AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene50534


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene50534.t1 MTR_1g071720 95.041 121 6 0 1 121 70 190 4.89e-80 233
MS.gene50534.t1 MTR_1g071720 94.215 121 6 1 1 121 70 189 1.81e-77 227
MS.gene50534.t1 MTR_5g006940 51.064 94 42 2 1 94 69 158 1.12e-19 80.5
MS.gene50534.t1 MTR_7g095250 41.593 113 54 4 1 112 34 135 8.27e-18 75.1
MS.gene50534.t1 MTR_1g103420 37.500 120 51 3 1 99 69 185 1.77e-17 75.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene50534.t1 AT2G48140 50.000 66 32 1 1 66 63 127 7.75e-15 66.2
MS.gene50534.t1 AT2G48140 53.571 56 26 0 1 56 63 118 1.01e-14 67.4
MS.gene50534.t1 AT1G05450 52.459 61 28 1 1 61 66 125 1.70e-14 67.0

Find 33 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGGCAGGTCCAGCTATATT+TGG 0.239605 1.2:-54851128 MS.gene50534:intron
ATCTATGATGAGTACTAGTA+TGG 0.275702 1.2:-54852417 None:intergenic
GAAGGAAAGAACTCTATTAA+TGG 0.297936 1.2:+54852346 None:intergenic
GAGTGTTGAATTGCATATTT+AGG 0.320907 1.2:+54850886 None:intergenic
CTTGGGCGACTATGCTTCAT+TGG 0.351622 1.2:+54850832 None:intergenic
CTCAAGGGAGAAGCATTAAT+TGG 0.353542 1.2:+54851083 None:intergenic
TTAATGGGTGGTAGTTGAAA+TGG 0.405959 1.2:+54852362 None:intergenic
AAGGAAAGAACTCTATTAAT+GGG 0.415197 1.2:+54852347 None:intergenic
TAGTCGCCCAAGAAAACTTC+AGG 0.419211 1.2:-54850821 MS.gene50534:CDS
GGCTCTCCTTTACCAGCTCC+AGG 0.442482 1.2:-54852138 MS.gene50534:intron
ATTGTGCATGGAATCCATTC+AGG 0.446420 1.2:+54852303 None:intergenic
CCATTCAGGTTGCATGATTG+TGG 0.485094 1.2:+54852317 None:intergenic
CATTAATTGGCGGAAGAGAC+GGG 0.492843 1.2:+54851096 None:intergenic
ATATTTACCTTGCGGACTCA+AGG 0.503866 1.2:+54851067 None:intergenic
ACATTTGATCCAAATATAGC+TGG 0.505446 1.2:+54851119 None:intergenic
CCACAATCATGCAACCTGAA+TGG 0.505888 1.2:-54852317 MS.gene50534:CDS
GCATTAATTGGCGGAAGAGA+CGG 0.508648 1.2:+54851095 None:intergenic
AGGAGAATCAGCTACCTCAA+TGG 0.512985 1.2:+54850906 None:intergenic
TGGATTCCATGCACAATGCA+AGG 0.527893 1.2:-54852297 MS.gene50534:CDS
TAAGTACCTGGAGCTGGTAA+AGG 0.529079 1.2:+54852132 None:intergenic
GCATGATTGTGGAAGGAAGA+AGG 0.544924 1.2:+54852328 None:intergenic
TAATAATAAGTACCTGGAGC+TGG 0.545527 1.2:+54852126 None:intergenic
TCAGGTTGCATGATTGTGGA+AGG 0.574464 1.2:+54852321 None:intergenic
TATTTACCTTGCGGACTCAA+GGG 0.591593 1.2:+54851068 None:intergenic
AAGGGAGAAGCATTAATTGG+CGG 0.596813 1.2:+54851086 None:intergenic
CGCAGTAGATGAAACCATTG+AGG 0.601013 1.2:-54850920 MS.gene50534:intron
GTGTACCCTTGCATTGTGCA+TGG 0.619403 1.2:+54852291 None:intergenic
GGATTCCATGCACAATGCAA+GGG 0.619466 1.2:-54852296 MS.gene50534:intron
TGCAATTCAACACTCAGCAA+AGG 0.626463 1.2:-54850878 MS.gene50534:CDS
GCTTCTCCCTTGAGTCCGCA+AGG 0.628732 1.2:-54851074 MS.gene50534:intron
GAAAGAACTCTATTAATGGG+TGG 0.644751 1.2:+54852350 None:intergenic
TCTATGATGAGTACTAGTAT+GGG 0.647243 1.2:-54852416 MS.gene50534:CDS
TGGTAGTTGAAATGGAACGT+TGG 0.743680 1.2:+54852370 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAAAAAAAACTTGAT+CGG + chr1.2:54851290-54851309 None:intergenic 10.0%
!!! ATTTTAAAGGAAATTAAAAT+AGG + chr1.2:54851005-54851024 None:intergenic 10.0%
!!! TTATATACAAATGATTTTAA+AGG + chr1.2:54851018-54851037 None:intergenic 10.0%
!! ATGTAAACACAAAATTAAAA+GGG - chr1.2:54852204-54852223 MS.gene50534:intron 15.0%
!! GTATATAAAATGTCTAATAA+AGG - chr1.2:54851030-54851049 MS.gene50534:intron 15.0%
!! TATGTAAACACAAAATTAAA+AGG - chr1.2:54852203-54852222 MS.gene50534:intron 15.0%
!! TATGTAATTAAAAACTTGAT+CGG + chr1.2:54851325-54851344 None:intergenic 15.0%
!! TTGCAAATAAAATGTTTAAA+AGG + chr1.2:54851255-54851274 None:intergenic 15.0%
!! TTTAATTAATAATAAGTACC+TGG + chr1.2:54851103-54851122 None:intergenic 15.0%
!!! ATATTTTTATGTCAACAAAT+TGG + chr1.2:54852266-54852285 None:intergenic 15.0%
!!! ATGATCTTTAAAAATTATTC+AGG - chr1.2:54852030-54852049 MS.gene50534:intron 15.0%
!!! TATTTTTATGTCAACAAATT+GGG + chr1.2:54852265-54852284 None:intergenic 15.0%
!!! TTGTGGTTATTTTATAATTT+TGG + chr1.2:54851627-54851646 None:intergenic 15.0%
!!! TTTTAAACATTTTATTTGCA+AGG - chr1.2:54851254-54851273 MS.gene50534:intron 15.0%
!! ATGTAACATTCATATATAAG+AGG + chr1.2:54851969-54851988 None:intergenic 20.0%
! AAACACAAAATTAAAAGGGT+TGG - chr1.2:54852208-54852227 MS.gene50534:intron 25.0%
! AAGGAAAGAACTCTATTAAT+GGG + chr1.2:54850876-54850895 None:intergenic 25.0%
! GAAAAAGAATAGGTTAAAGA+CGG + chr1.2:54851355-54851374 None:intergenic 25.0%
! GATGTTCTCAAAAAAATTAG+TGG + chr1.2:54851412-54851431 None:intergenic 25.0%
! TAACAATGATATTTACCTTG+CGG + chr1.2:54852164-54852183 None:intergenic 25.0%
!! AAATTGGGTTAGATGTATAA+TGG + chr1.2:54852250-54852269 None:intergenic 25.0%
!! ATCACATAATTTGTCACAAA+AGG + chr1.2:54850972-54850991 None:intergenic 25.0%
!! GTATCAAGTTTAAAACTACT+AGG + chr1.2:54851691-54851710 None:intergenic 25.0%
!! TGGAAATATATAAAGGTACA+TGG - chr1.2:54852005-54852024 MS.gene50534:intron 25.0%
!! TGGTCTCTTAAGTTAATTTT+AGG + chr1.2:54851607-54851626 None:intergenic 25.0%
!! TTTTGTGACAAATTATGTGA+TGG - chr1.2:54850971-54850990 MS.gene50534:intron 25.0%
!!! AAAAAATTAGTGGACTCATA+TGG + chr1.2:54851402-54851421 None:intergenic 25.0%
!!! CTCTCATTTGAGTTTTTAAA+CGG - chr1.2:54851443-54851462 MS.gene50534:intron 25.0%
!!! TGAGTTCTGGAAATATATAA+AGG - chr1.2:54851998-54852017 MS.gene50534:intron 25.0%
AAAAAGATGATAGCATGCTT+CGG + chr1.2:54851713-54851732 None:intergenic 30.0%
AAAGTGTGTCGAAAAAGAAT+AGG + chr1.2:54851365-54851384 None:intergenic 30.0%
AACCACAAATTTACTAGCTA+TGG - chr1.2:54851639-54851658 MS.gene50534:intron 30.0%
AATTTGTATATTGCAGCTTC+TGG - chr1.2:54851061-54851080 MS.gene50534:intron 30.0%
ACATTTGATCCAAATATAGC+TGG + chr1.2:54852104-54852123 None:intergenic 30.0%
GAAGGAAAGAACTCTATTAA+TGG + chr1.2:54850877-54850896 None:intergenic 30.0%
TAAATAAGCACTCACATTTC+AGG + chr1.2:54851802-54851821 None:intergenic 30.0%
TTCATGGACATTAGTACATA+GGG + chr1.2:54851203-54851222 None:intergenic 30.0%
TTCCATAGCTAGTAAATTTG+TGG + chr1.2:54851644-54851663 None:intergenic 30.0%
! TGAATTCCTGAAGTTTTCTT+GGG + chr1.2:54852408-54852427 None:intergenic 30.0%
! TTGAATTCCTGAAGTTTTCT+TGG + chr1.2:54852409-54852428 None:intergenic 30.0%
!! GAGTGTTGAATTGCATATTT+AGG + chr1.2:54852337-54852356 None:intergenic 30.0%
!!! CTTGTTTTTAAGTAGTCCAA+TGG - chr1.2:54851131-54851150 MS.gene50534:intron 30.0%
!!! TTCATTGGTACTAGTTTTGT+CGG + chr1.2:54852376-54852395 None:intergenic 30.0%
ACATTAGTACATAGGGATTG+AGG + chr1.2:54851196-54851215 None:intergenic 35.0%
CACAAATTCATGGTCAACAT+TGG + chr1.2:54851762-54851781 None:intergenic 35.0%
CTTCATGGACATTAGTACAT+AGG + chr1.2:54851204-54851223 None:intergenic 35.0%
GAAAGAACTCTATTAATGGG+TGG + chr1.2:54850873-54850892 None:intergenic 35.0%
TAATAATAAGTACCTGGAGC+TGG + chr1.2:54851097-54851116 None:intergenic 35.0%
! ATATCTGAGACCATCTATGA+TGG + chr1.2:54851866-54851885 None:intergenic 35.0%
! ATTTTCTTTGGCATAAGCCA+TGG + chr1.2:54851739-54851758 None:intergenic 35.0%
! GCTATCATCTTTTTATGCCA+TGG - chr1.2:54851719-54851738 MS.gene50534:intron 35.0%
! GGTCAACATTGGATTTTCTT+TGG + chr1.2:54851751-54851770 None:intergenic 35.0%
! TTAATGGGTGGTAGTTGAAA+TGG + chr1.2:54850861-54850880 None:intergenic 35.0%
!! AAGTTCAGTTGATAGCTTCA+TGG + chr1.2:54851219-54851238 None:intergenic 35.0%
ATAAGCACTCACATTTCAGG+AGG + chr1.2:54851799-54851818 None:intergenic 40.0%
ATATTTACCTTGCGGACTCA+AGG + chr1.2:54852156-54852175 None:intergenic 40.0%
ATTGTGCATGGAATCCATTC+AGG + chr1.2:54850920-54850939 None:intergenic 40.0%
CACACTGTCTCACAAATTCA+TGG + chr1.2:54851772-54851791 None:intergenic 40.0%
CCAACAAAAGCAATGGAAAG+AGG + chr1.2:54852076-54852095 None:intergenic 40.0%
TAAGCACTCACATTTCAGGA+GGG + chr1.2:54851798-54851817 None:intergenic 40.0%
TATTTACCTTGCGGACTCAA+GGG + chr1.2:54852155-54852174 None:intergenic 40.0%
TGCAATTCAACACTCAGCAA+AGG - chr1.2:54852342-54852361 MS.gene50534:CDS 40.0%
TGGTAGTTGAAATGGAACGT+TGG + chr1.2:54850853-54850872 None:intergenic 40.0%
!! AAGGGAGAAGCATTAATTGG+CGG + chr1.2:54852137-54852156 None:intergenic 40.0%
!! CCTCTTTCCATTGCTTTTGT+TGG - chr1.2:54852073-54852092 MS.gene50534:intron 40.0%
!! CTCAAGGGAGAAGCATTAAT+TGG + chr1.2:54852140-54852159 None:intergenic 40.0%
!! TTTCCATTGCTTTTGTTGGC+AGG - chr1.2:54852077-54852096 MS.gene50534:intron 40.0%
AAGCACTCACATTTCAGGAG+GGG + chr1.2:54851797-54851816 None:intergenic 45.0%
ACATGCTCAACGTTGAGTTC+TGG - chr1.2:54851985-54852004 MS.gene50534:intron 45.0%
AGGAGAATCAGCTACCTCAA+TGG + chr1.2:54852317-54852336 None:intergenic 45.0%
CATTAATTGGCGGAAGAGAC+GGG + chr1.2:54852127-54852146 None:intergenic 45.0%
CCACAATCATGCAACCTGAA+TGG - chr1.2:54850903-54850922 MS.gene50534:CDS 45.0%
CGCAGTAGATGAAACCATTG+AGG - chr1.2:54852300-54852319 MS.gene50534:CDS 45.0%
CTCCACATGAGTTTAGCCAT+TGG + chr1.2:54851150-54851169 None:intergenic 45.0%
GCATGATTGTGGAAGGAAGA+AGG + chr1.2:54850895-54850914 None:intergenic 45.0%
GCATTAATTGGCGGAAGAGA+CGG + chr1.2:54852128-54852147 None:intergenic 45.0%
GGATTCCATGCACAATGCAA+GGG - chr1.2:54850924-54850943 MS.gene50534:intron 45.0%
GTCCAATGGCTAAACTCATG+TGG - chr1.2:54851145-54851164 MS.gene50534:intron 45.0%
TAAGTACCTGGAGCTGGTAA+AGG + chr1.2:54851091-54851110 None:intergenic 45.0%
TAGTCGCCCAAGAAAACTTC+AGG - chr1.2:54852399-54852418 MS.gene50534:CDS 45.0%
TGGATTCCATGCACAATGCA+AGG - chr1.2:54850923-54850942 MS.gene50534:intron 45.0%
TTGGCAGGTCCAGCTATATT+TGG - chr1.2:54852092-54852111 MS.gene50534:intron 45.0%
TTTCTCCACGCCATCATAGA+TGG - chr1.2:54851853-54851872 MS.gene50534:intron 45.0%
! TCAGGTTGCATGATTGTGGA+AGG + chr1.2:54850902-54850921 None:intergenic 45.0%
! TCTATGATGGCGTGGAGAAA+AGG + chr1.2:54851853-54851872 None:intergenic 45.0%
!! CCATTCAGGTTGCATGATTG+TGG + chr1.2:54850906-54850925 None:intergenic 45.0%
CTTGGGCGACTATGCTTCAT+TGG + chr1.2:54852391-54852410 None:intergenic 50.0%
GGACCTGCCAACAAAAGCAA+TGG + chr1.2:54852083-54852102 None:intergenic 50.0%
GTGTACCCTTGCATTGTGCA+TGG + chr1.2:54850932-54850951 None:intergenic 50.0%
! TGAGACCATCTATGATGGCG+TGG + chr1.2:54851861-54851880 None:intergenic 50.0%
!!! GGTACTAGTTTTGTCGGTGC+TGG + chr1.2:54852370-54852389 None:intergenic 50.0%
GCTTCTCCCTTGAGTCCGCA+AGG - chr1.2:54852146-54852165 MS.gene50534:CDS 60.0%
GGCTCTCCTTTACCAGCTCC+AGG - chr1.2:54851082-54851101 MS.gene50534:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 54850807 54852435 54850807 ID=MS.gene50534
chr1.2 mRNA 54850807 54852435 54850807 ID=MS.gene50534.t1;Parent=MS.gene50534
chr1.2 exon 54852297 54852435 54852297 ID=MS.gene50534.t1.exon1;Parent=MS.gene50534.t1
chr1.2 CDS 54852297 54852435 54852297 ID=cds.MS.gene50534.t1;Parent=MS.gene50534.t1
chr1.2 exon 54852139 54852165 54852139 ID=MS.gene50534.t1.exon2;Parent=MS.gene50534.t1
chr1.2 CDS 54852139 54852165 54852139 ID=cds.MS.gene50534.t1;Parent=MS.gene50534.t1
chr1.2 exon 54851075 54851143 54851075 ID=MS.gene50534.t1.exon3;Parent=MS.gene50534.t1
chr1.2 CDS 54851075 54851143 54851075 ID=cds.MS.gene50534.t1;Parent=MS.gene50534.t1
chr1.2 exon 54850807 54850937 54850807 ID=MS.gene50534.t1.exon4;Parent=MS.gene50534.t1
chr1.2 CDS 54850807 54850937 54850807 ID=cds.MS.gene50534.t1;Parent=MS.gene50534.t1
Gene Sequence

>MS.gene50534

ATGATGAGTACTAGTATGGGTTGTGCTTGCTTGTTAATTACAGCCAACGTTCCATTTCAACTACCACCCATTAATAGAGTTCTTTCCTTCTTCCTTCCACAATCATGCAACCTGAATGGATTCCATGCACAATGCAAGGGTACACAATTCATATATATGTTTCCTTTTGTGACAAATTATGTGATGGATTTTCTTCCTATTTTAATTTCCTTTAAAATCATTTGTATATAAAATGTCTAATAAAGGTTTTTATAAATTTGTATATTGCAGCTTCTGGCTCTCCTTTACCAGCTCCAGGTACTTATTATTAATTAAATTAACTCACTTGTTTTTAAGTAGTCCAATGGCTAAACTCATGTGGAGAAGTGAGAAATTTGACGTTCGAACCTCAATCCCTATGTACTAATGTCCATGAAGCTATCAACTGAACTTCATTTAGAAGATTCCTTTTAAACATTTTATTTGCAAGGACAGTACTATCCGATCAAGTTTTTTTTTTTTTTTTTTGACGAAATCCGATCAAGTTTTTAATTACATAAATAACACCGTCTTTAACCTATTCTTTTTCGACACACTTTTTATAGATTAAAATCCATATGAGTCCACTAATTTTTTTGAGAACATCACAATGAAGCTCTCTCATTTGAGTTTTTAAACGGATCTTGTATTCTTATATATATATATATATATATATATATATATATATATATATATATATATATATATGTCACTTATATATATATATAATTTATAAAAACAAAGTGAAAAGAAAAAAAAAACTTAAAATCAAAGTGAAACCTAAAATTAACTTAAGAGACCAAAATTATAAAATAACCACAAATTTACTAGCTATGGAAAATGTTGTATCTCGCAAGAAAATTCCTAGTAGTTTTAAACTTGATACCGAAGCATGCTATCATCTTTTTATGCCATGGCTTATGCCAAAGAAAATCCAATGTTGACCATGAATTTGTGAGACAGTGTGAACCCCTCCTGAAATGTGAGTGCTTATTTAAACTACTCAATTCAATAAACATCTTCAACCTTTTCTCCACGCCATCATAGATGGTCTCAGATATAAATAATTAATAATACTCGTTTGAATTTCAATCAATAGTATATATATCATAAAGAGTGTGTTACACATTACATTATTAATCCTCTTATATATGAATGTTACATGCTCAACGTTGAGTTCTGGAAATATATAAAGGTACATGGATATGATCTTTAAAAATTATTCAGGATCATGTCATAAATCTTATTCCTCTTTCCATTGCTTTTGTTGGCAGGTCCAGCTATATTTGGATCAAATGTCCCGTCTCTTCCGCCAATTAATGCTTCTCCCTTGAGTCCGCAAGGTAAATATCATTGTTATTGTAAAAATTATATTTATTATGTAAACACAAAATTAAAAGGGTTGGTGACATTTATTTTCTTCCATTATACATCTAACCCAATTTGTTGACATAAAAATATTGTCTAAACTTCAACGCAGTAGATGAAACCATTGAGGTAGCTGATTCTCCTAAATATGCAATTCAACACTCAGCAAAGGCACCAGCACCGACAAAACTAGTACCAATGAAGCATAGTCGCCCAAGAAAACTTCAGGAATTCAACAAGTAG

Protein sequence

>MS.gene50534.t1

MMSTSMGCACLLITANVPFQLPPINRVLSFFLPQSCNLNGFHAQCKASGSPLPAPGPAIFGSNVPSLPPINASPLSPQVDETIEVADSPKYAIQHSAKAPAPTKLVPMKHSRPRKLQEFNK