AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene028119

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028119.t1 MTR_7g080390 74.242 132 32 1 1 132 1 130 1.92e-66 197
MS.gene028119.t1 MTR_7g080760 39.695 131 66 3 1 131 1 118 2.24e-26 95.9
MS.gene028119.t1 MTR_4g133928 36.290 124 66 2 18 132 4 123 1.62e-17 73.2
MS.gene028119.t1 MTR_0446s0010 37.500 104 52 2 18 112 4 103 9.36e-13 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028119.t1 AT1G65290 62.121 132 44 3 1 132 1 126 6.35e-49 153
MS.gene028119.t1 AT2G44620 43.939 132 62 5 1 131 1 121 1.07e-25 94.4
MS.gene028119.t1 AT5G47630 38.750 80 49 0 53 132 48 127 2.22e-13 62.8
MS.gene028119.t1 AT5G47630 38.750 80 49 0 53 132 48 127 2.22e-13 62.8
MS.gene028119.t1 AT5G47630 38.750 80 49 0 53 132 48 127 2.22e-13 62.8
MS.gene028119.t1 AT3G05020 35.955 89 57 0 37 125 41 129 3.43e-11 57.4

Find 30 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCGGCTCGGGGAAGCGGTTT+GGG 0.283525 5.3:-16290483 MS.gene028119:CDS
GGCGGCTCGGGGAAGCGGTT+TGG 0.290380 5.3:-16290484 MS.gene028119:CDS
TGACAATGTTGATCCTTCTA+AGG 0.294761 5.3:-16290286 MS.gene028119:intron
ATGGATCTTGATACAGAGTT+TGG 0.311699 5.3:-16289422 MS.gene028119:CDS
ATCAACAACAATGGCGGCTC+GGG 0.345626 5.3:-16290496 None:intergenic
AAGCATGAACCTCAACTCTT+AGG 0.355069 5.3:+16290448 None:intergenic
GAAATCAACAGCTTGATTAA+CGG 0.409809 5.3:+16289361 None:intergenic
ATGGAAGTGAAAACCTTAGA+AGG 0.418506 5.3:+16290273 None:intergenic
TTTCTATGATGACCTTGGAT+TGG 0.444522 5.3:-16289471 MS.gene028119:CDS
AAGATCCATACAGATCTCTA+TGG 0.455448 5.3:+16289436 None:intergenic
GTCGCTTCAGCGAAGAGATC+AGG 0.457126 5.3:-16290368 MS.gene028119:CDS
ACAATGGCGGCTCGGGGAAG+CGG 0.466910 5.3:-16290489 MS.gene028119:CDS
GAGGAGTACGCAAAGGAGAT+TGG 0.466971 5.3:+16290412 None:intergenic
CAGCGACGAAGGAAGGAATT+CGG 0.467889 5.3:+16290390 None:intergenic
CATCATAGAAATGAGCAGTT+GGG 0.468087 5.3:+16289483 None:intergenic
TTTCATTGCATCTCATCCTC+AGG 0.474149 5.3:-16289342 MS.gene028119:CDS
GCTCATTTCTATGATGACCT+TGG 0.491539 5.3:-16289476 MS.gene028119:CDS
TATCAACAACAATGGCGGCT+CGG 0.529312 5.3:-16290497 None:intergenic
TCATCATAGAAATGAGCAGT+TGG 0.537450 5.3:+16289482 None:intergenic
GAAGCGACAGCGACGAAGGA+AGG 0.545017 5.3:+16290383 None:intergenic
CGCTGAAGCGACAGCGACGA+AGG 0.552195 5.3:+16290379 None:intergenic
AGACGCCATAGAGATCTGTA+TGG 0.564613 5.3:-16289441 MS.gene028119:CDS
ATCATAGAAATGAGCAGTTG+GGG 0.586456 5.3:+16289484 None:intergenic
GATGAATTACCTAAGAGTTG+AGG 0.587013 5.3:-16290457 MS.gene028119:CDS
CGTCTAAACTATCCAATCCA+AGG 0.606873 5.3:+16289459 None:intergenic
GAGTACGCAAAGGAGATTGG+TGG 0.606939 5.3:+16290415 None:intergenic
TCAACAACAATGGCGGCTCG+GGG 0.630083 5.3:-16290495 None:intergenic
GAATTCGGAGGAGTACGCAA+AGG 0.668596 5.3:+16290405 None:intergenic
AGGTTAGACTACTTCGCCTG+AGG 0.672291 5.3:+16289326 None:intergenic
CGACGAAGGAAGGAATTCGG+AGG 0.686278 5.3:+16290393 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAAAATAAATGAAGAAATT+AGG + chr5.3:16289579-16289598 None:intergenic 15.0%
!!! CTATTTTCAATCTTTAATTT+AGG - chr5.3:16289615-16289634 MS.gene028119:intron 15.0%
!! AAGCCAAAGATATAATATAA+CGG + chr5.3:16290263-16290282 None:intergenic 20.0%
!! TAAATGAAGAAATTAGGTTA+AGG + chr5.3:16289573-16289592 None:intergenic 20.0%
! GTACCGTTATATTATATCTT+TGG - chr5.3:16290257-16290276 MS.gene028119:intron 25.0%
!! ATAAGTTGTCTTTTCAAACA+TGG + chr5.3:16289956-16289975 None:intergenic 25.0%
!! TTATCCTTTTATGTTGTGTT+TGG + chr5.3:16289796-16289815 None:intergenic 25.0%
GAAATCAACAGCTTGATTAA+CGG + chr5.3:16290462-16290481 None:intergenic 30.0%
GTTTATCTGAGCTTATTTAC+TGG + chr5.3:16290146-16290165 None:intergenic 30.0%
TAAAGTAAAAGTCTACACTG+AGG + chr5.3:16290182-16290201 None:intergenic 30.0%
TGAAGAAATTAGGTTAAGGA+TGG + chr5.3:16289569-16289588 None:intergenic 30.0%
TGATCCAAACACAACATAAA+AGG - chr5.3:16289789-16289808 MS.gene028119:intron 30.0%
! ATCTTGTCTACTTCATTTTC+AGG + chr5.3:16290434-16290453 None:intergenic 30.0%
! GCTAAGTGAAGACTATATTT+TGG - chr5.3:16289920-16289939 MS.gene028119:intron 30.0%
! TGACCAATTCTTGTAAGTTT+TGG - chr5.3:16289660-16289679 MS.gene028119:intron 30.0%
!! AAGTGAAGACTATATTTTGG+AGG - chr5.3:16289923-16289942 MS.gene028119:intron 30.0%
!!! ATTGTCAAATTTTTTGACGC+AGG + chr5.3:16289521-16289540 None:intergenic 30.0%
AAGATCCATACAGATCTCTA+TGG + chr5.3:16290387-16290406 None:intergenic 35.0%
AGGCCAAAACTTACAAGAAT+TGG + chr5.3:16289666-16289685 None:intergenic 35.0%
ATATAACGGTACACAAATGC+TGG + chr5.3:16290249-16290268 None:intergenic 35.0%
ATCATAGAAATGAGCAGTTG+GGG + chr5.3:16290339-16290358 None:intergenic 35.0%
ATGGAAGTGAAAACCTTAGA+AGG + chr5.3:16289550-16289569 None:intergenic 35.0%
ATGGATCTTGATACAGAGTT+TGG - chr5.3:16290398-16290417 MS.gene028119:CDS 35.0%
CATCATAGAAATGAGCAGTT+GGG + chr5.3:16290340-16290359 None:intergenic 35.0%
GATGAATTACCTAAGAGTTG+AGG - chr5.3:16289363-16289382 MS.gene028119:CDS 35.0%
GTACAATAAACCCAAAAGTG+CGG - chr5.3:16289874-16289893 MS.gene028119:intron 35.0%
TCATCATAGAAATGAGCAGT+TGG + chr5.3:16290341-16290360 None:intergenic 35.0%
TGACAATGTTGATCCTTCTA+AGG - chr5.3:16289534-16289553 MS.gene028119:intron 35.0%
TTAATGTGCTTGTGTCAGTT+TGG - chr5.3:16290205-16290224 MS.gene028119:intron 35.0%
TTATTTCCGTAAGCTATCCT+AGG + chr5.3:16290048-16290067 None:intergenic 35.0%
TTTCTATGATGACCTTGGAT+TGG - chr5.3:16290349-16290368 MS.gene028119:CDS 35.0%
! AAGTTCTAGTCCTCGAAATA+GGG - chr5.3:16289842-16289861 MS.gene028119:intron 35.0%
! CTGTTTTCATAAGCTATCCT+AGG - chr5.3:16290028-16290047 MS.gene028119:intron 35.0%
! GAGAACTTTTCTCGACAAAT+CGG - chr5.3:16289474-16289493 MS.gene028119:CDS 35.0%
! TTGTGTTTGGATCAGTGTTT+TGG + chr5.3:16289783-16289802 None:intergenic 35.0%
AAGCATGAACCTCAACTCTT+AGG + chr5.3:16289375-16289394 None:intergenic 40.0%
AGCTATCCTAGGATAGCTTA+CGG - chr5.3:16290039-16290058 MS.gene028119:intron 40.0%
CGTCTAAACTATCCAATCCA+AGG + chr5.3:16290364-16290383 None:intergenic 40.0%
GCTCATTTCTATGATGACCT+TGG - chr5.3:16290344-16290363 MS.gene028119:CDS 40.0%
GGAAACAGCTTATGACATGT+AGG + chr5.3:16290084-16290103 None:intergenic 40.0%
TTTCATTGCATCTCATCCTC+AGG - chr5.3:16290478-16290497 MS.gene028119:CDS 40.0%
! AACTTTTCTCGACAAATCGG+AGG - chr5.3:16289477-16289496 MS.gene028119:CDS 40.0%
! CAAGTTCTAGTCCTCGAAAT+AGG - chr5.3:16289841-16289860 MS.gene028119:intron 40.0%
! CATAGTCTTACCCTATTTCG+AGG + chr5.3:16289855-16289874 None:intergenic 40.0%
! TGACAAAAGCAAAGAAGCAC+AGG + chr5.3:16290311-16290330 None:intergenic 40.0%
!! TGTGCTTCTTTGCTTTTGTC+AGG - chr5.3:16290310-16290329 MS.gene028119:CDS 40.0%
AAGTTGTTGTCACCTGACTG+AGG - chr5.3:16289815-16289834 MS.gene028119:intron 45.0%
AGACGCCATAGAGATCTGTA+TGG - chr5.3:16290379-16290398 MS.gene028119:CDS 45.0%
AGACTGTGTGATAGAGCTTG+TGG + chr5.3:16290105-16290124 None:intergenic 45.0%
ATCAGCTCAAACGCACGTTT+GGG + chr5.3:16289714-16289733 None:intergenic 45.0%
TAGAACTTGTGACCTCAGTC+AGG + chr5.3:16289830-16289849 None:intergenic 45.0%
TTTGCCGCAGAAACAAACAG+AGG + chr5.3:16289686-16289705 None:intergenic 45.0%
!! TTGGCCTCTGTTTGTTTCTG+CGG - chr5.3:16289679-16289698 MS.gene028119:intron 45.0%
CAGCGACGAAGGAAGGAATT+CGG + chr5.3:16289433-16289452 None:intergenic 50.0%
CATCAGCTCAAACGCACGTT+TGG + chr5.3:16289715-16289734 None:intergenic 50.0%
GAGTACGCAAAGGAGATTGG+TGG + chr5.3:16289408-16289427 None:intergenic 50.0%
GGTACACAAATGCTGGCAGA+GGG + chr5.3:16290242-16290261 None:intergenic 50.0%
GTCTACACTGAGGCTCTGTT+TGG + chr5.3:16290172-16290191 None:intergenic 50.0%
! ATAAACCCAAAAGTGCGGCG+CGG - chr5.3:16289879-16289898 MS.gene028119:intron 50.0%
! GAATTCGGAGGAGTACGCAA+AGG + chr5.3:16289418-16289437 None:intergenic 50.0%
! GAGGAGTACGCAAAGGAGAT+TGG + chr5.3:16289411-16289430 None:intergenic 50.0%
CGACGAAGGAAGGAATTCGG+AGG + chr5.3:16289430-16289449 None:intergenic 55.0%
CGGTACACAAATGCTGGCAG+AGG + chr5.3:16290243-16290262 None:intergenic 55.0%
GTCGCTTCAGCGAAGAGATC+AGG - chr5.3:16289452-16289471 MS.gene028119:CDS 55.0%
GAAGCGACAGCGACGAAGGA+AGG + chr5.3:16289440-16289459 None:intergenic 60.0%
! AAGCTACCGCGCCGCACTTT+TGG + chr5.3:16289888-16289907 None:intergenic 60.0%
! AGCTACCGCGCCGCACTTTT+GGG + chr5.3:16289887-16289906 None:intergenic 60.0%
CGCTGAAGCGACAGCGACGA+AGG + chr5.3:16289444-16289463 None:intergenic 65.0%
! GCGGCTCGGGGAAGCGGTTT+GGG - chr5.3:16289337-16289356 MS.gene028119:CDS 70.0%
! GGCGGCTCGGGGAAGCGGTT+TGG - chr5.3:16289336-16289355 MS.gene028119:CDS 75.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 16289334 16290508 16289334 ID=MS.gene028119
chr5.3 mRNA 16289334 16290508 16289334 ID=MS.gene028119.t1;Parent=MS.gene028119
chr5.3 exon 16290287 16290508 16290287 ID=MS.gene028119.t1.exon1;Parent=MS.gene028119.t1
chr5.3 CDS 16290287 16290508 16290287 ID=cds.MS.gene028119.t1;Parent=MS.gene028119.t1
chr5.3 exon 16289334 16289510 16289334 ID=MS.gene028119.t1.exon2;Parent=MS.gene028119.t1
chr5.3 CDS 16289334 16289510 16289334 ID=cds.MS.gene028119.t1;Parent=MS.gene028119.t1
Gene Sequence

>MS.gene028119

ATGGCGGCTCGGGGAAGCGGTTTGGGTCTGATGAATTACCTAAGAGTTGAGGTTCATGCTTCTGCTCTCAACCACCAATCTCCTTTGCGTACTCCTCCGAATTCCTTCCTTCGTCGCTGTCGCTTCAGCGAAGAGATCAGGAGAACTTTTCTCGACAAATCGGAGGTCACTGATCGCGTCATTTCCTGCGTCAAAAAATTTGACAATGTTGATCCTTCTAAGGTTTTCACTTCCATCCTTAACCTAATTTCTTCATTTATTTTCATTTATTTTACAAATTTCTATTTTCAATCTTTAATTTAGGTCATATTTAGTATCTTAATTAATGACCAATTCTTGTAAGTTTTGGCCTCTGTTTGTTTCTGCGGCAAAACAAGCCCAAACGTGCGTTTGAGCTGATGCTACTAGTTGTAGCTTCTTAAAAATCAAGTTTATTTGATAGAAAACCAAAACACTGATCCAAACACAACATAAAAGGATAAAGTTGTTGTCACCTGACTGAGGTCACAAGTTCTAGTCCTCGAAATAGGGTAAGACTATGTACAATAAACCCAAAAGTGCGGCGCGGTAGCTTTATTGTATGAAAGCTAAGTGAAGACTATATTTTGGAGGATTAAGACCATGTTTGAAAAGACAACTTATTTAAGCGTTTTGTGTAAGCTATTTCTTTAACAAAAAATAAAATAAAATCAAACTGTTTTCATAAGCTATCCTAGGATAGCTTACGGAAATAAGTTTAAACATTTACCTACATGTCATAAGCTGTTTCCACAAGCTCTATCACACAGTCTCACTCACAATTTTCTTTTCCAGTAAATAAGCTCAGATAAACAATCCAAACAGAGCCTCAGTGTAGACTTTTACTTTACTTTTAATGTGCTTGTGTCAGTTTGGAGAATTTAAATCCCTCTGCCAGCATTTGTGTACCGTTATATTATATCTTTGGCTTATGTTATTTTGATAATAACACAGAACCTGTGCTTCTTTGCTTTTGTCAGGTTACCCCAACTGCTCATTTCTATGATGACCTTGGATTGGATAGTTTAGACGCCATAGAGATCTGTATGGATCTTGATACAGAGTTTGGATTTGAGATTCCTGAAAATGAAGTAGACAAGATCGTCTCCGTTAATCAAGCTGTTGATTTCATTGCATCTCATCCTCAGGCGAAGTAG
Protein sequence

>MS.gene028119.t1

MAARGSGLGLMNYLRVEVHASALNHQSPLRTPPNSFLRRCRFSEEIRRTFLDKSEVTDRVISCVKKFDNVDPSKVTPTAHFYDDLGLDSLDAIEICMDLDTEFGFEIPENEVDKIVSVNQAVDFIASHPQAK