AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene93754

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene93754.t1 MTR_8g107300 83.721 129 6 3 1 125 1 118 2.49e-70 206
MS.gene93754.t1 MTR_2g019190 76.471 136 19 3 1 125 1 134 9.65e-68 200
MS.gene93754.t1 MTR_8g107300 82.979 94 5 1 32 125 1 83 1.01e-48 150
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene93754.t1 AT1G30135 41.912 136 57 7 1 124 3 128 2.13e-21 83.2
MS.gene93754.t1 AT2G34600 39.062 128 72 5 1 124 20 145 1.25e-16 71.2

Find 26 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACTGATGTCACAGAGTTTC+AGG 0.192920 4.2:+232699 MS.gene93754:CDS
TGCCAGCATTAAGATGGATT+TGG 0.344981 4.2:-232833 None:intergenic
CAGAATCATAGAGAGGAAAA+AGG 0.376693 4.2:-232460 None:intergenic
CATCTTCCCATCATAGAATA+TGG 0.389620 4.2:-232671 None:intergenic
CCTCATCAATTGTATAGCCC+TGG 0.405940 4.2:+232931 MS.gene93754:CDS
GATGGTATGGAGATGCTTCT+TGG 0.408900 4.2:-233014 None:intergenic
GGAAAGCCCAATGCAAAATC+AGG 0.420902 4.2:+232636 MS.gene93754:CDS
TTTATTTGCCAGCATTAAGA+TGG 0.422633 4.2:-232839 None:intergenic
TTCTCTTATCTTACATGTGG+TGG 0.433401 4.2:-232502 None:intergenic
CCGCTGACCATATTCTATGA+TGG 0.457336 4.2:+232664 MS.gene93754:CDS
TCTACAGAAGAGAAAGAATA+GGG 0.468849 4.2:+232990 MS.gene93754:CDS
CTCATCAATTGTATAGCCCT+GGG 0.470700 4.2:+232932 MS.gene93754:CDS
TGAGGAGGCTGCACTATTGT+TGG 0.477785 4.2:-232913 None:intergenic
CAATTGTATAGCCCTGGGTC+TGG 0.482257 4.2:+232937 MS.gene93754:CDS
TTCTACAGAAGAGAAAGAAT+AGG 0.508590 4.2:+232989 MS.gene93754:CDS
CGCTGACCATATTCTATGAT+GGG 0.509614 4.2:+232665 MS.gene93754:CDS
GGCCAAATCCATCTTAATGC+TGG 0.519970 4.2:+232831 MS.gene93754:intron
GCAAAGATCTCTTCATTGAA+AGG 0.520559 4.2:-232960 None:intergenic
TTCATTGAAAGGCCAGACCC+AGG 0.532257 4.2:-232949 None:intergenic
GTTGTTCGCTCTGACCCTCT+CGG 0.542596 4.2:-232889 None:intergenic
CAATGAAGAGATCTTTGCAA+CGG 0.550495 4.2:+232965 MS.gene93754:CDS
GGGCTATACAATTGATGAGG+AGG 0.602793 4.2:-232928 None:intergenic
TCATTGAAAGGCCAGACCCA+GGG 0.615225 4.2:-232948 None:intergenic
CCAGGGCTATACAATTGATG+AGG 0.668057 4.2:-232931 None:intergenic
CCATCATAGAATATGGTCAG+CGG 0.671722 4.2:-232664 None:intergenic
TGATTGCCAGAATCATAGAG+AGG 0.688733 4.2:-232467 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGATTTTCTTTTTATATTT+GGG + chr4.2:232570-232589 MS.gene93754:intron 10.0%
!!! TATGATTTTCTTTTTATATT+TGG + chr4.2:232569-232588 MS.gene93754:intron 10.0%
!!! TCATTTTTTCATTTAGTTAT+TGG - chr4.2:232758-232777 None:intergenic 15.0%
!! ACAAATTGAAAAAATGGAAA+TGG - chr4.2:232544-232563 None:intergenic 20.0%
!! AGTCTAACAAATTGAAAAAA+TGG - chr4.2:232550-232569 None:intergenic 20.0%
! TAATTTCTATCTCCATTGAA+GGG + chr4.2:232612-232631 MS.gene93754:intron 25.0%
! TTAATTTCTATCTCCATTGA+AGG + chr4.2:232611-232630 MS.gene93754:intron 25.0%
TCTACAGAAGAGAAAGAATA+GGG + chr4.2:232990-233009 MS.gene93754:CDS 30.0%
TTCTACAGAAGAGAAAGAAT+AGG + chr4.2:232989-233008 MS.gene93754:CDS 30.0%
TTTATTTGCCAGCATTAAGA+TGG - chr4.2:232842-232861 None:intergenic 30.0%
CAATGAAGAGATCTTTGCAA+CGG + chr4.2:232965-232984 MS.gene93754:CDS 35.0%
CAGAATCATAGAGAGGAAAA+AGG - chr4.2:232463-232482 None:intergenic 35.0%
CATCTTCCCATCATAGAATA+TGG - chr4.2:232674-232693 None:intergenic 35.0%
GCAAAGATCTCTTCATTGAA+AGG - chr4.2:232963-232982 None:intergenic 35.0%
GCATTCTCTTATCTTACATG+TGG - chr4.2:232508-232527 None:intergenic 35.0%
TTCTCTTATCTTACATGTGG+TGG - chr4.2:232505-232524 None:intergenic 35.0%
! CTTTTTCCTCTCTATGATTC+TGG + chr4.2:232461-232480 MS.gene93754:CDS 35.0%
AAAAAGTGAAGACACCGAGA+GGG + chr4.2:232875-232894 MS.gene93754:CDS 40.0%
CCATCATAGAATATGGTCAG+CGG - chr4.2:232667-232686 None:intergenic 40.0%
CGCTGACCATATTCTATGAT+GGG + chr4.2:232665-232684 MS.gene93754:CDS 40.0%
CTCATCAATTGTATAGCCCT+GGG + chr4.2:232932-232951 MS.gene93754:CDS 40.0%
GGTTAATGTGAATGTTGTGC+AGG + chr4.2:232810-232829 MS.gene93754:intron 40.0%
TGATTGCCAGAATCATAGAG+AGG - chr4.2:232470-232489 None:intergenic 40.0%
TTTCTATCTCCATTGAAGGG+AGG + chr4.2:232615-232634 MS.gene93754:intron 40.0%
! GCTGTTCCTGATTTTGCATT+GGG - chr4.2:232645-232664 None:intergenic 40.0%
! TGCCAGCATTAAGATGGATT+TGG - chr4.2:232836-232855 None:intergenic 40.0%
CCAGGGCTATACAATTGATG+AGG - chr4.2:232934-232953 None:intergenic 45.0%
CCGCTGACCATATTCTATGA+TGG + chr4.2:232664-232683 MS.gene93754:CDS 45.0%
CCTCATCAATTGTATAGCCC+TGG + chr4.2:232931-232950 MS.gene93754:CDS 45.0%
GAAAAAGTGAAGACACCGAG+AGG + chr4.2:232874-232893 MS.gene93754:CDS 45.0%
GACTGATGTCACAGAGTTTC+AGG + chr4.2:232699-232718 MS.gene93754:CDS 45.0%
GATGGTATGGAGATGCTTCT+TGG - chr4.2:233017-233036 None:intergenic 45.0%
GGAAAGCCCAATGCAAAATC+AGG + chr4.2:232636-232655 MS.gene93754:CDS 45.0%
GGCCAAATCCATCTTAATGC+TGG + chr4.2:232831-232850 MS.gene93754:intron 45.0%
GGGCTATACAATTGATGAGG+AGG - chr4.2:232931-232950 None:intergenic 45.0%
TTGGCCTAGTCAAGAACAGA+GGG - chr4.2:232739-232758 None:intergenic 45.0%
! ATTGGCCTAGTCAAGAACAG+AGG - chr4.2:232740-232759 None:intergenic 45.0%
! GGCTGTTCCTGATTTTGCAT+TGG - chr4.2:232646-232665 None:intergenic 45.0%
!! CTTTATAAAAATAAATAAAT+GGG + chr4.2:232789-232808 MS.gene93754:intron 5.0%
!! TCTTTATAAAAATAAATAAA+TGG + chr4.2:232788-232807 MS.gene93754:intron 5.0%
CAATTGTATAGCCCTGGGTC+TGG + chr4.2:232937-232956 MS.gene93754:CDS 50.0%
TCATTGAAAGGCCAGACCCA+GGG - chr4.2:232951-232970 None:intergenic 50.0%
TGAGGAGGCTGCACTATTGT+TGG - chr4.2:232916-232935 None:intergenic 50.0%
TTCATTGAAAGGCCAGACCC+AGG - chr4.2:232952-232971 None:intergenic 50.0%
TTGGGCTTTCCTCCCTTCAA+TGG - chr4.2:232627-232646 None:intergenic 50.0%
ACCGCCCTCTGTTCTTGACT+AGG + chr4.2:232732-232751 MS.gene93754:intron 55.0%
GCCTAGTCAAGAACAGAGGG+CGG - chr4.2:232736-232755 None:intergenic 55.0%
GTTGTTCGCTCTGACCCTCT+CGG - chr4.2:232892-232911 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 232431 233041 232431 ID=MS.gene93754
chr4.2 mRNA 232431 233041 232431 ID=MS.gene93754.t1;Parent=MS.gene93754
chr4.2 exon 232431 232510 232431 ID=MS.gene93754.t1.exon1;Parent=MS.gene93754.t1
chr4.2 CDS 232431 232510 232431 ID=cds.MS.gene93754.t1;Parent=MS.gene93754.t1
chr4.2 exon 232633 232720 232633 ID=MS.gene93754.t1.exon2;Parent=MS.gene93754.t1
chr4.2 CDS 232633 232720 232633 ID=cds.MS.gene93754.t1;Parent=MS.gene93754.t1
chr4.2 exon 232832 233041 232832 ID=MS.gene93754.t1.exon3;Parent=MS.gene93754.t1
chr4.2 CDS 232832 233041 232832 ID=cds.MS.gene93754.t1;Parent=MS.gene93754.t1
Gene Sequence

>MS.gene93754

ATGAGGAGGAATTGTAACTTAGAACTCTGCCTTTTTCCTCTCTATGATTCTGGCAATCACAACAACAGCAACCACCACATGTAAGATAAGAGAATGCTTTTCTTTGTATACCATTTCCATTTTTTCAATTTGTTAGACTATGATTTTCTTTTTATATTTGGGTATTAAAGTAATTCTTTGTTAATTTCTATCTCCATTGAAGGGAGGAAAGCCCAATGCAAAATCAGGAACAGCCGCTGACCATATTCTATGATGGGAAGATGTGTCTGACTGATGTCACAGAGTTTCAGGTATACTCATTACCGCCCTCTGTTCTTGACTAGGCCAATAACTAAATGAAAAAATGATTTTGCAATCTCTTTATAAAAATAAATAAATGGGTTAATGTGAATGTTGTGCAGGCCAAATCCATCTTAATGCTGGCAAATAAAATTAAGTTGCAAGAAAAAGTGAAGACACCGAGAGGGTCAGAGCGAACAACACCAACAATAGTGCAGCCTCCTCATCAATTGTATAGCCCTGGGTCTGGCCTTTCAATGAAGAGATCTTTGCAACGGTTTCTACAGAAGAGAAAGAATAGGGTCCAAGAAGCATCTCCATACCATCACTAG
Protein sequence

>MS.gene93754.t1

MRRNCNLELCLFPLYDSGNHNNSNHHMEESPMQNQEQPLTIFYDGKMCLTDVTEFQAKSILMLANKIKLQEKVKTPRGSERTTPTIVQPPHQLYSPGSGLSMKRSLQRFLQKRKNRVQEASPYHH