AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene032201

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene032201.t1 MTR_4g123470 28.261 184 132 0 51 234 27 210 5.28e-22 91.3
MS.gene032201.t1 MTR_0014s0220 25.263 190 125 4 50 239 641 813 4.67e-13 68.9
MS.gene032201.t1 MTR_1g054495 22.613 199 153 1 51 249 24 221 1.03e-12 65.9
MS.gene032201.t1 MTR_4g085790 23.618 199 151 1 51 249 24 221 1.56e-11 62.4
MS.gene032201.t1 MTR_7g025150 23.000 200 153 1 50 249 23 221 2.18e-11 62.0
MS.gene032201.t1 MTR_4g053550 40.541 74 44 0 49 122 45 118 7.62e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 54 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGACACTGAACATTGAATT+TGG 0.191641 2.3:+4277280 MS.gene032201:intron
ACAAATGTGATGTACTAATA+AGG 0.256110 2.3:+4277365 MS.gene032201:CDS
AATGATCTTTATGAAGTTCT+TGG 0.265359 2.3:+4277033 MS.gene032201:CDS
CAAATGTAATGAAGGTTTCT+AGG 0.290265 2.3:+4277500 MS.gene032201:CDS
ATTGCTAAACATAAAATAAT+AGG 0.310278 2.3:-4276782 None:intergenic
ATGATCTTTATGAAGTTCTT+GGG 0.324200 2.3:+4277034 MS.gene032201:CDS
TGATAACCTGCAGCCATATA+AGG 0.324757 2.3:-4277175 None:intergenic
AATGATCTTAACTCCTTATA+TGG 0.327626 2.3:+4277162 MS.gene032201:CDS
TAAATTCTCTTCCAAGTTTG+TGG 0.333428 2.3:-4276892 None:intergenic
GAACTTAACTTTGTGTCTAT+AGG 0.374145 2.3:-4276933 None:intergenic
GTCCACGAAATGCAGTGAAT+TGG 0.385092 2.3:-4277069 None:intergenic
TCAAGGACTCATAGGGATAA+TGG 0.395623 2.3:+4276719 MS.gene032201:CDS
GATCAACTTCAAGGACTCAT+AGG 0.397052 2.3:+4276711 MS.gene032201:CDS
TAAGCTTAAGTTTAAGTTTG+TGG 0.399998 2.3:+4277465 MS.gene032201:CDS
GAGTTAAGATCATTTCATAA+TGG 0.420070 2.3:-4277153 None:intergenic
GGTGATTACATTAGAAGCTC+AGG 0.428748 2.3:+4277301 MS.gene032201:CDS
TTCTCTGCTATTAATATGTA+TGG 0.435001 2.3:+4277325 MS.gene032201:CDS
TTCCAATTCACTGCATTTCG+TGG 0.438395 2.3:+4277067 MS.gene032201:CDS
CAAATGTGATGTACTAATAA+GGG 0.442101 2.3:+4277366 MS.gene032201:CDS
TATGGCTGCAGGTTATCAAT+TGG 0.445570 2.3:+4277180 MS.gene032201:CDS
CTGAGGGACGGATCAACTTA+AGG 0.448111 2.3:+4276984 MS.gene032201:CDS
GTTGTTATCAATACAATGTC+TGG 0.455307 2.3:+4276683 None:intergenic
TTAACTCCTTATATGGCTGC+AGG 0.483063 2.3:+4277169 MS.gene032201:CDS
ATTAATATGTATGGACCTAC+AGG 0.484413 2.3:+4277334 MS.gene032201:CDS
CTGGTGGTGGATCAACTTCA+AGG 0.486585 2.3:+4276702 MS.gene032201:CDS
TGTAAAGACAATGGATTCCA+TGG 0.503947 2.3:+4277436 MS.gene032201:CDS
CACTTACAAGCAAGGAATTG+AGG 0.515012 2.3:+4277123 MS.gene032201:CDS
AAGTACATCAAATGTAATGA+AGG 0.524181 2.3:+4277492 MS.gene032201:CDS
ATGTCAACTCATTGCCATCA+TGG 0.539340 2.3:+4277098 MS.gene032201:CDS
ATATCTCATTTACAACCGTA+TGG 0.539468 2.3:+4276836 MS.gene032201:CDS
ATCCGTCCCTCAGTCAGAAG+TGG 0.551673 2.3:-4276974 None:intergenic
AAGACAATGGATTCCATGGT+GGG 0.554852 2.3:+4277440 MS.gene032201:CDS
ATCAATACAATGTCTGGTGG+TGG 0.560856 2.3:+4276689 None:intergenic
TGATCTTTATGAAGTTCTTG+GGG 0.561506 2.3:+4277035 MS.gene032201:CDS
TGCTTGTAAGTGTGCCATGA+TGG 0.567390 2.3:-4277112 None:intergenic
ATAAAATGCTCAACAAAGGA+AGG 0.574317 2.3:-4276869 None:intergenic
CAACAAAGATTGACAGTGGG+TGG 0.577374 2.3:+4277404 MS.gene032201:CDS
CATTTGTACTCGGTGCCTGT+AGG 0.588159 2.3:-4277349 None:intergenic
TAGTACATCACATTTGTACT+CGG 0.590498 2.3:-4277359 None:intergenic
TGTGATGTACTAATAAGGGA+TGG 0.597036 2.3:+4277370 MS.gene032201:CDS
TGAACATCCACTTCTGACTG+AGG 0.599795 2.3:+4276967 MS.gene032201:CDS
ATCAACTTCAAGGACTCATA+GGG 0.600193 2.3:+4276712 MS.gene032201:CDS
ATCCACTTCTGACTGAGGGA+CGG 0.606860 2.3:+4276972 MS.gene032201:CDS
GAAGGTCTAATCTCTCCATA+CGG 0.615379 2.3:-4276851 None:intergenic
GTGGATAAAATGCTCAACAA+AGG 0.618303 2.3:-4276873 None:intergenic
ACTTAAGCTTATCCCCACCA+TGG 0.632346 2.3:-4277453 None:intergenic
AAAGACAATGGATTCCATGG+TGG 0.635851 2.3:+4277439 MS.gene032201:CDS
AGACAATGGATTCCATGGTG+GGG 0.640570 2.3:+4277441 MS.gene032201:CDS
TCATGGCACACTTACAAGCA+AGG 0.641070 2.3:+4277115 MS.gene032201:CDS
GAACATCCACTTCTGACTGA+GGG 0.646274 2.3:+4276968 MS.gene032201:CDS
AAGGCAACAAAGATTGACAG+TGG 0.667273 2.3:+4277400 MS.gene032201:CDS
TACTGCTTATATCATCAATG+AGG 0.679458 2.3:+4276751 MS.gene032201:CDS
AGGCAACAAAGATTGACAGT+GGG 0.681607 2.3:+4277401 MS.gene032201:CDS
GTTATCAATACAATGTCTGG+TGG 0.684260 2.3:+4276686 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTGCTAAACATAAAATAAT+AGG - chr2.3:4276785-4276804 None:intergenic 15.0%
!!! AACAAATTTTGTAAAGACAA+TGG + chr2.3:4277427-4277446 MS.gene032201:CDS 20.0%
! AAGTACATCAAATGTAATGA+AGG + chr2.3:4277492-4277511 MS.gene032201:CDS 25.0%
! AATGATCTTAACTCCTTATA+TGG + chr2.3:4277162-4277181 MS.gene032201:CDS 25.0%
! AATGATCTTTATGAAGTTCT+TGG + chr2.3:4277033-4277052 MS.gene032201:CDS 25.0%
! ACAAATGTGATGTACTAATA+AGG + chr2.3:4277365-4277384 MS.gene032201:CDS 25.0%
! ATGATCTTTATGAAGTTCTT+GGG + chr2.3:4277034-4277053 MS.gene032201:CDS 25.0%
! CAAATGTGATGTACTAATAA+GGG + chr2.3:4277366-4277385 MS.gene032201:CDS 25.0%
! GAGTTAAGATCATTTCATAA+TGG - chr2.3:4277156-4277175 None:intergenic 25.0%
! TTCTCTGCTATTAATATGTA+TGG + chr2.3:4277325-4277344 MS.gene032201:CDS 25.0%
!! ATCAACTTAAGGAAGTTTTA+TGG + chr2.3:4276995-4277014 MS.gene032201:CDS 25.0%
!! TAAGCTTAAGTTTAAGTTTG+TGG + chr2.3:4277465-4277484 MS.gene032201:CDS 25.0%
!! TAGAGATGTATCATTTTAGA+AGG - chr2.3:4277221-4277240 None:intergenic 25.0%
AATAAGGGATGGAAAAAAGA+AGG + chr2.3:4277381-4277400 MS.gene032201:CDS 30.0%
ATAAAATGCTCAACAAAGGA+AGG - chr2.3:4276872-4276891 None:intergenic 30.0%
ATATCTCATTTACAACCGTA+TGG + chr2.3:4276836-4276855 MS.gene032201:CDS 30.0%
ATTAATATGTATGGACCTAC+AGG + chr2.3:4277334-4277353 MS.gene032201:CDS 30.0%
CAAATGTAATGAAGGTTTCT+AGG + chr2.3:4277500-4277519 MS.gene032201:CDS 30.0%
GAACTTAACTTTGTGTCTAT+AGG - chr2.3:4276936-4276955 None:intergenic 30.0%
TAAATTCTCTTCCAAGTTTG+TGG - chr2.3:4276895-4276914 None:intergenic 30.0%
TACTGCTTATATCATCAATG+AGG + chr2.3:4276751-4276770 MS.gene032201:CDS 30.0%
TAGTACATCACATTTGTACT+CGG - chr2.3:4277362-4277381 None:intergenic 30.0%
TGATCTTTATGAAGTTCTTG+GGG + chr2.3:4277035-4277054 MS.gene032201:CDS 30.0%
!! ACTTAAGGAAGTTTTATGGT+TGG + chr2.3:4276999-4277018 MS.gene032201:CDS 30.0%
!! ATCATTTTAGAAGGAGTTGT+TGG - chr2.3:4277212-4277231 None:intergenic 30.0%
ATCAACTTCAAGGACTCATA+GGG + chr2.3:4276712-4276731 MS.gene032201:CDS 35.0%
CAGACACTGAACATTGAATT+TGG + chr2.3:4277280-4277299 MS.gene032201:intron 35.0%
GTGGATAAAATGCTCAACAA+AGG - chr2.3:4276876-4276895 None:intergenic 35.0%
TGTGATGTACTAATAAGGGA+TGG + chr2.3:4277370-4277389 MS.gene032201:CDS 35.0%
! GAGCATTTTATCCACAAACT+TGG + chr2.3:4276881-4276900 MS.gene032201:CDS 35.0%
! TGTAAAGACAATGGATTCCA+TGG + chr2.3:4277436-4277455 MS.gene032201:CDS 35.0%
AAGGCAACAAAGATTGACAG+TGG + chr2.3:4277400-4277419 MS.gene032201:CDS 40.0%
AGGCAACAAAGATTGACAGT+GGG + chr2.3:4277401-4277420 MS.gene032201:CDS 40.0%
ATGTCAACTCATTGCCATCA+TGG + chr2.3:4277098-4277117 MS.gene032201:CDS 40.0%
CACTTACAAGCAAGGAATTG+AGG + chr2.3:4277123-4277142 MS.gene032201:CDS 40.0%
GAAGGTCTAATCTCTCCATA+CGG - chr2.3:4276854-4276873 None:intergenic 40.0%
GATCAACTTCAAGGACTCAT+AGG + chr2.3:4276711-4276730 MS.gene032201:CDS 40.0%
GGTGATTACATTAGAAGCTC+AGG + chr2.3:4277301-4277320 MS.gene032201:CDS 40.0%
TATGGCTGCAGGTTATCAAT+TGG + chr2.3:4277180-4277199 MS.gene032201:CDS 40.0%
TCAAGGACTCATAGGGATAA+TGG + chr2.3:4276719-4276738 MS.gene032201:CDS 40.0%
TGATAACCTGCAGCCATATA+AGG - chr2.3:4277178-4277197 None:intergenic 40.0%
TTAACTCCTTATATGGCTGC+AGG + chr2.3:4277169-4277188 MS.gene032201:CDS 40.0%
TTCCAATTCACTGCATTTCG+TGG + chr2.3:4277067-4277086 MS.gene032201:CDS 40.0%
! AAAGACAATGGATTCCATGG+TGG + chr2.3:4277439-4277458 MS.gene032201:CDS 40.0%
! AAGACAATGGATTCCATGGT+GGG + chr2.3:4277440-4277459 MS.gene032201:CDS 40.0%
ACTTAAGCTTATCCCCACCA+TGG - chr2.3:4277456-4277475 None:intergenic 45.0%
CAACAAAGATTGACAGTGGG+TGG + chr2.3:4277404-4277423 MS.gene032201:CDS 45.0%
GAACATCCACTTCTGACTGA+GGG + chr2.3:4276968-4276987 MS.gene032201:CDS 45.0%
GTCCACGAAATGCAGTGAAT+TGG - chr2.3:4277072-4277091 None:intergenic 45.0%
TCATGGCACACTTACAAGCA+AGG + chr2.3:4277115-4277134 MS.gene032201:CDS 45.0%
TGAACATCCACTTCTGACTG+AGG + chr2.3:4276967-4276986 MS.gene032201:CDS 45.0%
TGCTTGTAAGTGTGCCATGA+TGG - chr2.3:4277115-4277134 None:intergenic 45.0%
! AGACAATGGATTCCATGGTG+GGG + chr2.3:4277441-4277460 MS.gene032201:CDS 45.0%
ATCCACTTCTGACTGAGGGA+CGG + chr2.3:4276972-4276991 MS.gene032201:CDS 50.0%
CTGAGGGACGGATCAACTTA+AGG + chr2.3:4276984-4277003 MS.gene032201:CDS 50.0%
!! CATTTGTACTCGGTGCCTGT+AGG - chr2.3:4277352-4277371 None:intergenic 50.0%
!! CTGGTGGTGGATCAACTTCA+AGG + chr2.3:4276702-4276721 MS.gene032201:CDS 50.0%
ATCCGTCCCTCAGTCAGAAG+TGG - chr2.3:4276977-4276996 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 4276698 4277528 4276698 ID=MS.gene032201
chr2.3 mRNA 4276698 4277528 4276698 ID=MS.gene032201.t1;Parent=MS.gene032201
chr2.3 exon 4276698 4277201 4276698 ID=MS.gene032201.t1.exon1;Parent=MS.gene032201.t1
chr2.3 CDS 4276698 4277201 4276698 ID=cds.MS.gene032201.t1;Parent=MS.gene032201.t1
chr2.3 exon 4277283 4277528 4277283 ID=MS.gene032201.t1.exon2;Parent=MS.gene032201.t1
chr2.3 CDS 4277283 4277528 4277283 ID=cds.MS.gene032201.t1;Parent=MS.gene032201.t1
Gene Sequence

>MS.gene032201

ATGTCTGGTGGTGGATCAACTTCAAGGACTCATAGGGATAATGGAGAAATACTTACTGCTTATATCATCAATGAGGTAGAACTTCCTATTATTTTATGTTTAGCAATTGAATATTGTTTAGTGAATCATCTAAACTATATATCTCATTTACAACCGTATGGAGAGATTAGACCTTCCTTTGTTGAGCATTTTATCCACAAACTTGGAAGAGAATTTATATTGATTGATTCAAAATCCTATAGACACAAAGTTAAGTTCAATCAAAACATTGAACATCCACTTCTGACTGAGGGACGGATCAACTTAAGGAAGTTTTATGGTTGGAATGAAGATAAAATGATCTTTATGAAGTTCTTGGGGAATGATTGTTTCCAATTCACTGCATTTCGTGGACATTTGAATGTCAACTCATTGCCATCATGGCACACTTACAAGCAAGGAATTGAGGATCTCAACCATTATGAAATGATCTTAACTCCTTATATGGCTGCAGGTTATCAATTGGTAAGTACCAACAACTCCTTCTAAAATGATACATCTCTATAAAGTTGAAAGCTATTCTAATTGTCATTTTGTTTTTTTCAGACACTGAACATTGAATTTGGTGATTACATTAGAAGCTCAGGCTTCTCTGCTATTAATATGTATGGACCTACAGGCACCGAGTACAAATGTGATGTACTAATAAGGGATGGAAAAAAGAAGGCAACAAAGATTGACAGTGGGTGGAACAAATTTTGTAAAGACAATGGATTCCATGGTGGGGATAAGCTTAAGTTTAAGTTTGTGGATATAAGTACATCAAATGTAATGAAGGTTTCTAGGATTTAA
Protein sequence

>MS.gene032201.t1

MSGGGSTSRTHRDNGEILTAYIINEVELPIILCLAIEYCLVNHLNYISHLQPYGEIRPSFVEHFIHKLGREFILIDSKSYRHKVKFNQNIEHPLLTEGRINLRKFYGWNEDKMIFMKFLGNDCFQFTAFRGHLNVNSLPSWHTYKQGIEDLNHYEMILTPYMAAGYQLTLNIEFGDYIRSSGFSAINMYGPTGTEYKCDVLIRDGKKKATKIDSGWNKFCKDNGFHGGDKLKFKFVDISTSNVMKVSRI