AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene55992

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene55992.t1 MTR_7g062720 94.697 132 7 0 1 132 1 132 1.02e-87 261
MS.gene55992.t1 MTR_4g037355 70.769 130 24 3 151 280 1 116 3.60e-54 175
MS.gene55992.t1 MTR_5g061150 62.500 120 45 0 27 146 17 136 3.27e-46 154
MS.gene55992.t1 MTR_4g112730 75.000 64 16 0 138 201 1 64 2.79e-26 100
MS.gene55992.t1 MTR_1g036690 61.628 86 22 3 273 357 5 80 2.48e-24 95.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 65 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGAGGCCCTTAACATTTC+TGG 0.105015 2.3:-56593616 MS.gene55992:CDS
GCATCTCAACACAATCATTT+TGG 0.131367 2.3:-56593040 MS.gene55992:CDS
TTCCACTTCTGGTGGGAAAA+TGG 0.172180 2.3:+56592905 None:intergenic
TCTTAAGTGCTTCATTTATA+TGG 0.216688 2.3:+56593464 None:intergenic
ATCCAATCATATCTTGCTTT+TGG 0.220117 2.3:+56593358 None:intergenic
GATGCTGATTATGATATTTA+TGG 0.234910 2.3:-56592686 MS.gene55992:CDS
AATACTACTCCTTTGGATAT+TGG 0.253196 2.3:-56592656 MS.gene55992:CDS
TCCACTTCTGGTGGGAAAAT+GGG 0.275118 2.3:+56592906 None:intergenic
TTTGTATACTTCAGAATTAT+AGG 0.281074 2.3:+56593300 None:intergenic
TGTTGAGATGCATTCACTTC+AGG 0.293409 2.3:+56593052 None:intergenic
TGCCATAAAAGAAGGAAATA+AGG 0.335057 2.3:-56593530 MS.gene55992:CDS
AGTTGTTTCCAGAAATGTTA+AGG 0.345031 2.3:+56593608 None:intergenic
CACCAGCAGGGCGAGCTTCA+TGG 0.368055 2.3:+56593086 None:intergenic
CGCGGTCGTGGTCGTGGTCG+TGG 0.386944 2.3:-56592986 MS.gene55992:CDS
ATTGATCACCTTGTTGAAGA+TGG 0.391237 2.3:-56592605 MS.gene55992:CDS
GTTGTTTCCAGAAATGTTAA+GGG 0.399743 2.3:+56593609 None:intergenic
TAATTTAATTTCTTGTCTCC+TGG 0.400386 2.3:-56593143 MS.gene55992:CDS
CTGGAAACAACTATTTGACT+TGG 0.414379 2.3:-56593597 MS.gene55992:CDS
TACTTAGCTGCTGAAGGAAA+TGG 0.418999 2.3:-56593556 MS.gene55992:CDS
GTTGAGATGCATTCACTTCA+GGG 0.423894 2.3:+56593053 None:intergenic
CGCGGTCGCGGTCGTGGTCG+TGG 0.429172 2.3:-56592992 MS.gene55992:CDS
TAAAGGTCAACCAAATGCTT+TGG 0.429910 2.3:+56592773 None:intergenic
GGTCATGCCCACAATCCTAA+TGG 0.437132 2.3:-56592941 MS.gene55992:CDS
AACCATGAAGCTCGCCCTGC+TGG 0.438159 2.3:-56593088 MS.gene55992:CDS
TGACATGAATACTACTCCTT+TGG 0.440582 2.3:-56592663 MS.gene55992:CDS
GGGAATGGAGCTACACCAGC+AGG 0.445287 2.3:+56593073 None:intergenic
CGTGGTCGCGGTCGCGGTCG+TGG 0.450743 2.3:-56592998 MS.gene55992:CDS
CGTGGTCGTGGTCGCGGTCG+CGG 0.452026 2.3:-56593004 MS.gene55992:CDS
CCACTTCTGGTGGGAAAATG+GGG 0.456004 2.3:+56592907 None:intergenic
TCTCTCAAAACTTCACTTTG+AGG 0.457299 2.3:-56593632 MS.gene55992:CDS
ATGTCGTACTCCAAAGCATT+TGG 0.465557 2.3:-56592783 MS.gene55992:CDS
TTTGGGAGCGCTCGTGGTCG+TGG 0.467855 2.3:-56593022 MS.gene55992:CDS
TCCCAAAAGCAAGATATGAT+TGG 0.468237 2.3:-56593360 MS.gene55992:CDS
TGAAAGATCCACTTGTGCTC+TGG 0.468533 2.3:-56593426 MS.gene55992:CDS
AGCGCTCGTGGTCGTGGTCG+TGG 0.471808 2.3:-56593016 MS.gene55992:CDS
ACTCATTATGCTTATAAAGA+TGG 0.483040 2.3:-56592713 MS.gene55992:CDS
TTGTTGTTGCAAGAGCATAT+TGG 0.488960 2.3:+56593195 None:intergenic
CGTGGTCGTGGTCGTGGTCG+CGG 0.491270 2.3:-56593010 MS.gene55992:CDS
TGCAACAACAATACCGTGAA+AGG 0.491455 2.3:-56593183 MS.gene55992:CDS
CATTGTTCTGTTCAGCAACC+AGG 0.503364 2.3:+56593125 None:intergenic
AAAGTATCTGTTATCGATGT+GGG 0.505636 2.3:-56592829 MS.gene55992:CDS
GCAACAACAATACCGTGAAA+GGG 0.512293 2.3:-56593182 MS.gene55992:CDS
AGTTTATTCCAGAGCACAAG+TGG 0.512360 2.3:+56593418 None:intergenic
GATGCATTCACTTCAGGGAA+TGG 0.514758 2.3:+56593058 None:intergenic
GAAAAGAATGAAAATGAGAA+GGG 0.529787 2.3:-56592875 MS.gene55992:CDS
TAAGTACATTTCAGTATCTA+CGG 0.532057 2.3:+56593573 None:intergenic
TGGAAACAACTATTTGACTT+GGG 0.534823 2.3:-56593596 MS.gene55992:CDS
TGAAAAGAATGAAAATGAGA+AGG 0.541748 2.3:-56592876 MS.gene55992:CDS
AATATGCATGGTCGTGGTCG+TGG 0.544688 2.3:-56592962 MS.gene55992:CDS
AATGGAGATGCCATAAAAGA+AGG 0.547076 2.3:-56593538 MS.gene55992:CDS
GAGCATATTGGATGCATGAA+AGG 0.547906 2.3:+56593207 None:intergenic
AAGAATGAAAATGAGAAGGG+TGG 0.573649 2.3:-56592872 MS.gene55992:CDS
GAAAGTATCTGTTATCGATG+TGG 0.574435 2.3:-56592830 MS.gene55992:CDS
GAAATGTACTTAGCTGCTGA+AGG 0.580070 2.3:-56593562 MS.gene55992:CDS
ACTTCTCAATTAGAATTGTG+TGG 0.587587 2.3:-56593274 MS.gene55992:CDS
CAACAACAATACCGTGAAAG+GGG 0.610582 2.3:-56593181 MS.gene55992:CDS
AAGAAATCACCAATATCCAA+AGG 0.617484 2.3:+56592647 None:intergenic
AGTATCTGTTATCGATGTGG+GGG 0.620042 2.3:-56592827 MS.gene55992:CDS
CGTGGAAATATGCATGGTCG+TGG 0.624916 2.3:-56592968 MS.gene55992:CDS
CTTCATTTATATGGTGACGA+AGG 0.627090 2.3:+56593473 None:intergenic
AAGTATCTGTTATCGATGTG+GGG 0.635242 2.3:-56592828 MS.gene55992:CDS
TCACGATTCCATCTTCAACA+AGG 0.635824 2.3:+56592597 None:intergenic
CGTGGTCGTGGAAATATGCA+TGG 0.646225 2.3:-56592974 MS.gene55992:CDS
GGAATGGAGCTACACCAGCA+GGG 0.651331 2.3:+56593074 None:intergenic
CAAGTGGATCTTTCACAGTG+AGG 0.718603 2.3:+56593434 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAAAAAACAAAGGAAAAA+TGG - chr2.3:56593488-56593507 MS.gene55992:CDS 15.0%
!! TTTGTATACTTCAGAATTAT+AGG + chr2.3:56592932-56592951 None:intergenic 20.0%
!!! TTTTTAATGATTGCTGATAA+AGG + chr2.3:56593476-56593495 None:intergenic 20.0%
! ACTCATTATGCTTATAAAGA+TGG - chr2.3:56593516-56593535 MS.gene55992:CDS 25.0%
! CAGCAATCATTAAAAAACAA+AGG - chr2.3:56593480-56593499 MS.gene55992:CDS 25.0%
! GAAAAGAATGAAAATGAGAA+GGG - chr2.3:56593354-56593373 MS.gene55992:CDS 25.0%
! TAAGTACATTTCAGTATCTA+CGG + chr2.3:56592659-56592678 None:intergenic 25.0%
! TCTTAAGTGCTTCATTTATA+TGG + chr2.3:56592768-56592787 None:intergenic 25.0%
! TGAAAAGAATGAAAATGAGA+AGG - chr2.3:56593353-56593372 MS.gene55992:CDS 25.0%
! TGGTGAAAAAATAACAGATA+CGG - chr2.3:56592975-56592994 MS.gene55992:CDS 25.0%
!! GATGCTGATTATGATATTTA+TGG - chr2.3:56593543-56593562 MS.gene55992:CDS 25.0%
!! TAATTTAATTTCTTGTCTCC+TGG - chr2.3:56593086-56593105 MS.gene55992:CDS 25.0%
!!! TTTCATTATTTTTCCACTTC+TGG + chr2.3:56593338-56593357 None:intergenic 25.0%
AAGAAATCACCAATATCCAA+AGG + chr2.3:56593585-56593604 None:intergenic 30.0%
AATACTACTCCTTTGGATAT+TGG - chr2.3:56593573-56593592 MS.gene55992:CDS 30.0%
ACTTCTCAATTAGAATTGTG+TGG - chr2.3:56592955-56592974 MS.gene55992:CDS 30.0%
TGCCATAAAAGAAGGAAATA+AGG - chr2.3:56592699-56592718 MS.gene55992:CDS 30.0%
! AAAGTATCTGTTATCGATGT+GGG - chr2.3:56593400-56593419 MS.gene55992:CDS 30.0%
! AGTTGTTTCCAGAAATGTTA+AGG + chr2.3:56592624-56592643 None:intergenic 30.0%
! ATCCAATCATATCTTGCTTT+TGG + chr2.3:56592874-56592893 None:intergenic 30.0%
! CATCTCAACACAATCATTTT+GGG - chr2.3:56593190-56593209 MS.gene55992:CDS 30.0%
! GAATTTTCCATTAGGATTGT+GGG + chr2.3:56593298-56593317 None:intergenic 30.0%
! GTTGTTTCCAGAAATGTTAA+GGG + chr2.3:56592623-56592642 None:intergenic 30.0%
! TGAATTTTCCATTAGGATTG+TGG + chr2.3:56593299-56593318 None:intergenic 30.0%
! TGGAAACAACTATTTGACTT+GGG - chr2.3:56592633-56592652 MS.gene55992:CDS 30.0%
!! ATTATTTTTCCACTTCTGGT+GGG + chr2.3:56593334-56593353 None:intergenic 30.0%
!! TCCAATCATATCTTGCTTTT+GGG + chr2.3:56592873-56592892 None:intergenic 30.0%
!!! ATTTTTGAAATCCCCTTTCA+CGG + chr2.3:56593062-56593081 None:intergenic 30.0%
!!! TGCCTTATTTCCTTCTTTTA+TGG + chr2.3:56592704-56592723 None:intergenic 30.0%
AAGAATGAAAATGAGAAGGG+TGG - chr2.3:56593357-56593376 MS.gene55992:CDS 35.0%
AAGTATCTGTTATCGATGTG+GGG - chr2.3:56593401-56593420 MS.gene55992:CDS 35.0%
AATGGAGATGCCATAAAAGA+AGG - chr2.3:56592691-56592710 MS.gene55992:CDS 35.0%
ATTGATCACCTTGTTGAAGA+TGG - chr2.3:56593624-56593643 MS.gene55992:CDS 35.0%
CTGGAAACAACTATTTGACT+TGG - chr2.3:56592632-56592651 MS.gene55992:CDS 35.0%
TAAAGGTCAACCAAATGCTT+TGG + chr2.3:56593459-56593478 None:intergenic 35.0%
TCCCAAAAGCAAGATATGAT+TGG - chr2.3:56592869-56592888 MS.gene55992:CDS 35.0%
TCTCTCAAAACTTCACTTTG+AGG - chr2.3:56592597-56592616 MS.gene55992:CDS 35.0%
TGACATGAATACTACTCCTT+TGG - chr2.3:56593566-56593585 MS.gene55992:CDS 35.0%
! CTTCATTTATATGGTGACGA+AGG + chr2.3:56592759-56592778 None:intergenic 35.0%
! GCATCTCAACACAATCATTT+TGG - chr2.3:56593189-56593208 MS.gene55992:CDS 35.0%
! TTGTTGTTGCAAGAGCATAT+TGG + chr2.3:56593037-56593056 None:intergenic 35.0%
!! AATCATATCTTGCTTTTGGG+AGG + chr2.3:56592870-56592889 None:intergenic 35.0%
!! CATTATTTTTCCACTTCTGG+TGG + chr2.3:56593335-56593354 None:intergenic 35.0%
!! GAAAGTATCTGTTATCGATG+TGG - chr2.3:56593399-56593418 MS.gene55992:CDS 35.0%
!!! TGCTTTTGCTTTTTGTTGCT+CGG + chr2.3:56592728-56592747 None:intergenic 35.0%
AGTATCTGTTATCGATGTGG+GGG - chr2.3:56593402-56593421 MS.gene55992:CDS 40.0%
AGTTTATTCCAGAGCACAAG+TGG + chr2.3:56592814-56592833 None:intergenic 40.0%
CAACAACAATACCGTGAAAG+GGG - chr2.3:56593048-56593067 MS.gene55992:CDS 40.0%
GAAATGTACTTAGCTGCTGA+AGG - chr2.3:56592667-56592686 MS.gene55992:CDS 40.0%
GAGCATATTGGATGCATGAA+AGG + chr2.3:56593025-56593044 None:intergenic 40.0%
GCAACAACAATACCGTGAAA+GGG - chr2.3:56593047-56593066 MS.gene55992:CDS 40.0%
GTTGAGATGCATTCACTTCA+GGG + chr2.3:56593179-56593198 None:intergenic 40.0%
TACTTAGCTGCTGAAGGAAA+TGG - chr2.3:56592673-56592692 MS.gene55992:CDS 40.0%
TCACGATTCCATCTTCAACA+AGG + chr2.3:56593635-56593654 None:intergenic 40.0%
TGCAACAACAATACCGTGAA+AGG - chr2.3:56593046-56593065 MS.gene55992:CDS 40.0%
TGTTGAGATGCATTCACTTC+AGG + chr2.3:56593180-56593199 None:intergenic 40.0%
! ATGTCGTACTCCAAAGCATT+TGG - chr2.3:56593446-56593465 MS.gene55992:CDS 40.0%
! TTTGAGGCCCTTAACATTTC+TGG - chr2.3:56592613-56592632 MS.gene55992:CDS 40.0%
!! TCTTGCTTTTGGGAGGATAA+TGG + chr2.3:56592863-56592882 None:intergenic 40.0%
!!! GGGGTTCTGAATTTTCCATT+AGG + chr2.3:56593306-56593325 None:intergenic 40.0%
CAAGTGGATCTTTCACAGTG+AGG + chr2.3:56592798-56592817 None:intergenic 45.0%
CATTGTTCTGTTCAGCAACC+AGG + chr2.3:56593107-56593126 None:intergenic 45.0%
GATGCATTCACTTCAGGGAA+TGG + chr2.3:56593174-56593193 None:intergenic 45.0%
TCCACTTCTGGTGGGAAAAT+GGG + chr2.3:56593326-56593345 None:intergenic 45.0%
TGAAAGATCCACTTGTGCTC+TGG - chr2.3:56592803-56592822 MS.gene55992:CDS 45.0%
TGTTATCGATGTGGGGGAAA+AGG - chr2.3:56593408-56593427 MS.gene55992:CDS 45.0%
TTCCACTTCTGGTGGGAAAA+TGG + chr2.3:56593327-56593346 None:intergenic 45.0%
AATATGCATGGTCGTGGTCG+TGG - chr2.3:56593267-56593286 MS.gene55992:CDS 50.0%
CCACTTCTGGTGGGAAAATG+GGG + chr2.3:56593325-56593344 None:intergenic 50.0%
CGTGGAAATATGCATGGTCG+TGG - chr2.3:56593261-56593280 MS.gene55992:CDS 50.0%
CGTGGTCGTGGAAATATGCA+TGG - chr2.3:56593255-56593274 MS.gene55992:CDS 50.0%
GATGTGGGGGAAAAGGTCAT+TGG - chr2.3:56593415-56593434 MS.gene55992:CDS 50.0%
GGTCATGCCCACAATCCTAA+TGG - chr2.3:56593288-56593307 MS.gene55992:CDS 50.0%
!!! AATCATTTTGGGAGCGCTCG+TGG - chr2.3:56593201-56593220 MS.gene55992:CDS 50.0%
GGAATGGAGCTACACCAGCA+GGG + chr2.3:56593158-56593177 None:intergenic 55.0%
! CCCCATTTTCCCACCAGAAG+TGG - chr2.3:56593322-56593341 MS.gene55992:CDS 55.0%
AACCATGAAGCTCGCCCTGC+TGG - chr2.3:56593141-56593160 MS.gene55992:CDS 60.0%
GGGAATGGAGCTACACCAGC+AGG + chr2.3:56593159-56593178 None:intergenic 60.0%
CACCAGCAGGGCGAGCTTCA+TGG + chr2.3:56593146-56593165 None:intergenic 65.0%
!! TTTGGGAGCGCTCGTGGTCG+TGG - chr2.3:56593207-56593226 MS.gene55992:CDS 65.0%
AGCGCTCGTGGTCGTGGTCG+TGG - chr2.3:56593213-56593232 MS.gene55992:CDS 70.0%
CGTGGTCGTGGTCGTGGTCG+CGG - chr2.3:56593219-56593238 MS.gene55992:CDS 70.0%
CGCGGTCGTGGTCGTGGTCG+TGG - chr2.3:56593243-56593262 MS.gene55992:CDS 75.0%
CGTGGTCGTGGTCGCGGTCG+CGG - chr2.3:56593225-56593244 MS.gene55992:CDS 75.0%
! CGCGGTCGCGGTCGTGGTCG+TGG - chr2.3:56593237-56593256 MS.gene55992:CDS 80.0%
! CGTGGTCGCGGTCGCGGTCG+TGG - chr2.3:56593231-56593250 MS.gene55992:CDS 80.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 56592589 56593662 56592589 ID=MS.gene55992
chr2.3 mRNA 56592589 56593662 56592589 ID=MS.gene55992.t1;Parent=MS.gene55992
chr2.3 exon 56592589 56593662 56592589 ID=MS.gene55992.t1.exon1;Parent=MS.gene55992.t1
chr2.3 CDS 56592589 56593662 56592589 ID=cds.MS.gene55992.t1;Parent=MS.gene55992.t1
Gene Sequence

>MS.gene55992

ATGTCAAATCTCTCAAAACTTCACTTTGAGGCCCTTAACATTTCTGGAAACAACTATTTGACTTGGGCCGTAGATACTGAAATGTACTTAGCTGCTGAAGGAAATGGAGATGCCATAAAAGAAGGAAATAAGGCATCCGAGCAACAAAAAGCAAAAGCATTAATATTCCTTCGTCACCATATAAATGAAGCACTTAAGAATGAATACCTCACTGTGAAAGATCCACTTGTGCTCTGGAATAAACTAAAAGAAAGATATGAGCACTTGAAAGCCATTATCCTCCCAAAAGCAAGATATGATTGGATGCACTTGCGCTTACAAGACTTTAAGTCTGTAACTGCCTATAATTCTGAAGTATACAAAATTACTTCTCAATTAGAATTGTGTGGTGAAAAAATAACAGATACGGATCTGTTAGAGAAAACATTTTCAACCTTTCATGCATCCAATATGCTCTTGCAACAACAATACCGTGAAAGGGGATTTCAAAAATACTCTAATTTAATTTCTTGTCTCCTGGTTGCTGAACAGAACAATGAGCTTCTAATGAAAAACCATGAAGCTCGCCCTGCTGGTGTAGCTCCATTCCCTGAAGTGAATGCATCTCAACACAATCATTTTGGGAGCGCTCGTGGTCGTGGTCGTGGTCGCGGTCGCGGTCGTGGTCGTGGTCGTGGAAATATGCATGGTCGTGGTCGTGGTCATGCCCACAATCCTAATGGAAAATTCAGAACCCCATTTTCCCACCAGAAGTGGAAAAATAATGAAAAGAATGAAAATGAGAAGGGTGGACAAAGTAGCAAAACAAATGAAAGTATCTGTTATCGATGTGGGGGAAAAGGTCATTGGTCTCGTACATGTCGTACTCCAAAGCATTTGGTTGACCTTTATCAGCAATCATTAAAAAACAAAGGAAAAATGGTTGAAACTCATTATGCTTATAAAGATGGTGATGATGCTGATTATGATATTTATGGTGACATGAATACTACTCCTTTGGATATTGGTGATTTCTTTGAAAATAAAAATGAAAAAATTGATCACCTTGTTGAAGATGGAATCGTGAAGAAATAG
Protein sequence

>MS.gene55992.t1

MSNLSKLHFEALNISGNNYLTWAVDTEMYLAAEGNGDAIKEGNKASEQQKAKALIFLRHHINEALKNEYLTVKDPLVLWNKLKERYEHLKAIILPKARYDWMHLRLQDFKSVTAYNSEVYKITSQLELCGEKITDTDLLEKTFSTFHASNMLLQQQYRERGFQKYSNLISCLLVAEQNNELLMKNHEARPAGVAPFPEVNASQHNHFGSARGRGRGRGRGRGRGRGNMHGRGRGHAHNPNGKFRTPFSHQKWKNNEKNENEKGGQSSKTNESICYRCGGKGHWSRTCRTPKHLVDLYQQSLKNKGKMVETHYAYKDGDDADYDIYGDMNTTPLDIGDFFENKNEKIDHLVEDGIVKK