AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene57241

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene57241.t1 MTR_1g016200 55.357 112 35 4 9 114 2 104 1.77e-25 93.2
MS.gene57241.t1 MTR_1g016170 43.158 95 45 2 29 114 140 234 2.91e-14 67.8
MS.gene57241.t1 MTR_7g112330 44.068 59 33 0 70 128 22 80 2.59e-11 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene57241.t1 AT4G36620 47.368 57 30 0 70 126 75 131 8.77e-12 60.1
MS.gene57241.t1 AT5G26930 48.980 49 25 0 66 114 22 70 1.93e-11 57.4
MS.gene57241.t1 AT2G18380 49.123 57 29 0 70 126 92 148 9.02e-11 57.4
MS.gene57241.t1 AT5G56860 70.588 34 10 0 70 103 230 263 9.73e-11 58.2

Find 30 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAGTGTCAAGACCCTTAT+TGG 0.213155 1.4:-6110536 None:intergenic
TTCCTCTTTGTGACTGGAAT+TGG 0.242970 1.4:-6110088 None:intergenic
AGTATTCGCCATTGCCCTTT+TGG 0.253039 1.4:-6110205 None:intergenic
GGAAGAGGCAAAAGCCAATA+AGG 0.316264 1.4:+6110522 MS.gene57241:CDS
GAATACTATATCCAAGGAAT+TGG 0.396437 1.4:+6110221 MS.gene57241:CDS
ATACGAACACTACTCCTCTT+TGG 0.428715 1.4:+6110293 MS.gene57241:CDS
TAAGGGTCTTGACACTGAAA+AGG 0.459357 1.4:+6110540 MS.gene57241:CDS
TTGCCTCTTCCCTTCTTCGT+CGG 0.477939 1.4:-6110510 None:intergenic
ACTGAAAAGGGAAAGGGAAA+TGG 0.483033 1.4:+6110553 MS.gene57241:CDS
TCTTTGGCGGAGTGATCCTA+CGG 0.514022 1.4:+6110309 MS.gene57241:CDS
ACTGAATACGAATACCCAAA+AGG 0.514268 1.4:+6110190 MS.gene57241:CDS
GGAGGGCTGAACCAATTCCT+TGG 0.517307 1.4:-6110232 None:intergenic
AAGGGTCTTGACACTGAAAA+GGG 0.524508 1.4:+6110541 MS.gene57241:CDS
GAAGAGGCAAAAGCCAATAA+GGG 0.527753 1.4:+6110523 MS.gene57241:CDS
CTGAATACGAATACCCAAAA+GGG 0.530093 1.4:+6110191 MS.gene57241:CDS
ATGTGGACTCCGACGAAGAA+GGG 0.540307 1.4:+6110501 MS.gene57241:CDS
CATGTGGACTCCGACGAAGA+AGG 0.573346 1.4:+6110500 MS.gene57241:CDS
GAGTGATCCTACGGGTTCCA+AGG 0.575967 1.4:+6110318 MS.gene57241:CDS
CGAACACTACTCCTCTTTGG+CGG 0.584168 1.4:+6110296 MS.gene57241:CDS
CTTTGGCGGAGTGATCCTAC+GGG 0.586116 1.4:+6110310 MS.gene57241:CDS
ACTCCGACGAAGAAGGGAAG+AGG 0.589069 1.4:+6110507 MS.gene57241:CDS
ATCCAATTCCAGTCACAAAG+AGG 0.594857 1.4:+6110086 MS.gene57241:CDS
TCTTGACACTGAAAAGGGAA+AGG 0.595440 1.4:+6110546 MS.gene57241:CDS
CTTGACACTGAAAAGGGAAA+GGG 0.607329 1.4:+6110547 MS.gene57241:CDS
CAGTCGTTGTGCAATGCATG+TGG 0.610062 1.4:+6110484 MS.gene57241:intron
ACGAATACCCAAAAGGGCAA+TGG 0.610371 1.4:+6110197 MS.gene57241:CDS
AATGGCGAATACTATATCCA+AGG 0.653439 1.4:+6110215 MS.gene57241:CDS
ATCGCAATCGAAACAAACCC+TGG 0.664892 1.4:-6110272 None:intergenic
GTAGGATCACTCCGCCAAAG+AGG 0.691241 1.4:-6110307 None:intergenic
AGTAATACCTTGGAACCCGT+AGG 0.710916 1.4:-6110325 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATCAATATGTATAAGTA+TGG - chr1.4:6110417-6110436 None:intergenic 15.0%
!! ATAGTTAACAAGAAATATGT+TGG + chr1.4:6110459-6110478 MS.gene57241:intron 20.0%
!!! AGCAGTTTTTATTTTCTTTT+TGG - chr1.4:6110170-6110189 None:intergenic 20.0%
!!! ATTTGATAGTAAATAAGTTG+TGG - chr1.4:6110364-6110383 None:intergenic 20.0%
!!! TTACTATCAAATTTCACTTT+TGG + chr1.4:6110372-6110391 MS.gene57241:intron 20.0%
!!! TAAAACTTTTTCACATTCTC+AGG - chr1.4:6110592-6110611 None:intergenic 25.0%
AGACAGATTAAGTAATACCT+TGG - chr1.4:6110338-6110357 None:intergenic 30.0%
GAATACTATATCCAAGGAAT+TGG + chr1.4:6110221-6110240 MS.gene57241:CDS 30.0%
AATGGCGAATACTATATCCA+AGG + chr1.4:6110215-6110234 MS.gene57241:CDS 35.0%
ACTGAATACGAATACCCAAA+AGG + chr1.4:6110190-6110209 MS.gene57241:CDS 35.0%
CTGAATACGAATACCCAAAA+GGG + chr1.4:6110191-6110210 MS.gene57241:CDS 35.0%
TCCTAGTAAAAACACAACCA+GGG + chr1.4:6110255-6110274 MS.gene57241:CDS 35.0%
!! TTGTGTTTTTACTAGGAGGA+GGG - chr1.4:6110252-6110271 None:intergenic 35.0%
AAGGGTCTTGACACTGAAAA+GGG + chr1.4:6110541-6110560 MS.gene57241:CDS 40.0%
ACTGAAAAGGGAAAGGGAAA+TGG + chr1.4:6110553-6110572 MS.gene57241:CDS 40.0%
ATACGAACACTACTCCTCTT+TGG + chr1.4:6110293-6110312 MS.gene57241:CDS 40.0%
ATCCAATTCCAGTCACAAAG+AGG + chr1.4:6110086-6110105 MS.gene57241:CDS 40.0%
CTCCTAGTAAAAACACAACC+AGG + chr1.4:6110254-6110273 MS.gene57241:CDS 40.0%
CTTGACACTGAAAAGGGAAA+GGG + chr1.4:6110547-6110566 MS.gene57241:CDS 40.0%
GAAGAGGCAAAAGCCAATAA+GGG + chr1.4:6110523-6110542 MS.gene57241:CDS 40.0%
TAAGGGTCTTGACACTGAAA+AGG + chr1.4:6110540-6110559 MS.gene57241:CDS 40.0%
TCTTGACACTGAAAAGGGAA+AGG + chr1.4:6110546-6110565 MS.gene57241:CDS 40.0%
TTCAGTGTCAAGACCCTTAT+TGG - chr1.4:6110539-6110558 None:intergenic 40.0%
TTCCTCTTTGTGACTGGAAT+TGG - chr1.4:6110091-6110110 None:intergenic 40.0%
!! ACCCTGGTTGTGTTTTTACT+AGG - chr1.4:6110259-6110278 None:intergenic 40.0%
!! CTGGTTGTGTTTTTACTAGG+AGG - chr1.4:6110256-6110275 None:intergenic 40.0%
!! GTTGTGTTTTTACTAGGAGG+AGG - chr1.4:6110253-6110272 None:intergenic 40.0%
!!! GCTTTTTTCCTCTTTGTGAC+TGG - chr1.4:6110097-6110116 None:intergenic 40.0%
ACGAATACCCAAAAGGGCAA+TGG + chr1.4:6110197-6110216 MS.gene57241:CDS 45.0%
AGAGGAAAAAAGCTGCTGCT+AGG + chr1.4:6110104-6110123 MS.gene57241:CDS 45.0%
AGTAATACCTTGGAACCCGT+AGG - chr1.4:6110328-6110347 None:intergenic 45.0%
ATCGCAATCGAAACAAACCC+TGG - chr1.4:6110275-6110294 None:intergenic 45.0%
GAGGAAAAAAGCTGCTGCTA+GGG + chr1.4:6110105-6110124 MS.gene57241:CDS 45.0%
GGAAGAGGCAAAAGCCAATA+AGG + chr1.4:6110522-6110541 MS.gene57241:CDS 45.0%
! AGTATTCGCCATTGCCCTTT+TGG - chr1.4:6110208-6110227 None:intergenic 45.0%
! GTATTCGCCATTGCCCTTTT+GGG - chr1.4:6110207-6110226 None:intergenic 45.0%
ATGTGGACTCCGACGAAGAA+GGG + chr1.4:6110501-6110520 MS.gene57241:CDS 50.0%
CAGTCGTTGTGCAATGCATG+TGG + chr1.4:6110484-6110503 MS.gene57241:intron 50.0%
CGAACACTACTCCTCTTTGG+CGG + chr1.4:6110296-6110315 MS.gene57241:CDS 50.0%
TCTTTGGCGGAGTGATCCTA+CGG + chr1.4:6110309-6110328 MS.gene57241:CDS 50.0%
TTGCCTCTTCCCTTCTTCGT+CGG - chr1.4:6110513-6110532 None:intergenic 50.0%
ACTCCGACGAAGAAGGGAAG+AGG + chr1.4:6110507-6110526 MS.gene57241:CDS 55.0%
CATGTGGACTCCGACGAAGA+AGG + chr1.4:6110500-6110519 MS.gene57241:CDS 55.0%
CTTTGGCGGAGTGATCCTAC+GGG + chr1.4:6110310-6110329 MS.gene57241:CDS 55.0%
GAGTGATCCTACGGGTTCCA+AGG + chr1.4:6110318-6110337 MS.gene57241:CDS 55.0%
GGAGGGCTGAACCAATTCCT+TGG - chr1.4:6110235-6110254 None:intergenic 55.0%
GTAGGATCACTCCGCCAAAG+AGG - chr1.4:6110310-6110329 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 6110067 6110612 6110067 ID=MS.gene57241
chr1.4 mRNA 6110067 6110612 6110067 ID=MS.gene57241.t1;Parent=MS.gene57241
chr1.4 exon 6110067 6110339 6110067 ID=MS.gene57241.t1.exon1;Parent=MS.gene57241.t1
chr1.4 CDS 6110067 6110339 6110067 ID=cds.MS.gene57241.t1;Parent=MS.gene57241.t1
chr1.4 exon 6110487 6110612 6110487 ID=MS.gene57241.t1.exon2;Parent=MS.gene57241.t1
chr1.4 CDS 6110487 6110612 6110487 ID=cds.MS.gene57241.t1;Parent=MS.gene57241.t1
Gene Sequence

>MS.gene57241

ATGAGAGTATGTAACGATGATCCAATTCCAGTCACAAAGAGGAAAAAAGCTGCTGCTAGGGCTACAAAAAAGAAGAAAACAGCTGCTACTGCTAGTGCTGCCAAAAAGAAAATAAAAACTGCTACTGAATACGAATACCCAAAAGGGCAATGGCGAATACTATATCCAAGGAATTGGTTCAGCCCTCCTCCTAGTAAAAACACAACCAGGGTTTGTTTCGATTGCGATACGAACACTACTCCTCTTTGGCGGAGTGATCCTACGGGTTCCAAGGTATTACTTAATCTGTCTTCTCCACAACTTATTTACTATCAAATTTCACTTTTGGTTCATTCAAAAGTGTTATTCCATACTTATACATATTGATTAATAATTTGAATATCTAGTTATATATAGTTAACAAGAAATATGTTGGTGCAGTCGTTGTGCAATGCATGTGGACTCCGACGAAGAAGGGAAGAGGCAAAAGCCAATAAGGGTCTTGACACTGAAAAGGGAAAGGGAAATGGCGAAAGCTCATCACCTGAGAATGTGAAAAAGTTTTAA
Protein sequence

>MS.gene57241.t1

MRVCNDDPIPVTKRKKAAARATKKKKTAATASAAKKKIKTATEYEYPKGQWRILYPRNWFSPPPSKNTTRVCFDCDTNTTPLWRSDPTGSKSLCNACGLRRRREEAKANKGLDTEKGKGNGESSSPENVKKF