AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene99024

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99024.t1 MTR_5g038260 76.115 381 28 3 1 318 3 383 0.0 580
MS.gene99024.t1 MTR_5g038230 68.421 380 33 4 1 318 1 355 1.90e-180 502
MS.gene99024.t1 MTR_1g064570 41.687 403 147 8 1 318 1 400 7.00e-100 300
MS.gene99024.t1 MTR_1g108740 39.071 366 148 12 2 316 3 344 1.52e-69 220
MS.gene99024.t1 MTR_5g082770 46.094 256 98 8 1 229 1 243 4.50e-63 202
MS.gene99024.t1 MTR_7g077620 35.620 379 165 15 4 316 5 370 8.31e-52 175
MS.gene99024.t1 MTR_7g077660 33.420 383 168 15 4 318 5 368 4.14e-49 168
MS.gene99024.t1 MTR_7g077650 33.676 389 163 17 4 318 5 372 4.74e-49 168
MS.gene99024.t1 MTR_1g016150 33.803 284 107 11 2 254 3 236 1.20e-35 129
MS.gene99024.t1 MTR_5g082780 35.391 243 92 9 103 289 1 234 1.50e-27 107
MS.gene99024.t1 MTR_7g076100 29.526 359 145 13 4 318 6 300 3.52e-26 105
MS.gene99024.t1 MTR_7g076110 28.758 306 141 10 77 318 21 313 6.12e-23 97.1
MS.gene99024.t1 MTR_1g108750 40.000 120 43 3 1 117 1 94 5.00e-20 84.3
MS.gene99024.t1 MTR_6g023955 57.377 61 26 0 257 317 149 209 4.18e-18 81.6
MS.gene99024.t1 MTR_6g023955 59.091 66 25 2 126 190 87 151 3.69e-17 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 64 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATTATATTGCTCCTAAAT+TGG 0.217987 5.4:-27513678 None:intergenic
AATAGTAAATTGAATCCTTT+TGG 0.242301 5.4:-27514490 None:intergenic
TGGTGAGAAGGTTTATAAAT+AGG 0.247820 5.4:+27514294 MS.gene99024:CDS
ATACAAGACACTGACCATTT+TGG 0.281472 5.4:+27514074 MS.gene99024:CDS
TAAAAGCAGGACAAGAGTTT+TGG 0.281524 5.4:+27514045 MS.gene99024:CDS
CTTCTTTGTAACAAAACATT+TGG 0.292647 5.4:-27514209 None:intergenic
TTAAGCATTGTCAATTCTAA+TGG 0.313392 5.4:-27513775 None:intergenic
TTGTTATTCAAGTGACCCTT+GGG 0.317511 5.4:+27514172 MS.gene99024:CDS
ATAGCAGCAACATCCTTAAA+AGG 0.324907 5.4:-27513874 None:intergenic
GCCACCCATCGATAATTATA+TGG 0.327281 5.4:+27513903 MS.gene99024:CDS
ATCAACACGATCACCAATTT+AGG 0.336169 5.4:+27513665 MS.gene99024:CDS
TTGAACCAATTGATCACATT+TGG 0.344806 5.4:+27513596 MS.gene99024:CDS
CCAATTGATCACATTTGGTT+TGG 0.352054 5.4:+27513601 MS.gene99024:CDS
GCATAACCATGGAGCGAGAT+TGG 0.373158 5.4:+27513527 None:intergenic
CCAAACCAAATGTGATCAAT+TGG 0.396537 5.4:-27513601 None:intergenic
GGTGAGAAGGTTTATAAATA+GGG 0.399787 5.4:+27514295 MS.gene99024:CDS
TACTTATTTAGTGAAATCAT+TGG 0.416138 5.4:+27514256 MS.gene99024:CDS
CATTACATTCTACAATGGTT+TGG 0.419262 5.4:+27514106 MS.gene99024:CDS
TAATGTCGATGAAACCAAAA+TGG 0.420892 5.4:-27514088 None:intergenic
AAAAGGTGGCACAACCCATA+TGG 0.432547 5.4:-27514645 None:intergenic
AAGGTATGACACCTCCCATA+TGG 0.446486 5.4:+27514630 MS.gene99024:CDS
CATAACCATGGAGCGAGATT+GGG 0.451858 5.4:+27513528 None:intergenic
TCAAAAGGACCTCTAGGATA+AGG 0.452966 5.4:-27514542 None:intergenic
CCTAATCAATTCCATTGAAA+AGG 0.460995 5.4:-27514662 None:intergenic
GAGAGTTGTGGATGGTGAGA+AGG 0.464771 5.4:+27514282 MS.gene99024:CDS
CGTTACAAATCTTACTTCAA+AGG 0.467196 5.4:+27514611 MS.gene99024:CDS
TTTGTTATTCAAGTGACCCT+TGG 0.473541 5.4:+27514171 MS.gene99024:CDS
TTTCTCAAGTTACCTCCAAA+AGG 0.480419 5.4:+27514475 MS.gene99024:CDS
TTCAAGTGACCCTTGGGGTG+AGG 0.511989 5.4:+27514178 MS.gene99024:CDS
AGGTATGACACCTCCCATAT+GGG 0.519021 5.4:+27514631 MS.gene99024:CDS
ACTTGAGCCACAACATCTCT+TGG 0.521360 5.4:-27513800 None:intergenic
TTGTAGATTCCCATATCAAA+AGG 0.521611 5.4:-27514557 None:intergenic
GTTGTGGCTCAAGTCATGGC+TGG 0.535182 5.4:+27513809 MS.gene99024:CDS
GATTTCACTAAATAAGTAAG+TGG 0.538843 5.4:-27514251 None:intergenic
AAAGGTGGCACAACCCATAT+GGG 0.541900 5.4:-27514644 None:intergenic
TGTCTAGCTTTCATAAAAGC+AGG 0.542520 5.4:+27514032 MS.gene99024:CDS
CTTTGAAGTAAGATTTGTAA+CGG 0.546410 5.4:-27514610 None:intergenic
TATTTAGTGAAATCATTGGA+GGG 0.549492 5.4:+27514260 MS.gene99024:CDS
ACATACCATATAATTATCGA+TGG 0.552414 5.4:-27513908 None:intergenic
GGACCTCTAGGATAAGGAAT+CGG 0.552728 5.4:-27514536 None:intergenic
GTTTGCCCAATCTCGCTCCA+TGG 0.556567 5.4:-27513533 None:intergenic
CCCATATCAAAAGGACCTCT+AGG 0.561580 5.4:-27514548 None:intergenic
TTATTTAGTGAAATCATTGG+AGG 0.564804 5.4:+27514259 MS.gene99024:CDS
GGAATTCTTTCCTCACCCCA+AGG 0.565481 5.4:-27514188 None:intergenic
ACGAAGAAGATGTCATCACT+TGG 0.566470 5.4:+27513845 MS.gene99024:CDS
GGAATCTACAACGTAAAGCA+TGG 0.570743 5.4:+27514569 MS.gene99024:CDS
AATCAATTCCATTGAAAAGG+TGG 0.576430 5.4:-27514659 None:intergenic
TCTGAAGGGATCATTAGCAT+AGG 0.577323 5.4:-27513700 None:intergenic
ATCGACATTACATTCTACAA+TGG 0.582494 5.4:+27514101 MS.gene99024:CDS
GAATTCTTTCCTCACCCCAA+GGG 0.583805 5.4:-27514187 None:intergenic
CTTAACACCAAGAGATGTTG+TGG 0.590075 5.4:+27513793 MS.gene99024:CDS
GGTGATCGTGTTGATGACTA+AGG 0.595842 5.4:-27513657 None:intergenic
AATCATTGGAGGGAGAGTTG+TGG 0.606251 5.4:+27514270 MS.gene99024:CDS
TGGTGTATGCTGTAACTCGT+TGG 0.616114 5.4:+27514126 MS.gene99024:CDS
CGAAGAAGATGTCATCACTT+GGG 0.623448 5.4:+27513846 MS.gene99024:CDS
ACCATATAATTATCGATGGG+TGG 0.627867 5.4:-27513904 None:intergenic
AGATGTTGTGGCTCAAGTCA+TGG 0.635745 5.4:+27513805 MS.gene99024:CDS
TTATGAAAGCTAGACAGCCA+CGG 0.638641 5.4:-27514025 None:intergenic
GAACCGATTCCTTATCCTAG+AGG 0.645299 5.4:+27514533 MS.gene99024:CDS
CATACCATATAATTATCGAT+GGG 0.648701 5.4:-27513907 None:intergenic
TGTTATTCAAGTGACCCTTG+GGG 0.675329 5.4:+27514173 MS.gene99024:CDS
GCAGCAATTTACACTGACCG+TGG 0.685734 5.4:+27514008 MS.gene99024:intron
ATTGGAGGGAGAGTTGTGGA+TGG 0.690403 5.4:+27514274 MS.gene99024:CDS
GGTGGCACAACCCATATGGG+AGG 0.700789 5.4:-27514641 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TACTTATTTAGTGAAATCAT+TGG + chr5.4:27514256-27514275 MS.gene99024:CDS 20.0%
!! TTCTTTACATGTATTTAAGT+TGG + chr5.4:27514343-27514362 MS.gene99024:intron 20.0%
!!! AATAGTAAATTGAATCCTTT+TGG - chr5.4:27514493-27514512 None:intergenic 20.0%
!!! AATATTTTATTTGTAGGTGA+CGG + chr5.4:27514425-27514444 MS.gene99024:intron 20.0%
! ACATACCATATAATTATCGA+TGG - chr5.4:27513911-27513930 None:intergenic 25.0%
! CATACCATATAATTATCGAT+GGG - chr5.4:27513910-27513929 None:intergenic 25.0%
! CGATAATTATATGGTATGTA+AGG + chr5.4:27513912-27513931 MS.gene99024:intron 25.0%
! CTTCTTTGTAACAAAACATT+TGG - chr5.4:27514212-27514231 None:intergenic 25.0%
! GATTTCACTAAATAAGTAAG+TGG - chr5.4:27514254-27514273 None:intergenic 25.0%
! TATTTAGTGAAATCATTGGA+GGG + chr5.4:27514260-27514279 MS.gene99024:CDS 25.0%
! TTATTTAGTGAAATCATTGG+AGG + chr5.4:27514259-27514278 MS.gene99024:CDS 25.0%
!! TTAAGCATTGTCAATTCTAA+TGG - chr5.4:27513778-27513797 None:intergenic 25.0%
!!! ATCATTTGGACTTGTTATAT+AGG - chr5.4:27513979-27513998 None:intergenic 25.0%
!!! CTTTGAAGTAAGATTTGTAA+CGG - chr5.4:27514613-27514632 None:intergenic 25.0%
!!! GGAGACAATATTTTATTTGT+AGG + chr5.4:27514419-27514438 MS.gene99024:intron 25.0%
AACAAGTCCAAATGATTATG+TGG + chr5.4:27513983-27514002 MS.gene99024:intron 30.0%
AAGTTGGAATTGAATGACAA+AGG + chr5.4:27514359-27514378 MS.gene99024:intron 30.0%
AGGGTCAAAAATATCAACAA+AGG + chr5.4:27514314-27514333 MS.gene99024:CDS 30.0%
ATCGACATTACATTCTACAA+TGG + chr5.4:27514101-27514120 MS.gene99024:CDS 30.0%
CATTACATTCTACAATGGTT+TGG + chr5.4:27514106-27514125 MS.gene99024:CDS 30.0%
CGTTACAAATCTTACTTCAA+AGG + chr5.4:27514611-27514630 MS.gene99024:CDS 30.0%
GCATTATATTGCTCCTAAAT+TGG - chr5.4:27513681-27513700 None:intergenic 30.0%
GGTGAGAAGGTTTATAAATA+GGG + chr5.4:27514295-27514314 MS.gene99024:CDS 30.0%
TAATGTCGATGAAACCAAAA+TGG - chr5.4:27514091-27514110 None:intergenic 30.0%
TGGTGAGAAGGTTTATAAAT+AGG + chr5.4:27514294-27514313 MS.gene99024:CDS 30.0%
TTGAACCAATTGATCACATT+TGG + chr5.4:27513596-27513615 MS.gene99024:CDS 30.0%
TTGTAGATTCCCATATCAAA+AGG - chr5.4:27514560-27514579 None:intergenic 30.0%
! AATGGATACACTCTATTTTC+AGG - chr5.4:27513760-27513779 None:intergenic 30.0%
! AGTAAATTGAATCCTTTTGG+AGG - chr5.4:27514490-27514509 None:intergenic 30.0%
ACCATATAATTATCGATGGG+TGG - chr5.4:27513907-27513926 None:intergenic 35.0%
ATAGCAGCAACATCCTTAAA+AGG - chr5.4:27513877-27513896 None:intergenic 35.0%
ATCAACACGATCACCAATTT+AGG + chr5.4:27513665-27513684 MS.gene99024:CDS 35.0%
CCAAACCAAATGTGATCAAT+TGG - chr5.4:27513604-27513623 None:intergenic 35.0%
CCAATTGATCACATTTGGTT+TGG + chr5.4:27513601-27513620 MS.gene99024:CDS 35.0%
TGTGCATAAGGTTACATTGT+CGG + chr5.4:27513948-27513967 MS.gene99024:intron 35.0%
TTACGACTACAATGTGCATA+AGG + chr5.4:27513936-27513955 MS.gene99024:intron 35.0%
TTGTCGAAACTTGAGAGTTT+AGG + chr5.4:27514398-27514417 MS.gene99024:intron 35.0%
TTTCTCAAGTTACCTCCAAA+AGG + chr5.4:27514475-27514494 MS.gene99024:CDS 35.0%
! ATACAAGACACTGACCATTT+TGG + chr5.4:27514074-27514093 MS.gene99024:CDS 35.0%
! TAAAAGCAGGACAAGAGTTT+TGG + chr5.4:27514045-27514064 MS.gene99024:CDS 35.0%
! TTGTTATTCAAGTGACCCTT+GGG + chr5.4:27514172-27514191 MS.gene99024:CDS 35.0%
! TTTCTGGACACTTTTCTGAA+GGG - chr5.4:27513717-27513736 None:intergenic 35.0%
! TTTTCTGGACACTTTTCTGA+AGG - chr5.4:27513718-27513737 None:intergenic 35.0%
!! CTATACAAACATCGCTTTTC+TGG - chr5.4:27513733-27513752 None:intergenic 35.0%
!! TGTCTAGCTTTCATAAAAGC+AGG + chr5.4:27514032-27514051 MS.gene99024:CDS 35.0%
!! TTGGTTCTGTCTGCAAAAAT+TGG + chr5.4:27513620-27513639 MS.gene99024:CDS 35.0%
!! TTTGTTATTCAAGTGACCCT+TGG + chr5.4:27514171-27514190 MS.gene99024:CDS 35.0%
ACGAAGAAGATGTCATCACT+TGG + chr5.4:27513845-27513864 MS.gene99024:CDS 40.0%
CGAAGAAGATGTCATCACTT+GGG + chr5.4:27513846-27513865 MS.gene99024:CDS 40.0%
CTTAACACCAAGAGATGTTG+TGG + chr5.4:27513793-27513812 MS.gene99024:CDS 40.0%
GCCACCCATCGATAATTATA+TGG + chr5.4:27513903-27513922 MS.gene99024:CDS 40.0%
GCTGCAACCACATAATCATT+TGG - chr5.4:27513993-27514012 None:intergenic 40.0%
GGAATCTACAACGTAAAGCA+TGG + chr5.4:27514569-27514588 MS.gene99024:CDS 40.0%
TCTGAAGGGATCATTAGCAT+AGG - chr5.4:27513703-27513722 None:intergenic 40.0%
TGTTATTCAAGTGACCCTTG+GGG + chr5.4:27514173-27514192 MS.gene99024:CDS 40.0%
TTATGAAAGCTAGACAGCCA+CGG - chr5.4:27514028-27514047 None:intergenic 40.0%
! CACTTGGGAGAATCCTTTTA+AGG + chr5.4:27513861-27513880 MS.gene99024:CDS 40.0%
! CCTAGAGGTCCTTTTGATAT+GGG + chr5.4:27514548-27514567 MS.gene99024:CDS 40.0%
! TCCTAGAGGTCCTTTTGATA+TGG + chr5.4:27514547-27514566 MS.gene99024:CDS 40.0%
!! TCAAAAGGACCTCTAGGATA+AGG - chr5.4:27514545-27514564 None:intergenic 40.0%
AAAAGGTGGCACAACCCATA+TGG - chr5.4:27514648-27514667 None:intergenic 45.0%
AAAGGTGGCACAACCCATAT+GGG - chr5.4:27514647-27514666 None:intergenic 45.0%
AAGGTATGACACCTCCCATA+TGG + chr5.4:27514630-27514649 MS.gene99024:CDS 45.0%
AATCATTGGAGGGAGAGTTG+TGG + chr5.4:27514270-27514289 MS.gene99024:CDS 45.0%
ACTTGAGCCACAACATCTCT+TGG - chr5.4:27513803-27513822 None:intergenic 45.0%
AGATGTTGTGGCTCAAGTCA+TGG + chr5.4:27513805-27513824 MS.gene99024:CDS 45.0%
AGGTATGACACCTCCCATAT+GGG + chr5.4:27514631-27514650 MS.gene99024:CDS 45.0%
CCCATATCAAAAGGACCTCT+AGG - chr5.4:27514551-27514570 None:intergenic 45.0%
GAATTCTTTCCTCACCCCAA+GGG - chr5.4:27514190-27514209 None:intergenic 45.0%
TGGTGTATGCTGTAACTCGT+TGG + chr5.4:27514126-27514145 MS.gene99024:CDS 45.0%
! GAACCGATTCCTTATCCTAG+AGG + chr5.4:27514533-27514552 MS.gene99024:CDS 45.0%
!! GGACCTCTAGGATAAGGAAT+CGG - chr5.4:27514539-27514558 None:intergenic 45.0%
!! GGTGATCGTGTTGATGACTA+AGG - chr5.4:27513660-27513679 None:intergenic 45.0%
ATTGGAGGGAGAGTTGTGGA+TGG + chr5.4:27514274-27514293 MS.gene99024:CDS 50.0%
GAGAGTTGTGGATGGTGAGA+AGG + chr5.4:27514282-27514301 MS.gene99024:CDS 50.0%
GCAGCAATTTACACTGACCG+TGG + chr5.4:27514008-27514027 MS.gene99024:intron 50.0%
GGAATTCTTTCCTCACCCCA+AGG - chr5.4:27514191-27514210 None:intergenic 50.0%
! GGGTTGTGCCACCTTTTCAA+TGG + chr5.4:27514651-27514670 MS.gene99024:CDS 50.0%
GTTGTGGCTCAAGTCATGGC+TGG + chr5.4:27513809-27513828 MS.gene99024:CDS 55.0%
TTCAAGTGACCCTTGGGGTG+AGG + chr5.4:27514178-27514197 MS.gene99024:CDS 55.0%
GGTGGCACAACCCATATGGG+AGG - chr5.4:27514644-27514663 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 27513535 27514679 27513535 ID=MS.gene99024
chr5.4 mRNA 27513535 27514679 27513535 ID=MS.gene99024.t1;Parent=MS.gene99024
chr5.4 exon 27513535 27513928 27513535 ID=MS.gene99024.t1.exon1;Parent=MS.gene99024.t1
chr5.4 CDS 27513535 27513928 27513535 ID=cds.MS.gene99024.t1;Parent=MS.gene99024.t1
chr5.4 exon 27514012 27514335 27514012 ID=MS.gene99024.t1.exon2;Parent=MS.gene99024.t1
chr5.4 CDS 27514012 27514335 27514012 ID=cds.MS.gene99024.t1;Parent=MS.gene99024.t1
chr5.4 exon 27514441 27514679 27514441 ID=MS.gene99024.t1.exon3;Parent=MS.gene99024.t1
chr5.4 CDS 27514441 27514679 27514441 ID=cds.MS.gene99024.t1;Parent=MS.gene99024.t1
Gene Sequence

>MS.gene99024

ATGGAGCGAGATTGGGCAAACTTAGATTCACTCGCTCTCAACATGATTCTTGAGAAGTTAATTGAACCAATTGATCACATTTGGTTTGGTTCTGTCTGCAAAAATTGGCACTCAGTTGCAGACCTTAGTCATCAACACGATCACCAATTTAGGAGCAATATAATGCCTATGCTAATGATCCCTTCAGAAAAGTGTCCAGAAAAGCGATGTTTGTATAGCATACCTGAAAATAGAGTGTATCCATTAGAATTGACAATGCTTAACACCAAGAGATGTTGTGGCTCAAGTCATGGCTGGCTCGCAACGTTAGACGAAGAAGATGTCATCACTTGGGAGAATCCTTTTAAGGATGTTGCTGCTATTAGTTTGCCACCCATCGATAATTATATGGTATGTAAGGATTACGACTACAATGTGCATAAGGTTACATTGTCGGTTGATCCTATATAACAAGTCCAAATGATTATGTGGTTGCAGCAATTTACACTGACCGTGGCTGTCTAGCTTTCATAAAAGCAGGACAAGAGTTTTGGACATACATACAAGACACTGACCATTTTGGTTTCATCGACATTACATTCTACAATGGTTTGGTGTATGCTGTAACTCGTTGGAGAAAAATTGTCTGCTTTGATCTTTGTTATTCAAGTGACCCTTGGGGTGAGGAAAGAATTCCAAATGTTTTGTTACAAAGAAGCGATGATGCAACTTACTCTCCACTTACTTATTTAGTGAAATCATTGGAGGGAGAGTTGTGGATGGTGAGAAGGTTTATAAATAGGGTCAAAAATATCAACAAAGGTACTAATTCTTTACATGTATTTAAGTTGGAATTGAATGACAAAGGTGAGAAGCTTATGCATTTGTCGAAACTTGAGAGTTTAGGAGACAATATTTTATTTGTAGGTGACGGCGACTCAATGTCTGTATCAGCTTCATATTTCTCAAGTTACCTCCAAAAGGATTCAATTTACTATTCTGATAATTATTATAACGAAGAACCGATTCCTTATCCTAGAGGTCCTTTTGATATGGGAATCTACAACGTAAAGCATGGAAGCTTTGATGTTCATTGCCGTTACAAATCTTACTTCAAAGGTATGACACCTCCCATATGGGTTGTGCCACCTTTTCAATGGAATTGA
Protein sequence

>MS.gene99024.t1

MERDWANLDSLALNMILEKLIEPIDHIWFGSVCKNWHSVADLSHQHDHQFRSNIMPMLMIPSEKCPEKRCLYSIPENRVYPLELTMLNTKRCCGSSHGWLATLDEEDVITWENPFKDVAAISLPPIDNYMVSIYTDRGCLAFIKAGQEFWTYIQDTDHFGFIDITFYNGLVYAVTRWRKIVCFDLCYSSDPWGEERIPNVLLQRSDDATYSPLTYLVKSLEGELWMVRRFINRVKNINKGDGDSMSVSASYFSSYLQKDSIYYSDNYYNEEPIPYPRGPFDMGIYNVKHGSFDVHCRYKSYFKGMTPPIWVVPPFQWN