AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54540


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54540.t1 MTR_1g007905 91.005 189 16 1 1 189 1 188 4.52e-123 346
MS.gene54540.t1 MTR_3g091680 55.844 154 53 5 37 189 1 140 6.26e-44 144
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54540.t1 AT5G53030 38.333 180 70 9 45 189 40 213 1.70e-19 82.8
MS.gene54540.t1 AT5G53030 38.333 180 70 9 45 189 40 213 1.94e-19 83.2
MS.gene54540.t1 AT4G27810 35.176 199 78 11 9 188 1 167 5.51e-11 59.3

Find 47 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAAGGGCAGTGTGAATTT+TGG 0.173203 1.2:-12051318 MS.gene54540:CDS
TCCTCCTAGGTTGTTGTCTT+TGG 0.204117 1.2:-12051448 MS.gene54540:CDS
TTGTTACCTTCTCTTTCTTT+TGG 0.308850 1.2:+12051492 None:intergenic
ACCATCACCAACAACTGTTT+TGG 0.363972 1.2:-12051397 MS.gene54540:CDS
TAACAACGTTGTTAGAGCTT+TGG 0.381783 1.2:-12051475 MS.gene54540:CDS
CACATGGTACTTCACATTTG+TGG 0.395630 1.2:-12051164 MS.gene54540:CDS
TTGGGTCTAGTAGGTGGGGT+GGG 0.401963 1.2:-12051299 MS.gene54540:CDS
ATCATGATGATGATGAATTA+AGG 0.404054 1.2:-12051680 MS.gene54540:CDS
ACATGGTACTTCACATTTGT+GGG 0.406088 1.2:-12051163 None:intergenic
ATAGCCGTCGTTCGCGGTGG+TGG 0.414893 1.2:+12051579 None:intergenic
TTTCAAGTTGGAGTGTTGAT+GGG 0.452572 1.2:-12051233 MS.gene54540:CDS
TTTAAGTGGGAGGAAGCACC+AGG 0.462547 1.2:-12051546 MS.gene54540:CDS
GTCGTTCGCGGTGGTGGAGT+TGG 0.473237 1.2:+12051585 None:intergenic
TAGGTTGTTGTCTTTGGAGA+GGG 0.474181 1.2:-12051442 MS.gene54540:CDS
GGACCTTCCAAAACAGTTGT+TGG 0.481823 1.2:+12051390 None:intergenic
TGACATGACCTAGGCTTCCC+TGG 0.485647 1.2:+12051528 None:intergenic
GGTGCTTCCTCCCACTTAAA+CGG 0.493829 1.2:+12051549 None:intergenic
GAGCTTTGGAACTTCCTCCT+AGG 0.498331 1.2:-12051461 MS.gene54540:CDS
TTTGGGTCTAGTAGGTGGGG+TGG 0.500229 1.2:-12051300 MS.gene54540:CDS
GACACTGCACGTCCAACGTA+TGG 0.515972 1.2:+12051369 None:intergenic
GATCACAAGAGTTAAGAGAA+GGG 0.526664 1.2:-12051196 MS.gene54540:CDS
CTAGGTTGTTGTCTTTGGAG+AGG 0.533267 1.2:-12051443 MS.gene54540:CDS
TTCAAGTTGGAGTGTTGATG+GGG 0.539072 1.2:-12051232 MS.gene54540:CDS
CTATATCGATACCGTTTAAG+TGG 0.539738 1.2:-12051560 MS.gene54540:CDS
AACTCCACCACCGCGAACGA+CGG 0.539846 1.2:-12051583 MS.gene54540:CDS
AGGAAGCACCAGGGAAGCCT+AGG 0.540552 1.2:-12051536 MS.gene54540:CDS
ATCGATATAGCCGTCGTTCG+CGG 0.559277 1.2:+12051573 None:intergenic
AGATCACAAGAGTTAAGAGA+AGG 0.565850 1.2:-12051197 MS.gene54540:CDS
ATCACAAGAGTTAAGAGAAG+GGG 0.589130 1.2:-12051195 MS.gene54540:CDS
TCCAAAACAGTTGTTGGTGA+TGG 0.590521 1.2:+12051396 None:intergenic
ATCGATACCGTTTAAGTGGG+AGG 0.600972 1.2:-12051556 MS.gene54540:CDS
CCAGAGCCAAAAGAAAGAGA+AGG 0.615358 1.2:-12051498 MS.gene54540:CDS
GTATAGGGATAGTAATAACA+AGG 0.626999 1.2:-12051334 MS.gene54540:CDS
CACGGTCGTGATAACACTGG+TGG 0.632454 1.2:+12051624 None:intergenic
TCCAAAGACAACAACCTAGG+AGG 0.639929 1.2:+12051447 None:intergenic
GGTCGTGTATGACATGACCT+AGG 0.639981 1.2:+12051519 None:intergenic
TATATCGATACCGTTTAAGT+GGG 0.641926 1.2:-12051559 MS.gene54540:CDS
TCAAGTTGGAGTGTTGATGG+GGG 0.642096 1.2:-12051231 MS.gene54540:CDS
AAAAGTCAAAACTACCCTCA+CGG 0.642581 1.2:+12051253 None:intergenic
AATAATAGAATTGACCGTGA+GGG 0.656653 1.2:-12051267 MS.gene54540:CDS
CTCTCCAAAGACAACAACCT+AGG 0.661580 1.2:+12051444 None:intergenic
AAACACGGTCGTGATAACAC+TGG 0.682213 1.2:+12051621 None:intergenic
AAATAATAGAATTGACCGTG+AGG 0.684752 1.2:-12051268 MS.gene54540:CDS
GATATAGCCGTCGTTCGCGG+TGG 0.697862 1.2:+12051576 None:intergenic
TATAGGGATAGTAATAACAA+GGG 0.698970 1.2:-12051333 MS.gene54540:CDS
AGAAGGGGAAGCTTCTCACA+TGG 0.717228 1.2:-12051180 MS.gene54540:CDS
TTAAGTGGGAGGAAGCACCA+GGG 0.769568 1.2:-12051545 MS.gene54540:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TATAGGGATAGTAATAACAA+GGG - chr1.2:12051539-12051558 MS.gene54540:CDS 25.0%
!! ATCATGATGATGATGAATTA+AGG - chr1.2:12051192-12051211 MS.gene54540:CDS 25.0%
AAATAATAGAATTGACCGTG+AGG - chr1.2:12051604-12051623 MS.gene54540:CDS 30.0%
AATAATAGAATTGACCGTGA+GGG - chr1.2:12051605-12051624 MS.gene54540:CDS 30.0%
GTATAGGGATAGTAATAACA+AGG - chr1.2:12051538-12051557 MS.gene54540:CDS 30.0%
TATATCGATACCGTTTAAGT+GGG - chr1.2:12051313-12051332 MS.gene54540:CDS 30.0%
! TTGTTACCTTCTCTTTCTTT+TGG + chr1.2:12051383-12051402 None:intergenic 30.0%
!!! GTAGTTTTGACTTTTCAAGT+TGG - chr1.2:12051627-12051646 MS.gene54540:CDS 30.0%
AAAAGTCAAAACTACCCTCA+CGG + chr1.2:12051622-12051641 None:intergenic 35.0%
AGATCACAAGAGTTAAGAGA+AGG - chr1.2:12051675-12051694 MS.gene54540:CDS 35.0%
ATCACAAGAGTTAAGAGAAG+GGG - chr1.2:12051677-12051696 MS.gene54540:CDS 35.0%
CTATATCGATACCGTTTAAG+TGG - chr1.2:12051312-12051331 MS.gene54540:CDS 35.0%
GATCACAAGAGTTAAGAGAA+GGG - chr1.2:12051676-12051695 MS.gene54540:CDS 35.0%
TAACAACGTTGTTAGAGCTT+TGG - chr1.2:12051397-12051416 MS.gene54540:CDS 35.0%
!! TTTCAAGTTGGAGTGTTGAT+GGG - chr1.2:12051639-12051658 MS.gene54540:CDS 35.0%
!!! TTTTCAAGTTGGAGTGTTGA+TGG - chr1.2:12051638-12051657 MS.gene54540:CDS 35.0%
CACATGGTACTTCACATTTG+TGG - chr1.2:12051708-12051727 MS.gene54540:CDS 40.0%
! AACAAGGGCAGTGTGAATTT+TGG - chr1.2:12051554-12051573 MS.gene54540:CDS 40.0%
! ACAAGGGCAGTGTGAATTTT+GGG - chr1.2:12051555-12051574 MS.gene54540:CDS 40.0%
! ACCATCACCAACAACTGTTT+TGG - chr1.2:12051475-12051494 MS.gene54540:CDS 40.0%
! GGTGGAAGAGAAAGTTTTTG+TGG + chr1.2:12051233-12051252 None:intergenic 40.0%
! GTCTTTTACGACGTCGTATA+GGG - chr1.2:12051523-12051542 MS.gene54540:CDS 40.0%
! TAGGTTGTTGTCTTTGGAGA+GGG - chr1.2:12051430-12051449 MS.gene54540:CDS 40.0%
! TCCAAAACAGTTGTTGGTGA+TGG + chr1.2:12051479-12051498 None:intergenic 40.0%
! TGTCTTTTACGACGTCGTAT+AGG - chr1.2:12051522-12051541 MS.gene54540:CDS 40.0%
!! AATTTTGGGTCTAGTAGGTG+GGG - chr1.2:12051569-12051588 MS.gene54540:CDS 40.0%
!! GAATTTTGGGTCTAGTAGGT+GGG - chr1.2:12051568-12051587 MS.gene54540:CDS 40.0%
!! GTGTGAATTTTGGGTCTAGT+AGG - chr1.2:12051564-12051583 MS.gene54540:CDS 40.0%
!! TCACCAACAACTGTTTTGGA+AGG - chr1.2:12051479-12051498 MS.gene54540:CDS 40.0%
!! TGAATTTTGGGTCTAGTAGG+TGG - chr1.2:12051567-12051586 MS.gene54540:CDS 40.0%
!! TTCAAGTTGGAGTGTTGATG+GGG - chr1.2:12051640-12051659 MS.gene54540:CDS 40.0%
AAACACGGTCGTGATAACAC+TGG + chr1.2:12051254-12051273 None:intergenic 45.0%
ATCGATACCGTTTAAGTGGG+AGG - chr1.2:12051316-12051335 MS.gene54540:CDS 45.0%
CCAGAGCCAAAAGAAAGAGA+AGG - chr1.2:12051374-12051393 MS.gene54540:CDS 45.0%
CTCTCCAAAGACAACAACCT+AGG + chr1.2:12051431-12051450 None:intergenic 45.0%
GGACCTTCCAAAACAGTTGT+TGG + chr1.2:12051485-12051504 None:intergenic 45.0%
TCCAAAGACAACAACCTAGG+AGG + chr1.2:12051428-12051447 None:intergenic 45.0%
TCCTCCTAGGTTGTTGTCTT+TGG - chr1.2:12051424-12051443 MS.gene54540:CDS 45.0%
! ATCACGACCGTGTTTTTCGT+CGG - chr1.2:12051259-12051278 MS.gene54540:CDS 45.0%
! CTAGGTTGTTGTCTTTGGAG+AGG - chr1.2:12051429-12051448 MS.gene54540:CDS 45.0%
!! TCAAGTTGGAGTGTTGATGG+GGG - chr1.2:12051641-12051660 MS.gene54540:CDS 45.0%
!!! CCTTCTCTTTCTTTTGGCTC+TGG + chr1.2:12051377-12051396 None:intergenic 45.0%
!!! GTTTTGGAAGGTCCATACGT+TGG - chr1.2:12051491-12051510 MS.gene54540:CDS 45.0%
AGAAGGGGAAGCTTCTCACA+TGG - chr1.2:12051692-12051711 MS.gene54540:CDS 50.0%
ATCGATATAGCCGTCGTTCG+CGG + chr1.2:12051302-12051321 None:intergenic 50.0%
GGTCGTGTATGACATGACCT+AGG + chr1.2:12051356-12051375 None:intergenic 50.0%
GGTGCTTCCTCCCACTTAAA+CGG + chr1.2:12051326-12051345 None:intergenic 50.0%
!! GAGCTTTGGAACTTCCTCCT+AGG - chr1.2:12051411-12051430 MS.gene54540:CDS 50.0%
!! GAGTGTTGATGGGGGTGATA+AGG - chr1.2:12051649-12051668 MS.gene54540:CDS 50.0%
!! TTAAGTGGGAGGAAGCACCA+GGG - chr1.2:12051327-12051346 MS.gene54540:CDS 50.0%
!! TTTAAGTGGGAGGAAGCACC+AGG - chr1.2:12051326-12051345 MS.gene54540:CDS 50.0%
CACGGTCGTGATAACACTGG+TGG + chr1.2:12051251-12051270 None:intergenic 55.0%
GACACTGCACGTCCAACGTA+TGG + chr1.2:12051506-12051525 None:intergenic 55.0%
GGTGCCTCCGACGAAAAACA+CGG + chr1.2:12051269-12051288 None:intergenic 55.0%
TGACATGACCTAGGCTTCCC+TGG + chr1.2:12051347-12051366 None:intergenic 55.0%
TTGGGTCTAGTAGGTGGGGT+GGG - chr1.2:12051573-12051592 MS.gene54540:CDS 55.0%
TTTGGGTCTAGTAGGTGGGG+TGG - chr1.2:12051572-12051591 MS.gene54540:CDS 55.0%
! ACGACCGTGTTTTTCGTCGG+AGG - chr1.2:12051262-12051281 MS.gene54540:CDS 55.0%
AACTCCACCACCGCGAACGA+CGG - chr1.2:12051289-12051308 MS.gene54540:CDS 60.0%
GATATAGCCGTCGTTCGCGG+TGG + chr1.2:12051299-12051318 None:intergenic 60.0%
!! AGGAAGCACCAGGGAAGCCT+AGG - chr1.2:12051336-12051355 MS.gene54540:CDS 60.0%
ATAGCCGTCGTTCGCGGTGG+TGG + chr1.2:12051296-12051315 None:intergenic 65.0%
!! GTCGTTCGCGGTGGTGGAGT+TGG + chr1.2:12051290-12051309 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 12051164 12051730 12051164 ID=MS.gene54540
chr1.2 mRNA 12051164 12051730 12051164 ID=MS.gene54540.t1;Parent=MS.gene54540
chr1.2 exon 12051164 12051730 12051164 ID=MS.gene54540.t1.exon1;Parent=MS.gene54540.t1
chr1.2 CDS 12051164 12051730 12051164 ID=cds.MS.gene54540.t1;Parent=MS.gene54540.t1
Gene Sequence

>MS.gene54540

ATGACTTCAGAGAATAACAAGAAACTTGATCATGATGATGATGAATTAAGGAGCAACTACAACACACCACAAAAACTTTCTCTTCCACCAGTGTTATCACGACCGTGTTTTTCGTCGGAGGCACCAACTCCACCACCGCGAACGACGGCTATATCGATACCGTTTAAGTGGGAGGAAGCACCAGGGAAGCCTAGGTCATGTCATACACGACCAGAGCCAAAAGAAAGAGAAGGTAACAACGTTGTTAGAGCTTTGGAACTTCCTCCTAGGTTGTTGTCTTTGGAGAGGGAGAGTACTAGCAATATTTACGCACCATCACCAACAACTGTTTTGGAAGGTCCATACGTTGGACGTGCAGTGTCTTTTACGACGTCGTATAGGGATAGTAATAACAAGGGCAGTGTGAATTTTGGGTCTAGTAGGTGGGGTGGGTTGAAGAAAAATAATAGAATTGACCGTGAGGGTAGTTTTGACTTTTCAAGTTGGAGTGTTGATGGGGGTGATAAGGTGAAGATCACAAGAGTTAAGAGAAGGGGAAGCTTCTCACATGGTACTTCACATTTGTGG

Protein sequence

>MS.gene54540.t1

MTSENNKKLDHDDDELRSNYNTPQKLSLPPVLSRPCFSSEAPTPPPRTTAISIPFKWEEAPGKPRSCHTRPEPKEREGNNVVRALELPPRLLSLERESTSNIYAPSPTTVLEGPYVGRAVSFTTSYRDSNNKGSVNFGSSRWGGLKKNNRIDREGSFDFSSWSVDGGDKVKITRVKRRGSFSHGTSHLW