AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24565

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24565.t1 MTR_1g016200 55.340 103 35 3 9 100 2 104 7.94e-25 90.9
MS.gene24565.t1 MTR_1g016170 62.500 48 15 1 56 100 187 234 3.78e-13 64.3
MS.gene24565.t1 MTR_7g112330 42.373 59 34 0 56 114 22 80 2.07e-11 57.4
MS.gene24565.t1 MTR_4g121110 48.276 58 25 2 54 111 28 80 4.12e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24565.t1 AT5G56860 46.154 65 31 1 25 89 203 263 5.90e-12 61.6
MS.gene24565.t1 AT5G49300 44.928 69 32 2 56 120 36 102 7.81e-12 58.5
MS.gene24565.t1 AT4G26150 71.875 32 9 0 56 87 199 230 4.41e-11 58.9
MS.gene24565.t1 AT5G26930 60.000 35 14 0 56 90 26 60 9.62e-11 55.5

Find 27 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTCTTTGTGGCTGGAAC+TGG 0.239072 1.2:-6296957 None:intergenic
AGTATTCGCCATTGCCCTTT+TGG 0.253039 1.2:-6297068 None:intergenic
ATGAGTATCAAGACCCTTAT+CGG 0.303482 1.2:-6297363 None:intergenic
ATACAAACACTACTCCTCTT+TGG 0.387924 1.2:+6297120 MS.gene24565:CDS
GGAAGAGGCAAAAGCCGATA+AGG 0.448770 1.2:+6297349 MS.gene24565:CDS
CAATCGAAACAAACCCTAGT+TGG 0.460017 1.2:-6297095 None:intergenic
TCTTGATACTCATAAGGAAA+AGG 0.465163 1.2:+6297373 MS.gene24565:CDS
TTGCCTCTTCCCTTCTTCGT+CGG 0.477939 1.2:-6297337 None:intergenic
CTTGATACTCATAAGGAAAA+GGG 0.489428 1.2:+6297374 MS.gene24565:CDS
TAAGGGTCTTGATACTCATA+AGG 0.492473 1.2:+6297367 MS.gene24565:CDS
ACCGAATACGAATACCCAAA+AGG 0.493067 1.2:+6297053 MS.gene24565:CDS
CCGAATACGAATACCCAAAA+GGG 0.528839 1.2:+6297054 MS.gene24565:CDS
GAAGAGGCAAAAGCCGATAA+GGG 0.529120 1.2:+6297350 MS.gene24565:CDS
ATGTGGACTCCGACGAAGAA+GGG 0.540307 1.2:+6297328 MS.gene24565:CDS
CTTTGGAGGAGTGATCCTAC+AGG 0.546346 1.2:+6297137 MS.gene24565:CDS
GGCGAATACTATATCCAACT+AGG 0.572160 1.2:+6297081 MS.gene24565:CDS
CATGTGGACTCCGACGAAGA+AGG 0.573346 1.2:+6297327 MS.gene24565:CDS
GAGTGATCCTACAGGTTCCA+AGG 0.583772 1.2:+6297145 MS.gene24565:CDS
ACTCCGACGAAGAAGGGAAG+AGG 0.589069 1.2:+6297334 MS.gene24565:CDS
CAAACACTACTCCTCTTTGG+AGG 0.592172 1.2:+6297123 MS.gene24565:CDS
GCGAATACTATATCCAACTA+GGG 0.606852 1.2:+6297082 MS.gene24565:CDS
CAGTCGTTGTGCAATGCATG+TGG 0.610062 1.2:+6297311 MS.gene24565:intron
ACGAATACCCAAAAGGGCAA+TGG 0.610371 1.2:+6297060 MS.gene24565:CDS
ACTCATAAGGAAAAGGGCAA+TGG 0.616678 1.2:+6297380 MS.gene24565:CDS
TGGCGAACGCTCATCATCTG+AGG 0.618644 1.2:+6297400 MS.gene24565:CDS
CTAATTACCTTGGAACCTGT+AGG 0.643620 1.2:-6297152 None:intergenic
GTAGGATCACTCCTCCAAAG+AGG 0.666474 1.2:-6297134 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATCAATATGTATAAGTA+TGG - chr1.2:6297244-6297263 None:intergenic 15.0%
!!! AAATTTGATAGTAAATAAGT+TGG - chr1.2:6297193-6297212 None:intergenic 15.0%
!!! AATTTGATAGTAAATAAGTT+GGG - chr1.2:6297192-6297211 None:intergenic 15.0%
!!! AGCAATTTTTATTTTCTTTT+TGG - chr1.2:6297033-6297052 None:intergenic 15.0%
!! ATAGTTAACAAGAAATATGT+TGG + chr1.2:6297286-6297305 MS.gene24565:intron 20.0%
!!! TTACTATCAAATTTCACTTT+TGG + chr1.2:6297199-6297218 MS.gene24565:intron 20.0%
!!! AGTAGTTTTTTTCTTCTTTG+TGG - chr1.2:6296970-6296989 None:intergenic 25.0%
CTTGATACTCATAAGGAAAA+GGG + chr1.2:6297374-6297393 MS.gene24565:CDS 30.0%
TCTTGATACTCATAAGGAAA+AGG + chr1.2:6297373-6297392 MS.gene24565:CDS 30.0%
ATACAAACACTACTCCTCTT+TGG + chr1.2:6297120-6297139 MS.gene24565:CDS 35.0%
ATGAGTATCAAGACCCTTAT+CGG - chr1.2:6297366-6297385 None:intergenic 35.0%
GAGAGATGAACTAATTACCT+TGG - chr1.2:6297165-6297184 None:intergenic 35.0%
GCGAATACTATATCCAACTA+GGG + chr1.2:6297082-6297101 MS.gene24565:CDS 35.0%
TAAGGGTCTTGATACTCATA+AGG + chr1.2:6297367-6297386 MS.gene24565:CDS 35.0%
!! AGCAGCTGATTTCTTCTTTT+TGG - chr1.2:6297003-6297022 None:intergenic 35.0%
!!! GTTTTTTTCTTCTTTGTGGC+TGG - chr1.2:6296966-6296985 None:intergenic 35.0%
ACCGAATACGAATACCCAAA+AGG + chr1.2:6297053-6297072 MS.gene24565:CDS 40.0%
ACTCATAAGGAAAAGGGCAA+TGG + chr1.2:6297380-6297399 MS.gene24565:CDS 40.0%
CAATCGAAACAAACCCTAGT+TGG - chr1.2:6297098-6297117 None:intergenic 40.0%
CCGAATACGAATACCCAAAA+GGG + chr1.2:6297054-6297073 MS.gene24565:CDS 40.0%
CTAATTACCTTGGAACCTGT+AGG - chr1.2:6297155-6297174 None:intergenic 40.0%
GGCGAATACTATATCCAACT+AGG + chr1.2:6297081-6297100 MS.gene24565:CDS 40.0%
!! CCCTTTTGGGTATTCGTATT+CGG - chr1.2:6297057-6297076 None:intergenic 40.0%
ACGAATACCCAAAAGGGCAA+TGG + chr1.2:6297060-6297079 MS.gene24565:CDS 45.0%
CAAACACTACTCCTCTTTGG+AGG + chr1.2:6297123-6297142 MS.gene24565:CDS 45.0%
GAAGAGGCAAAAGCCGATAA+GGG + chr1.2:6297350-6297369 MS.gene24565:CDS 45.0%
TTCTTCTTTGTGGCTGGAAC+TGG - chr1.2:6296960-6296979 None:intergenic 45.0%
! AGTATTCGCCATTGCCCTTT+TGG - chr1.2:6297071-6297090 None:intergenic 45.0%
! GTATTCGCCATTGCCCTTTT+GGG - chr1.2:6297070-6297089 None:intergenic 45.0%
ATGTGGACTCCGACGAAGAA+GGG + chr1.2:6297328-6297347 MS.gene24565:CDS 50.0%
CAGTCGTTGTGCAATGCATG+TGG + chr1.2:6297311-6297330 MS.gene24565:intron 50.0%
GAGTGATCCTACAGGTTCCA+AGG + chr1.2:6297145-6297164 MS.gene24565:CDS 50.0%
GGAAGAGGCAAAAGCCGATA+AGG + chr1.2:6297349-6297368 MS.gene24565:CDS 50.0%
GTAGGATCACTCCTCCAAAG+AGG - chr1.2:6297137-6297156 None:intergenic 50.0%
TTGCCTCTTCCCTTCTTCGT+CGG - chr1.2:6297340-6297359 None:intergenic 50.0%
! CTTTGGAGGAGTGATCCTAC+AGG + chr1.2:6297137-6297156 MS.gene24565:CDS 50.0%
ACTCCGACGAAGAAGGGAAG+AGG + chr1.2:6297334-6297353 MS.gene24565:CDS 55.0%
CATGTGGACTCCGACGAAGA+AGG + chr1.2:6297327-6297346 MS.gene24565:CDS 55.0%
TGGCGAACGCTCATCATCTG+AGG + chr1.2:6297400-6297419 MS.gene24565:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 6296936 6297451 6296936 ID=MS.gene24565
chr1.2 mRNA 6296936 6297451 6296936 ID=MS.gene24565.t1;Parent=MS.gene24565
chr1.2 exon 6296936 6297166 6296936 ID=MS.gene24565.t1.exon1;Parent=MS.gene24565.t1
chr1.2 CDS 6296936 6297166 6296936 ID=cds.MS.gene24565.t1;Parent=MS.gene24565.t1
chr1.2 exon 6297314 6297451 6297314 ID=MS.gene24565.t1.exon2;Parent=MS.gene24565.t1
chr1.2 CDS 6297314 6297451 6297314 ID=cds.MS.gene24565.t1;Parent=MS.gene24565.t1
Gene Sequence

>MS.gene24565

ATGAGAGTAAGTAACGATGATCCAGTTCCAGCCACAAAGAAGAAAAAAACTACTGCTAGTGCTGCCAAAAAGAAGAAATCAGCTGCTAGTGCTGCCAAAAAGAAAATAAAAATTGCTACCGAATACGAATACCCAAAAGGGCAATGGCGAATACTATATCCAACTAGGGTTTGTTTCGATTGCAATACAAACACTACTCCTCTTTGGAGGAGTGATCCTACAGGTTCCAAGGTAATTAGTTCATCTCTCTTCTCCCAACTTATTTACTATCAAATTTCACTTTTGGTTCATGCAAAAGTGTTATTCCATACTTATACATATTGATTAATAATTTGAGTATCTAGTTATATATAGTTAACAAGAAATATGTTGGTGCAGTCGTTGTGCAATGCATGTGGACTCCGACGAAGAAGGGAAGAGGCAAAAGCCGATAAGGGTCTTGATACTCATAAGGAAAAGGGCAATGGCGAACGCTCATCATCTGAGGATGTGAAGAATGTTTTAATGTTCATCTGA
Protein sequence

>MS.gene24565.t1

MRVSNDDPVPATKKKKTTASAAKKKKSAASAAKKKIKIATEYEYPKGQWRILYPTRVCFDCNTNTTPLWRSDPTGSKSLCNACGLRRRREEAKADKGLDTHKEKGNGERSSSEDVKNVLMFI