AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene65492

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene65492.t1 MTR_1g043050 78.409 176 32 1 1 176 85 254 5.46e-97 281
MS.gene65492.t1 MTR_1g043080 81.921 177 25 3 1 176 85 255 7.55e-90 263
MS.gene65492.t1 MTR_1g076150 52.809 178 72 5 4 176 36 206 4.94e-46 150
MS.gene65492.t1 MTR_1g076150 51.934 181 75 5 1 176 85 258 3.22e-45 149
MS.gene65492.t1 MTR_7g096930 34.826 201 99 6 1 176 85 278 5.51e-20 84.7
MS.gene65492.t1 MTR_7g115650 71.875 32 9 0 1 32 85 116 2.90e-11 60.1
MS.gene65492.t1 MTR_5g014990 48.571 70 28 3 1 68 86 149 5.05e-11 60.5
MS.gene65492.t1 MTR_2g089620 72.727 33 9 0 1 33 85 117 5.59e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene65492.t1 AT3G23250 38.308 201 92 7 1 173 28 224 5.64e-25 96.7
MS.gene65492.t1 AT3G23250 38.308 201 92 7 1 173 85 281 3.14e-24 96.3
MS.gene65492.t1 AT1G06180 37.433 187 81 9 1 176 85 246 3.39e-18 79.3
MS.gene65492.t1 AT2G31180 35.135 185 91 7 1 176 85 249 7.25e-18 78.6
MS.gene65492.t1 AT1G16490 93.103 29 2 0 4 32 21 49 4.75e-13 64.7
MS.gene65492.t1 AT4G28110 78.788 33 7 0 1 33 1 33 1.16e-12 63.5
MS.gene65492.t1 AT3G61250 45.205 73 34 1 1 67 85 157 2.44e-12 63.9
MS.gene65492.t1 AT1G16490 89.655 29 3 0 4 32 90 118 8.94e-12 62.4
MS.gene65492.t1 AT4G05100 75.758 33 8 0 1 33 86 118 1.89e-11 61.6
MS.gene65492.t1 AT1G79180 78.125 32 7 0 4 35 90 121 3.00e-11 60.8
MS.gene65492.t1 AT1G79180 86.207 29 4 0 4 32 123 151 3.07e-11 61.2
MS.gene65492.t1 AT4G28110 68.571 35 11 0 1 35 85 119 9.85e-11 59.3

Find 19 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTCATTATCAAAAGGGTTT+TGG 0.211007 1.3:+25753735 None:intergenic
CAAAAGCTTTCATCAATTTC+AGG 0.250594 1.3:+25753872 None:intergenic
GAAAATTACACATGAATAAA+AGG 0.253458 1.3:-25754368 None:intergenic
ATTTCATTGTCTGTTCTTCC+AGG 0.291634 1.3:+25754139 None:intergenic
CTGAAATTGATGAAAGCTTT+TGG 0.299877 1.3:-25753871 MS.gene65492:CDS
GAAACTGTCATAGGATTTGA+TGG 0.346331 1.3:+25753809 None:intergenic
AATTCATTTGAAACTGTCAT+AGG 0.356516 1.3:+25753800 None:intergenic
AGCTTCCATTGAGTTGGAAT+TGG 0.389117 1.3:+25753997 None:intergenic
CATGAAAATGTTTAGAACTC+TGG 0.425811 1.3:+25753656 None:intergenic
TATAACGTGTTCATCAAATC+AGG 0.457240 1.3:-25753695 MS.gene65492:CDS
ATGCCATCGTCATTATCAAA+AGG 0.461830 1.3:+25753728 None:intergenic
ATTGTCACAAAAGAGTCTTC+AGG 0.488694 1.3:+25753896 None:intergenic
AAATGCCAATTCCAACTCAA+TGG 0.490366 1.3:-25754002 MS.gene65492:CDS
TGCCATCGTCATTATCAAAA+GGG 0.500463 1.3:+25753729 None:intergenic
TTGTCACAAAAGAGTCTTCA+GGG 0.515022 1.3:+25753897 None:intergenic
TGATGTAGCTTCCATTGAGT+TGG 0.515373 1.3:+25753991 None:intergenic
GCAATAGCAGCAAAATTACC+TGG 0.544673 1.3:-25754157 MS.gene65492:CDS
TGTCATAGGATTTGATGGCA+TGG 0.664505 1.3:+25753814 None:intergenic
CATAGGATTTGATGGCATGG+TGG 0.687440 1.3:+25753817 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAATGAAATAAAAAATGTA+TGG - chr1.3:25753898-25753917 MS.gene65492:CDS 15.0%
!! TTAAAAATATATTGTTGATC+TGG + chr1.3:25754251-25754270 None:intergenic 15.0%
! AAATATGTTGTAATTGCATG+TGG + chr1.3:25753717-25753736 None:intergenic 25.0%
! ACAAATTAATGCTTAGTTGT+CGG + chr1.3:25753686-25753705 None:intergenic 25.0%
!! AATTCATTTGAAACTGTCAT+AGG + chr1.3:25754227-25754246 None:intergenic 25.0%
!! TCTAGTAATTTTTCATCACA+AGG - chr1.3:25754071-25754090 MS.gene65492:CDS 25.0%
!!! CTTTTTTTGGTATTTGAATG+AGG + chr1.3:25753969-25753988 None:intergenic 25.0%
!!! TTCTGATTTTTGTTTTCAGA+TGG - chr1.3:25753841-25753860 MS.gene65492:CDS 25.0%
!!! TTGTTTTGACACTCTTTTTT+TGG + chr1.3:25753982-25754001 None:intergenic 25.0%
CAAAAGCTTTCATCAATTTC+AGG + chr1.3:25754155-25754174 None:intergenic 30.0%
TATAACGTGTTCATCAAATC+AGG - chr1.3:25754329-25754348 MS.gene65492:intron 30.0%
! CTGAAATTGATGAAAGCTTT+TGG - chr1.3:25754153-25754172 MS.gene65492:CDS 30.0%
! TTTTGGTATTTGAATGAGGT+TGG + chr1.3:25753965-25753984 None:intergenic 30.0%
!! TGAATGAGGTTGGTTATTTT+TGG + chr1.3:25753955-25753974 None:intergenic 30.0%
AAATGCCAATTCCAACTCAA+TGG - chr1.3:25754022-25754041 MS.gene65492:CDS 35.0%
ATGCCATCGTCATTATCAAA+AGG + chr1.3:25754299-25754318 None:intergenic 35.0%
ATGTTGTAATTGCATGTGGT+TGG + chr1.3:25753713-25753732 None:intergenic 35.0%
ATTGTCACAAAAGAGTCTTC+AGG + chr1.3:25754131-25754150 None:intergenic 35.0%
ATTTCATTGTCTGTTCTTCC+AGG + chr1.3:25753888-25753907 None:intergenic 35.0%
GAAACTGTCATAGGATTTGA+TGG + chr1.3:25754218-25754237 None:intergenic 35.0%
TGCCATCGTCATTATCAAAA+GGG + chr1.3:25754298-25754317 None:intergenic 35.0%
TTGTCACAAAAGAGTCTTCA+GGG + chr1.3:25754130-25754149 None:intergenic 35.0%
! CGTCATTATCAAAAGGGTTT+TGG + chr1.3:25754292-25754311 None:intergenic 35.0%
! GAGATTCGAATTTTGCTTCT+TGG + chr1.3:25753812-25753831 None:intergenic 35.0%
!!! AACCCTTTTGATAATGACGA+TGG - chr1.3:25754293-25754312 MS.gene65492:intron 35.0%
!!! TTTTGATAATGACGATGGCA+TGG - chr1.3:25754298-25754317 MS.gene65492:intron 35.0%
GCAATAGCAGCAAAATTACC+TGG - chr1.3:25753867-25753886 MS.gene65492:CDS 40.0%
TGATGTAGCTTCCATTGAGT+TGG + chr1.3:25754036-25754055 None:intergenic 40.0%
! ATGACGATGGCATGGATTTT+TGG - chr1.3:25754306-25754325 MS.gene65492:intron 40.0%
! TGTCATAGGATTTGATGGCA+TGG + chr1.3:25754213-25754232 None:intergenic 40.0%
!! AGCTTCCATTGAGTTGGAAT+TGG + chr1.3:25754030-25754049 None:intergenic 40.0%
! CATAGGATTTGATGGCATGG+TGG + chr1.3:25754210-25754229 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 25753667 25754379 25753667 ID=MS.gene65492
chr1.3 mRNA 25753667 25754379 25753667 ID=MS.gene65492.t1;Parent=MS.gene65492
chr1.3 exon 25754369 25754379 25754369 ID=MS.gene65492.t1.exon1;Parent=MS.gene65492.t1
chr1.3 CDS 25754369 25754379 25754369 ID=cds.MS.gene65492.t1;Parent=MS.gene65492.t1
chr1.3 exon 25753667 25754186 25753667 ID=MS.gene65492.t1.exon2;Parent=MS.gene65492.t1
chr1.3 CDS 25753667 25754186 25753667 ID=cds.MS.gene65492.t1;Parent=MS.gene65492.t1
Gene Sequence

>MS.gene65492

ATGAATAAAAGGTAAGCCGACAACTAAGCATTAATTTGTAATACCAACCACATGCAATTACAACATATTTATATATATTATTGACATACATAGCACTATGCATGAATACAGTCAAAATTTGTTGTTTTCTCAATAACTTTATCCAAGAAGCAAAATTCGAATCTCATACATTAATTCTGATTTTTGTTTTCAGATGGTCAGCAATAGCAGCAAAATTACCTGGAAGAACAGACAATGAAATAAAAAATGTATGGCACACTCACTTGAAGAAAAGACTACTGAATACCAAAAATAACCAACCTCATTCAAATACCAAAAAAAGAGTGTCAAAACAAAAAATCAAAAGATATGATTCAAATGCCAATTCCAACTCAATGGAAGCTACATCATCAAATTGCACTTTTTCTAGTAATTTTTCATCACAAGGAAGAAATGTTGACAACATCATCAATTGTGAAGACCCTGAAGACTCTTTTGTGACAATGCCTGAAATTGATGAAAGCTTTTGGTCAGAGAAAATAAATGATGACGAAATTAGCTCCACCATGCCATCAAATCCTATGACAGTTTCAAATGAATTACCAGATCAACAATATATTTTTAATAATTCAGTAGAAAATTTCCAAAACCCTTTTGATAATGACGATGGCATGGATTTTTGGTATAACGTGTTCATCAAATCAGGAGAATCAACAGAATTGCCAGAGTTCTAA
Protein sequence

>MS.gene65492.t1

MNKRWSAIAAKLPGRTDNEIKNVWHTHLKKRLLNTKNNQPHSNTKKRVSKQKIKRYDSNANSNSMEATSSNCTFSSNFSSQGRNVDNIINCEDPEDSFVTMPEIDESFWSEKINDDEISSTMPSNPMTVSNELPDQQYIFNNSVENFQNPFDNDDGMDFWYNVFIKSGESTELPEF