGG - tig0023524:3761-3780 Msa1409410:CDS 25.0%
! GAGAAAATGAAAAGCAAATA+TGG - tig0023524:3792-3811 Msa1409410:CDS 25.0%
TGAAATTCAAAGAGCAAAGA+AGG + tig0023524:3266-3285 None:intergenic 30.0%
GAAAATTTGTCCTATCAAAG+AGG + tig0023524:3466-3485 None:intergenic 30.0%
! TTGATGACTTTAACATTTGG+AGG + tig0023524:3524-3543 None:intergenic 30.0%
TCCAAATGTTAAAGTCATCA+AGG - tig0023524:3523-3542 Msa1409410:CDS 30.0%
CCAAATGTTAAAGTCATCAA+GGG - tig0023524:3524-3543 Msa1409410:CDS 30.0%
!! CCAATAGTTTAGCTTCTTTT+GGG + tig0023524:3551-3570 None:intergenic 30.0%
!! ACCAATAGTTTAGCTTCTTT+TGG + tig0023524:3552-3571 None:intergenic 30.0%
AAGAAGCTAAACTATTGGTA+AGG - tig0023524:3553-3572 Msa1409410:CDS 30.0%
! TGCTTTTCTAATCTTGGAAG+AGG + tig0023524:3226-3245 None:intergenic 35.0%
! GGAACATGCTTTTCTAATCT+TGG + tig0023524:3232-3251 None:intergenic 35.0%
AATTCAAAGAGCAAAGAAGG+AGG + tig0023524:3263-3282 None:intergenic 35.0%
AAAATGCCACCAACTTCATT+TGG - tig0023524:3333-3352 Msa1409410:CDS 35.0%
TATCAAAGAGGCTAGTGTAA+GGG + tig0023524:3454-3473 None:intergenic 35.0%
! CCCTTGATGACTTTAACATT+TGG + tig0023524:3527-3546 None:intergenic 35.0%
CCCAAAAGAAGCTAAACTAT+TGG - tig0023524:3548-3567 Msa1409410:CDS 35.0%
TATTGGTAAGGCTTGAATGT+GGG - tig0023524:3565-3584 Msa1409410:CDS 35.0%
!! TATGTTGCAGTTTGTTGTGT+TGG - tig0023524:3605-3624 Msa1409410:CDS 35.0%
!! AAGGATTTCTAAAGTGCAAG+AGG - tig0023524:3716-3735 Msa1409410:CDS 35.0%
AATCTTAGCTACATTTGCAG+TGG + tig0023524:3745-3764 None:intergenic 35.0%
!!! ATGAAGTTGGTGGCATTTTG+AGG + tig0023524:3332-3351 None:intergenic 40.0%
AATGCCATGCCAAATGAAGT+TGG + tig0023524:3345-3364 None:intergenic 40.0%
GAAAGACGAGAAAAGTGAGA+TGG + tig0023524:3382-3401 None:intergenic 40.0%
!! TCACTTTTCTCGTCTTTCGT+CGG - tig0023524:3384-3403 Msa1409410:CDS 40.0%
TGAGAAAACACAAGTGTGTG+AGG + tig0023524:3422-3441 None:intergenic 40.0%
CTATCAAAGAGGCTAGTGTA+AGG + tig0023524:3455-3474 None:intergenic 40.0%
! CTTACACTAGCCTCTTTGAT+AGG - tig0023524:3453-3472 Msa1409410:CDS 40.0%
CTATTGGTAAGGCTTGAATG+TGG - tig0023524:3564-3583 Msa1409410:CDS 40.0%
ATTGGTAAGGCTTGAATGTG+GGG - tig0023524:3566-3585 Msa1409410:CDS 40.0%
!! CTTGAATGTGGGGTTTTGAT+GGG - tig0023524:3576-3595 Msa1409410:CDS 40.0%
TTGTGTAGTGCATAGTTGTG+TGG - tig0023524:3635-3654 Msa1409410:CDS 40.0%
AGAACTTGAAGCTGAGAAAG+AGG - tig0023524:3671-3690 Msa1409410:CDS 40.0%
AAGAGGCTATTGCAAGAAAG+AGG - tig0023524:3688-3707 Msa1409410:CDS 40.0%
TTGCAAGAAAGAGGAGTAGA+AGG - tig0023524:3697-3716 Msa1409410:CDS 40.0%
TGAAAAGCAAATATGGGCAG+TGG - tig0023524:3799-3818 Msa1409410:CDS 40.0%
GAAAAGCAAATATGGGCAGT+GGG - tig0023524:3800-3819 Msa1409410:CDS 40.0%
CAAAGAGCAAAGAAGGAGGA+CGG + tig0023524:3259-3278 None:intergenic 45.0%
GTGCAAATGAGGTAGCACAA+AGG + tig0023524:3299-3318 None:intergenic 45.0%
! GAGAATGGTTGGTGCAAATG+AGG + tig0023524:3310-3329 None:intergenic 45.0%
!! GGCATTTTGAGGAGAATGGT+TGG + tig0023524:3321-3340 None:intergenic 45.0%
!! TGGTGGCATTTTGAGGAGAA+TGG + tig0023524:3325-3344 None:intergenic 45.0%
ATTTGGCATGGCATTCCTCA+TGG - tig0023524:3350-3369 Msa1409410:CDS 45.0%
AGACGAGAAAAGTGAGATGG+TGG + tig0023524:3379-3398 None:intergenic 45.0%
TTGGAGGCTTGCATTCTCTT+TGG + tig0023524:3508-3527 None:intergenic 45.0%
!! GCTTGAATGTGGGGTTTTGA+TGG - tig0023524:3575-3594 Msa1409410:CDS 45.0%
GCCACCAACTTCATTTGGCA+TGG - tig0023524:3338-3357 Msa1409410:CDS 50.0%
GCCATGCCAAATGAAGTTGG+TGG + tig0023524:3342-3361 None:intergenic 50.0%
!! GTGAGATGGTGGAAACCATG+AGG + tig0023524:3368-3387 None:intergenic 50.0%
GCAAAGAAGGAGGACGGTGA+AGG + tig0023524:3253-3272 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0023524 gene 3219 3845 3219 ID=Msa1409410;Name=Msa1409410
tig0023524 mRNA 3219 3845 3219 ID=Msa1409410-mRNA-1;Parent=Msa1409410;Name=Msa1409410-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|208
tig0023524 exon 3219 3845 3219 ID=Msa1409410-mRNA-1:exon:26033;Parent=Msa1409410-mRNA-1
tig0023524 CDS 3219 3845 3219 ID=Msa1409410-mRNA-1:cds;Parent=Msa1409410-mRNA-1
Gene Sequence

>Msa1409410

ATGGCCTCTTCCAAGATTAGAAAAGCATGTTCCTTCACCGTCCTCCTTCTTTGCTCTTTGAATTTCACACTTTTTATCCTTTGTGCTACCTCATTTGCACCAACCATTCTCCTCAAAATGCCACCAACTTCATTTGGCATGGCATTCCTCATGGTTTCCACCATCTCACTTTTCTCGTCTTTCGTCGGCTTCTATTCACACCTCACACACTTGTGTTTTCTCACTCACATTTCCCTTACACTAGCCTCTTTGATAGGACAAATTTTCACCATATTTGCTTTGTTTACCAAAGAGAATGCAAGCCTCCAAATGTTAAAGTCATCAAGGGACCCAAAAGAAGCTAAACTATTGGTAAGGCTTGAATGTGGGGTTTTGATGGGAATGTGTATGTTGCAGTTTGTTGTGTTGGTGTTGAGTTGTGTAGTGCATAGTTGTGTGGTGAAAGATTATGAAGAACTTGAAGCTGAGAAAGAGGCTATTGCAAGAAAGAGGAGTAGAAGGATTTCTAAAGTGCAAGAGGAATCCACTGCAAATGTAGCTAAGATTGACGAAATTAAAGATAAGGAGTTCGATGAGAAAATGAAAAGCAAATATGGGCAGTGGGTAAAAACTGATTTTGAACCATGA

Protein sequence

>Msa1409410

MASSKIRKACSFTVLLLCSLNFTLFILCATSFAPTILLKMPPTSFGMAFLMVSTISLFSSFVGFYSHLTHLCFLTHISLTLASLIGQIFTIFALFTKENASLQMLKSSRDPKEAKLLVRLECGVLMGMCMLQFVVLVLSCVVHSCVVKDYEELEAEKEAIARKRSRRISKVQEESTANVAKIDEIKDKEFDEKMKSKYGQWVKTDFEP*