AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24502

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24502.t1 MTR_1g017500 94.194 155 9 0 3 157 4 158 2.53e-107 303
MS.gene24502.t1 MTR_4g097480 36.424 151 79 7 9 154 12 150 1.20e-14 67.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCTTCCAAGAAGGGTATT+TGG 0.166363 1.1:-5028097 MS.gene24502:CDS
ATGAGTACTAACACTTTCTT+TGG 0.167473 1.1:+5028274 None:intergenic
CAATGTTCGTGATAATAATT+TGG 0.187740 1.1:-5027916 MS.gene24502:CDS
CTTACCACCTTTCTTACTTT+TGG 0.205917 1.1:+5028031 None:intergenic
TTGAACCCAAATACCCTTCT+TGG 0.237720 1.1:+5028091 None:intergenic
CTCTCATTCTCCACAGAATA+TGG 0.249335 1.1:-5027886 MS.gene24502:CDS
TTGGAAGAAGTTCTATAATA+AGG 0.277422 1.1:+5028110 None:intergenic
AAATCATGAACAAGATTTCT+AGG 0.278610 1.1:+5028167 None:intergenic
TTCTTCCAAGAAGGGTATTT+GGG 0.323054 1.1:-5028096 MS.gene24502:CDS
CCTCCAATTTCTTCACTTGA+AGG 0.323798 1.1:-5028200 MS.gene24502:CDS
GCTCCTTCAAGTGAAGAAAT+TGG 0.323964 1.1:+5028197 None:intergenic
AATGATATCTTTCTTGTTAG+TGG 0.354774 1.1:+5028323 None:intergenic
TGAGTACTAACACTTTCTTT+GGG 0.383987 1.1:+5028275 None:intergenic
AAAGAAAGTGTTAGTACTCA+TGG 0.470475 1.1:-5028272 MS.gene24502:CDS
AAAGTAAGAAAGGTGGTAAG+AGG 0.472280 1.1:-5028028 MS.gene24502:CDS
CAAGAAAGATATCATTCTCA+TGG 0.473616 1.1:-5028316 MS.gene24502:CDS
TTCGTGATAATAATTTGGTT+AGG 0.477674 1.1:-5027911 MS.gene24502:CDS
TTATAGAACTTCTTCCAAGA+AGG 0.493929 1.1:-5028105 MS.gene24502:CDS
ACACTTTCTTTGGGGATACC+CGG 0.505002 1.1:+5028284 None:intergenic
TTCTCATGGGAAAAGAAGCC+GGG 0.513115 1.1:-5028302 MS.gene24502:CDS
TATAGAACTTCTTCCAAGAA+GGG 0.516874 1.1:-5028104 MS.gene24502:CDS
TGAAAAGCACAAGGAGGAAG+TGG 0.520857 1.1:+5028137 None:intergenic
TTCAAGTGAAGAAATTGGAG+GGG 0.525754 1.1:+5028202 None:intergenic
GAGTGTACCAAAAGTAAGAA+AGG 0.526631 1.1:-5028038 MS.gene24502:CDS
ATTCTCATGGGAAAAGAAGC+CGG 0.529047 1.1:-5028303 MS.gene24502:CDS
TCTTTGTAAGCTGCTAAGAA+AGG 0.554304 1.1:+5028059 None:intergenic
AAGAAAGATATCATTCTCAT+GGG 0.573446 1.1:-5028315 MS.gene24502:CDS
AAGTAAGAAAGGTGGTAAGA+GGG 0.577764 1.1:-5028027 MS.gene24502:CDS
CCTTCAAGTGAAGAAATTGG+AGG 0.579659 1.1:+5028200 None:intergenic
CTTCAAGTGAAGAAATTGGA+GGG 0.583909 1.1:+5028201 None:intergenic
GAGTACTAACACTTTCTTTG+GGG 0.584297 1.1:+5028276 None:intergenic
CAATCTCAATCCATATTCTG+TGG 0.592980 1.1:+5027876 None:intergenic
GAAGAAGTTCTATAATAAGG+AGG 0.615153 1.1:+5028113 None:intergenic
TCAAGTGAAGAAATTGGAGG+GGG 0.624631 1.1:+5028203 None:intergenic
TGTACCAAAAGTAAGAAAGG+TGG 0.672007 1.1:-5028035 MS.gene24502:CDS
TAAGGAGGTTGAAAAGCACA+AGG 0.678388 1.1:+5028128 None:intergenic
GGAGGTTGAAAAGCACAAGG+AGG 0.741035 1.1:+5028131 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAATCATGAACAAGATTTCT+AGG + chr1.1:5028049-5028068 None:intergenic 25.0%
! AAGAAAGATATCATTCTCAT+GGG - chr1.1:5027898-5027917 MS.gene24502:CDS 25.0%
! AATGATATCTTTCTTGTTAG+TGG + chr1.1:5027893-5027912 None:intergenic 25.0%
! CAATGTTCGTGATAATAATT+TGG - chr1.1:5028297-5028316 MS.gene24502:CDS 25.0%
! TTCGTGATAATAATTTGGTT+AGG - chr1.1:5028302-5028321 MS.gene24502:CDS 25.0%
! TTGGAAGAAGTTCTATAATA+AGG + chr1.1:5028106-5028125 None:intergenic 25.0%
ATGAGTACTAACACTTTCTT+TGG + chr1.1:5027942-5027961 None:intergenic 30.0%
CAAGAAAGATATCATTCTCA+TGG - chr1.1:5027897-5027916 MS.gene24502:CDS 30.0%
GAAGAAGTTCTATAATAAGG+AGG + chr1.1:5028103-5028122 None:intergenic 30.0%
GCAAAAATTCATTCTCTCTT+TGG + chr1.1:5027979-5027998 None:intergenic 30.0%
TATAGAACTTCTTCCAAGAA+GGG - chr1.1:5028109-5028128 MS.gene24502:CDS 30.0%
TGAGTACTAACACTTTCTTT+GGG + chr1.1:5027941-5027960 None:intergenic 30.0%
TTATAGAACTTCTTCCAAGA+AGG - chr1.1:5028108-5028127 MS.gene24502:CDS 30.0%
! GTAGTAGTTTTTGTGAATCA+AGG - chr1.1:5028233-5028252 MS.gene24502:CDS 30.0%
!! AAAGAAAGTGTTAGTACTCA+TGG - chr1.1:5027941-5027960 MS.gene24502:CDS 30.0%
AAAGTAAGAAAGGTGGTAAG+AGG - chr1.1:5028185-5028204 MS.gene24502:CDS 35.0%
AAGTAAGAAAGGTGGTAAGA+GGG - chr1.1:5028186-5028205 MS.gene24502:CDS 35.0%
CTTCAAGTGAAGAAATTGGA+GGG + chr1.1:5028015-5028034 None:intergenic 35.0%
GACAAAAAGATTAGTAGAGC+TGG - chr1.1:5028208-5028227 MS.gene24502:CDS 35.0%
GAGTACTAACACTTTCTTTG+GGG + chr1.1:5027940-5027959 None:intergenic 35.0%
GAGTGTACCAAAAGTAAGAA+AGG - chr1.1:5028175-5028194 MS.gene24502:CDS 35.0%
TCTTTGTAAGCTGCTAAGAA+AGG + chr1.1:5028157-5028176 None:intergenic 35.0%
TGTACCAAAAGTAAGAAAGG+TGG - chr1.1:5028178-5028197 MS.gene24502:CDS 35.0%
TTCAAGTGAAGAAATTGGAG+GGG + chr1.1:5028014-5028033 None:intergenic 35.0%
! CTTACCACCTTTCTTACTTT+TGG + chr1.1:5028185-5028204 None:intergenic 35.0%
!! TTCTTCCAAGAAGGGTATTT+GGG - chr1.1:5028117-5028136 MS.gene24502:CDS 35.0%
ATTCTCATGGGAAAAGAAGC+CGG - chr1.1:5027910-5027929 MS.gene24502:CDS 40.0%
CCTCCAATTTCTTCACTTGA+AGG - chr1.1:5028013-5028032 MS.gene24502:CDS 40.0%
CCTTCAAGTGAAGAAATTGG+AGG + chr1.1:5028016-5028035 None:intergenic 40.0%
CTCTCATTCTCCACAGAATA+TGG - chr1.1:5028327-5028346 MS.gene24502:CDS 40.0%
GCTCCTTCAAGTGAAGAAAT+TGG + chr1.1:5028019-5028038 None:intergenic 40.0%
TCAAGTGAAGAAATTGGAGG+GGG + chr1.1:5028013-5028032 None:intergenic 40.0%
TTGAACCCAAATACCCTTCT+TGG + chr1.1:5028125-5028144 None:intergenic 40.0%
! TAAGGAGGTTGAAAAGCACA+AGG + chr1.1:5028088-5028107 None:intergenic 40.0%
!! CTTCTTCCAAGAAGGGTATT+TGG - chr1.1:5028116-5028135 MS.gene24502:CDS 40.0%
TTCTCATGGGAAAAGAAGCC+GGG - chr1.1:5027911-5027930 MS.gene24502:CDS 45.0%
! ACACTTTCTTTGGGGATACC+CGG + chr1.1:5027932-5027951 None:intergenic 45.0%
! TGAAAAGCACAAGGAGGAAG+TGG + chr1.1:5028079-5028098 None:intergenic 45.0%
AGTGAAGAAATTGGAGGGGG+TGG + chr1.1:5028010-5028029 None:intergenic 50.0%
ATTGGAGGGGGTGGTAACTT+AGG + chr1.1:5028001-5028020 None:intergenic 50.0%
! GGAGGTTGAAAAGCACAAGG+AGG + chr1.1:5028085-5028104 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 5027881 5028354 5027881 ID=MS.gene24502
chr1.1 mRNA 5027881 5028354 5027881 ID=MS.gene24502.t1;Parent=MS.gene24502
chr1.1 exon 5027881 5028354 5027881 ID=MS.gene24502.t1.exon1;Parent=MS.gene24502.t1
chr1.1 CDS 5027881 5028354 5027881 ID=cds.MS.gene24502.t1;Parent=MS.gene24502.t1
Gene Sequence

>MS.gene24502

ATGAGTCAACCACTAACAAGAAAGATATCATTCTCATGGGAAAAGAAGCCGGGTATCCCCAAAGAAAGTGTTAGTACTCATGGTGAAAATTTAATCCAAAGAGAGAATGAATTTTTGCCTAAGTTACCACCCCCTCCAATTTCTTCACTTGAAGGAGCAACTACTCCTAGAAATCTTGTTCATGATTTTCAAATTCCACTTCCTCCTTGTGCTTTTCAACCTCCTTATTATAGAACTTCTTCCAAGAAGGGTATTTGGGTTCAAGATGATGATCCTTTCTTAGCAGCTTACAAAGAGTGTACCAAAAGTAAGAAAGGTGGTAAGAGGGACAAAAAGATTAGTAGAGCTGGTAGTAGTAGTTTTTGTGAATCAAGGTTAGTGAAAAACATGTCTTTTTTCTCATGTAAGAGATCTTGCAATGTTCGTGATAATAATTTGGTTAGGATCTCTCATTCTCCACAGAATATGGATTGA
Protein sequence

>MS.gene24502.t1

MSQPLTRKISFSWEKKPGIPKESVSTHGENLIQRENEFLPKLPPPPISSLEGATTPRNLVHDFQIPLPPCAFQPPYYRTSSKKGIWVQDDDPFLAAYKECTKSKKGGKRDKKISRAGSSSFCESRLVKNMSFFSCKRSCNVRDNNLVRISHSPQNMD