AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene029777

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene029777.t1 MTR_1g063150 64.407 236 25 4 38 271 21 199 3.53e-92 271
MS.gene029777.t1 MTR_1g085590 52.797 286 82 12 6 269 15 269 9.71e-69 214
MS.gene029777.t1 MTR_1g063140 62.011 179 23 5 91 265 1 138 4.40e-58 184
MS.gene029777.t1 MTR_1g046810 44.681 235 67 10 53 242 94 310 3.85e-41 144
MS.gene029777.t1 MTR_1g053530 31.818 176 94 7 72 225 68 239 2.51e-13 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAAGAGAAAGAAGGGTATT+TGG 0.170547 1.2:-48312347 None:intergenic
AATGAAGGTGAAACAGAATT+AGG 0.205798 1.2:+48312940 MS.gene029777:CDS
CTTAGCACTTGCCGTTTCTT+AGG 0.240976 1.2:-48312622 None:intergenic
CTCTTCAATACTTTGATTAG+AGG 0.294988 1.2:-48312908 None:intergenic
TGAATCACCGTGGTGCTAAA+AGG 0.300323 1.2:+48312743 MS.gene029777:CDS
AAAGAGAAAGAAGGGTATTT+GGG 0.313760 1.2:-48312346 None:intergenic
ACTTCTAACAAAGCTTTGAA+TGG 0.400226 1.2:+48312529 MS.gene029777:CDS
ACGGTGATTCAAATTGATAT+TGG 0.408428 1.2:-48312731 None:intergenic
TATATCTCGTGGCGGTTTCG+AGG 0.421737 1.2:+48312699 MS.gene029777:CDS
ATGAAGGTGAAACAGAATTA+GGG 0.423059 1.2:+48312941 MS.gene029777:CDS
TATTCAGTTCCTAATGATGC+TGG 0.435072 1.2:+48312463 MS.gene029777:CDS
TCTTCAACAACTAATGATGC+TGG 0.461941 1.2:+48312412 MS.gene029777:CDS
GAAGCTATGATGAACATGAT+TGG 0.471650 1.2:-48312314 None:intergenic
CTGGAAAACAGAAGATCATA+TGG 0.475072 1.2:+48312431 MS.gene029777:CDS
ATACTTTGATTAGAGGCAGC+AGG 0.495332 1.2:-48312901 None:intergenic
GAAGAGAAGAAGATTAATGA+AGG 0.510676 1.2:+48312925 MS.gene029777:CDS
CTCATGTGATGTTTGCAACA+AGG 0.514548 1.2:+48312501 MS.gene029777:CDS
AATCAATGAAAGAGAAAGAA+GGG 0.516168 1.2:-48312354 None:intergenic
ATATCTCGTGGCGGTTTCGA+GGG 0.521594 1.2:+48312700 MS.gene029777:CDS
ATCTTCCTCTGCAAGCTATG+AGG 0.522500 1.2:+48312585 MS.gene029777:CDS
TATGATGGATGCTAATATGA+TGG 0.534594 1.2:+48312783 MS.gene029777:CDS
TGATATTGAGAAGACGAAGA+AGG 0.543732 1.2:+48312807 MS.gene029777:CDS
TAATCAATGAAAGAGAAAGA+AGG 0.544898 1.2:-48312355 None:intergenic
TCATAGCTTGCAGAGGAAGA+TGG 0.548781 1.2:-48312583 None:intergenic
ACTTTCTACCACCTAAGAAA+CGG 0.555851 1.2:+48312611 MS.gene029777:CDS
TCATCTTCAAAATCATCACT+TGG 0.561254 1.2:-48313069 None:intergenic
AAATTCTTCACATCATCACT+TGG 0.564670 1.2:-48313030 None:intergenic
AGCACTTGCCGTTTCTTAGG+TGG 0.568114 1.2:-48312619 None:intergenic
TATTGCAGCTGAAACTCTGT+TGG 0.580874 1.2:+48312675 MS.gene029777:CDS
AAATTCATCACATCATCACT+TGG 0.595232 1.2:-48313000 None:intergenic
GTGTTGCTAACAAGTGCCAC+AGG 0.600284 1.2:+48312844 MS.gene029777:CDS
GAGGAAGATGGTGCAACAGT+TGG 0.627306 1.2:-48312571 None:intergenic
ACGAAGAAGGAGAAAGAACA+AGG 0.647791 1.2:+48312820 MS.gene029777:CDS
CTGTTGGATATATCTCGTGG+CGG 0.650335 1.2:+48312691 MS.gene029777:CDS
GTGATCCTCATAGCTTGCAG+AGG 0.672732 1.2:-48312590 None:intergenic
ACTCTGTTGGATATATCTCG+TGG 0.678764 1.2:+48312688 MS.gene029777:CDS
AATATCAATTTGAATCACCG+TGG 0.727003 1.2:+48312733 MS.gene029777:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTGGTTTTGTTATGATTA+GGG - chr1.2:48312387-48312406 None:intergenic 20.0%
!!! TTTTTGGTTTTGTTATGATT+AGG - chr1.2:48312388-48312407 None:intergenic 20.0%
! AATCAATGAAAGAGAAAGAA+GGG - chr1.2:48312357-48312376 None:intergenic 25.0%
! TAATCAATGAAAGAGAAAGA+AGG - chr1.2:48312358-48312377 None:intergenic 25.0%
!! AAAACTCTTTTGCAATATGA+TGG + chr1.2:48312768-48312787 MS.gene029777:CDS 25.0%
!! AGTTGTTGAAGAAAAGTTTT+TGG - chr1.2:48312404-48312423 None:intergenic 25.0%
!!! ATTGGTTTTTGGTTTATGAT+CGG - chr1.2:48312299-48312318 None:intergenic 25.0%
AAATTCATCACATCATCACT+TGG - chr1.2:48313003-48313022 None:intergenic 30.0%
AAATTCTTCACATCATCACT+TGG - chr1.2:48313033-48313052 None:intergenic 30.0%
AATATCAATTTGAATCACCG+TGG + chr1.2:48312733-48312752 MS.gene029777:CDS 30.0%
AATGAAGGTGAAACAGAATT+AGG + chr1.2:48312940-48312959 MS.gene029777:CDS 30.0%
ACGGTGATTCAAATTGATAT+TGG - chr1.2:48312734-48312753 None:intergenic 30.0%
ATGAAGGTGAAACAGAATTA+GGG + chr1.2:48312941-48312960 MS.gene029777:CDS 30.0%
CTCTTCAATACTTTGATTAG+AGG - chr1.2:48312911-48312930 None:intergenic 30.0%
GAAGAGAAGAAGATTAATGA+AGG + chr1.2:48312925-48312944 MS.gene029777:CDS 30.0%
TCATCTTCAAAATCATCACT+TGG - chr1.2:48313072-48313091 None:intergenic 30.0%
!! AAAGAGAAAGAAGGGTATTT+GGG - chr1.2:48312349-48312368 None:intergenic 30.0%
!! ACTTCTAACAAAGCTTTGAA+TGG + chr1.2:48312529-48312548 MS.gene029777:CDS 30.0%
!! TATGATGGATGCTAATATGA+TGG + chr1.2:48312783-48312802 MS.gene029777:CDS 30.0%
!!! TGATGAACATGATTGGTTTT+TGG - chr1.2:48312310-48312329 None:intergenic 30.0%
!!! TTTTGGTTTATGATCGGAAA+AGG - chr1.2:48312293-48312312 None:intergenic 30.0%
!!! TTTTGTTTTCCAGCATCATT+AGG - chr1.2:48312475-48312494 None:intergenic 30.0%
ACTTTCTACCACCTAAGAAA+CGG + chr1.2:48312611-48312630 MS.gene029777:CDS 35.0%
CTGGAAAACAGAAGATCATA+TGG + chr1.2:48312431-48312450 MS.gene029777:CDS 35.0%
GAAGCTATGATGAACATGAT+TGG - chr1.2:48312317-48312336 None:intergenic 35.0%
TATTCAGTTCCTAATGATGC+TGG + chr1.2:48312463-48312482 MS.gene029777:CDS 35.0%
TCTTCAACAACTAATGATGC+TGG + chr1.2:48312412-48312431 MS.gene029777:CDS 35.0%
TGATATTGAGAAGACGAAGA+AGG + chr1.2:48312807-48312826 MS.gene029777:CDS 35.0%
TGTTTGAAAAATCATGCCTG+TGG - chr1.2:48312863-48312882 None:intergenic 35.0%
!! GAAAGAGAAAGAAGGGTATT+TGG - chr1.2:48312350-48312369 None:intergenic 35.0%
!!! AAGGGTATTTGGGTTTTTGA+AGG - chr1.2:48312339-48312358 None:intergenic 35.0%
ACGAAGAAGGAGAAAGAACA+AGG + chr1.2:48312820-48312839 MS.gene029777:CDS 40.0%
ACTCTGTTGGATATATCTCG+TGG + chr1.2:48312688-48312707 MS.gene029777:CDS 40.0%
ATACTTTGATTAGAGGCAGC+AGG - chr1.2:48312904-48312923 None:intergenic 40.0%
CTCATGTGATGTTTGCAACA+AGG + chr1.2:48312501-48312520 MS.gene029777:CDS 40.0%
TATTGCAGCTGAAACTCTGT+TGG + chr1.2:48312675-48312694 MS.gene029777:CDS 40.0%
! GTTTTTGCCTTTTAGCACCA+CGG - chr1.2:48312753-48312772 None:intergenic 40.0%
ATCTTCCTCTGCAAGCTATG+AGG + chr1.2:48312585-48312604 MS.gene029777:CDS 45.0%
CTGTTGGATATATCTCGTGG+CGG + chr1.2:48312691-48312710 MS.gene029777:CDS 45.0%
! CTTAGCACTTGCCGTTTCTT+AGG - chr1.2:48312625-48312644 None:intergenic 45.0%
! TCATAGCTTGCAGAGGAAGA+TGG - chr1.2:48312586-48312605 None:intergenic 45.0%
! TGAATCACCGTGGTGCTAAA+AGG + chr1.2:48312743-48312762 MS.gene029777:CDS 45.0%
ATATCTCGTGGCGGTTTCGA+GGG + chr1.2:48312700-48312719 MS.gene029777:CDS 50.0%
GAGGAAGATGGTGCAACAGT+TGG - chr1.2:48312574-48312593 None:intergenic 50.0%
TATATCTCGTGGCGGTTTCG+AGG + chr1.2:48312699-48312718 MS.gene029777:CDS 50.0%
! AGCACTTGCCGTTTCTTAGG+TGG - chr1.2:48312622-48312641 None:intergenic 50.0%
! GTGATCCTCATAGCTTGCAG+AGG - chr1.2:48312593-48312612 None:intergenic 50.0%
! GTGTTGCTAACAAGTGCCAC+AGG + chr1.2:48312844-48312863 MS.gene029777:CDS 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 48312286 48313101 48312286 ID=MS.gene029777
chr1.2 mRNA 48312286 48313101 48312286 ID=MS.gene029777.t1;Parent=MS.gene029777
chr1.2 exon 48312286 48313101 48312286 ID=MS.gene029777.t1.exon1;Parent=MS.gene029777.t1
chr1.2 CDS 48312286 48313101 48312286 ID=cds.MS.gene029777.t1;Parent=MS.gene029777.t1
Gene Sequence

>MS.gene029777

ATGTCCTTTTCCGATCATAAACCAAAAACCAATCATGTTCATCATAGCTTCCTTCAAAAACCCAAATACCCTTCTTTCTCTTTCATTGATTATTCAAACCCTAATCATAACAAAACCAAAAACTTTTCTTCAACAACTAATGATGCTGGAAAACAGAAGATCATATGGTTTTTTTCTTATTCAGTTCCTAATGATGCTGGAAAACAAAAGAAACACTCATGTGATGTTTGCAACAAGGTTTTTACTTCTAACAAAGCTTTGAATGGACATATGATATGTCACTCACCAACTGTTGCACCATCTTCCTCTGCAAGCTATGAGGATCACTTTCTACCACCTAAGAAACGGCAAGTGCTAAGAAGAAGTTATATGAATAATGATGATGATGCTATTGCAGCTGAAACTCTGTTGGATATATCTCGTGGCGGTTTCGAGGGATCAACTACCAATATCAATTTGAATCACCGTGGTGCTAAAAGGCAAAAACTCTTTTGCAATATGATGGATGCTAATATGATGGATGATATTGAGAAGACGAAGAAGGAGAAAGAACAAGGTGTGTTGCTAACAAGTGCCACAGGCATGATTTTTCAAACATCACAAGATTGCAAGCAACCTGCTGCCTCTAATCAAAGTATTGAAGAGAAGAAGATTAATGAAGGTGAAACAGAATTAGGGTCAAAAGTTGTGAAGAATTTTGATTTGAACGAGCTTCCAAGTGATGATGTGATGAATTTTGAGCTTCCAAGTGATGATGTGAAGAATTTTGATTTGAACGAGCTTCCAAGTGATGATTTTGAAGATGAAATCAATTAG
Protein sequence

>MS.gene029777.t1

MSFSDHKPKTNHVHHSFLQKPKYPSFSFIDYSNPNHNKTKNFSSTTNDAGKQKIIWFFSYSVPNDAGKQKKHSCDVCNKVFTSNKALNGHMICHSPTVAPSSSASYEDHFLPPKKRQVLRRSYMNNDDDAIAAETLLDISRGGFEGSTTNINLNHRGAKRQKLFCNMMDANMMDDIEKTKKEKEQGVLLTSATGMIFQTSQDCKQPAASNQSIEEKKINEGETELGSKVVKNFDLNELPSDDVMNFELPSDDVKNFDLNELPSDDFEDEIN