AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene049662


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049662.t1 MTR_3g064070 97.581 124 3 0 1 124 54 177 4.62e-85 246
MS.gene049662.t1 MTR_8g005175 29.524 105 74 0 20 124 127 231 6.94e-12 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.gene049662.t1 AT2G01918 44.531 128 65 3 3 124 60 187 1.26e-29 105
MS.gene049662.t1 AT4G21280 31.967 122 77 1 9 124 102 223 5.33e-17 73.9
MS.gene049662.t1 AT4G21280 31.967 122 77 1 9 124 101 222 6.27e-17 73.9
MS.gene049662.t1 AT4G05180 29.508 122 80 1 9 124 108 229 1.28e-15 70.5
MS.gene049662.t1 AT4G05180 29.508 122 80 1 9 124 108 229 1.28e-15 70.5

Find 15 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTGCAAATGCATTTGATTT+TGG 0.133260 3.2:-59633200 MS.gene049662:CDS
AACTGTGACCTTTCACTTCC+AGG 0.232695 3.2:+59632999 None:intergenic
GCCTCTTCAACTGTTTGATC+AGG 0.315431 3.2:+59633167 None:intergenic
TCATAACGCTGCCACACTTC+AGG 0.379368 3.2:+59632785 None:intergenic
GTCATGGAAAATAGCACAAA+AGG 0.423780 3.2:-59633081 MS.gene049662:CDS
TTAGTGGAGAGTGCATGTTT+AGG 0.480583 3.2:-59633229 None:intergenic
ACCATAATTCAAAACAAGCC+TGG 0.511434 3.2:-59633017 MS.gene049662:CDS
GAAGTGAAAGGTCACAGTTA+AGG 0.517020 3.2:-59632995 MS.gene049662:CDS
CCTCTTCAACTGTTTGATCA+GGG 0.547039 3.2:+59633168 None:intergenic
CCCTGATCAAACAGTTGAAG+AGG 0.549247 3.2:-59633168 MS.gene049662:CDS
AAAACAAGCCTGGAAGTGAA+AGG 0.596015 3.2:-59633007 MS.gene049662:CDS
ATTTGTTAGAGTCAAAGTCA+TGG 0.608950 3.2:-59633097 MS.gene049662:CDS
ATCAAGATGGACCTGAAGTG+TGG 0.634230 3.2:-59632796 MS.gene049662:CDS
GCGTTATGAGAACATTGTTG+TGG 0.635212 3.2:-59632771 MS.gene049662:CDS
TATGCAGCAAGAGATCAAGA+TGG 0.661307 3.2:-59632809 MS.gene049662:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATTGTTTTTGTTGTGTA+AGG - chr3.2:59633066-59633085 MS.gene049662:CDS 20.0%
!!! ATTGATGTTTAGTTTTGCAT+TGG - chr3.2:59633104-59633123 MS.gene049662:CDS 25.0%
!!! ATTGCAAATGCATTTGATTT+TGG - chr3.2:59632757-59632776 MS.gene049662:CDS 25.0%
TCAACAATGTTACTAGAGTA+AGG - chr3.2:59633004-59633023 MS.gene049662:CDS 30.0%
! ATTTGTTAGAGTCAAAGTCA+TGG - chr3.2:59632860-59632879 MS.gene049662:intron 30.0%
ACCATAATTCAAAACAAGCC+TGG - chr3.2:59632940-59632959 MS.gene049662:intron 35.0%
GTCATGGAAAATAGCACAAA+AGG - chr3.2:59632876-59632895 MS.gene049662:intron 35.0%
!! AAGTTCAGCACTTTTGAAGA+AGG - chr3.2:59632909-59632928 MS.gene049662:intron 35.0%
!! TGACAAAGTGTCCTAGTTTT+AGG + chr3.2:59633039-59633058 None:intergenic 35.0%
!!! TCCAGGCTTGTTTTGAATTA+TGG + chr3.2:59632944-59632963 None:intergenic 35.0%
AAAACAAGCCTGGAAGTGAA+AGG - chr3.2:59632950-59632969 MS.gene049662:intron 40.0%
CCTCTTCAACTGTTTGATCA+GGG + chr3.2:59632792-59632811 None:intergenic 40.0%
GAAGTGAAAGGTCACAGTTA+AGG - chr3.2:59632962-59632981 MS.gene049662:CDS 40.0%
GCGTTATGAGAACATTGTTG+TGG - chr3.2:59633186-59633205 MS.gene049662:CDS 40.0%
GGAGACTTTGTCCTAAAACT+AGG - chr3.2:59633025-59633044 MS.gene049662:CDS 40.0%
TATGCAGCAAGAGATCAAGA+TGG - chr3.2:59633148-59633167 MS.gene049662:CDS 40.0%
AACTGTGACCTTTCACTTCC+AGG + chr3.2:59632961-59632980 None:intergenic 45.0%
ATCAAGATGGACCTGAAGTG+TGG - chr3.2:59633161-59633180 MS.gene049662:CDS 45.0%
CCCTGATCAAACAGTTGAAG+AGG - chr3.2:59632789-59632808 MS.gene049662:CDS 45.0%
GCCTCTTCAACTGTTTGATC+AGG + chr3.2:59632793-59632812 None:intergenic 45.0%
TCATAACGCTGCCACACTTC+AGG + chr3.2:59633175-59633194 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 59632742 59633237 59632742 ID=MS.gene049662
chr3.2 mRNA 59632742 59633237 59632742 ID=MS.gene049662.t1;Parent=MS.gene049662
chr3.2 exon 59632959 59633237 59632959 ID=MS.gene049662.t1.exon1;Parent=MS.gene049662.t1
chr3.2 CDS 59632959 59633237 59632959 ID=cds.MS.gene049662.t1;Parent=MS.gene049662.t1
chr3.2 exon 59632742 59632837 59632742 ID=MS.gene049662.t1.exon2;Parent=MS.gene049662.t1
chr3.2 CDS 59632742 59632837 59632742 ID=cds.MS.gene049662.t1;Parent=MS.gene049662.t1
Gene Sequence

>MS.gene049662

ATGTTTAGGACAAAGATTGCAAATGCATTTGATTTTGGACTTGTTGTCCCTGATCAAACAGTTGAAGAGGCACAAAATGTAGTGAGAGTTCATGCACAAGATTTATTGCAAGTTAGAGATTTGTTAGAGTCAAAGTCATGGAAAATAGCACAAAAGGAATTGAGAAGAAGTTCAGCACTTTTGAAGAAGGATATATACACCATAATTCAAAACAAGCCTGGAAGTGAAAGGTCACAGTTAAGGAAGCTCTATTCTACTCTCTTCAACAATGTTACTAGAGTAAGGAGACTTTGTCCTAAAACTAGGACACTTTGTCATGAAGAGTTTATTGTTTTTGTTGTGTAAGGTTTTATTACTTTTCAATTGATGTTTAGTTTTGCATTGGTGAAAAATAACGCAGCTAGATTATGCAGCAAGAGATCAAGATGGACCTGAAGTGTGGCAGCGTTATGAGAACATTGTTGTGGCTGTGAATGAAATTCTATCAAGAATATAA

Protein sequence

>MS.gene049662.t1

MFRTKIANAFDFGLVVPDQTVEEAQNVVRVHAQDLLQVRDLLESKSWKIAQKELRRSSALLKKDIYTIIQNKPGSERSQLRKLYSTLFNNVTRLDYAARDQDGPEVWQRYENIVVAVNEILSRI