AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene65425

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 39 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATACCTTTGTGAAGATAAA+AGG 0.212182 4.3:+87807874 None:intergenic
GTGATCTCATCCAGGATGAT+AGG 0.356626 4.3:+87807157 None:intergenic
CCAGGATGATAGGGTGGATA+GGG 0.403549 4.3:+87807167 None:intergenic
ATGTTGAAGGAGGCAAGAAC+TGG 0.403774 4.3:-87807270 MS.gene65425:CDS
TAAGGACGGGAAGGAACATT+TGG 0.428961 4.3:-87807672 MS.gene65425:CDS
TCTTATAAAATCATCATGAT+AGG 0.434799 4.3:+87807095 None:intergenic
GCAAGAGGTGTGATGGCAGC+AGG 0.439246 4.3:+87807226 None:intergenic
GAAGAAGCACGAGAAAATAA+AGG 0.445989 4.3:-87808925 MS.gene65425:CDS
AAATGTTCCTTCCCGTCCTT+AGG 0.450368 4.3:+87807674 None:intergenic
TGATGGCAGCAGGGGTAAGT+TGG 0.456592 4.3:+87807236 None:intergenic
CATACTACCTCTGCTAAGAT+TGG 0.469905 4.3:-87807202 MS.gene65425:CDS
CCCTATCCACCCTATCATCC+TGG 0.477480 4.3:-87807167 MS.gene65425:CDS
ACCATGTTGCAGAATGTTGA+AGG 0.481802 4.3:-87807283 MS.gene65425:CDS
TAAGATAGTAACATATCCTA+AGG 0.501123 4.3:-87807690 MS.gene65425:intron
ATTCTGCAACATGGTGGAAG+GGG 0.513075 4.3:+87807291 None:intergenic
TTGCAGGAGTGATCTCATCC+AGG 0.524797 4.3:+87807149 None:intergenic
TGTCTTTGAACAACAAGTGC+AGG 0.532648 4.3:-87807908 MS.gene65425:CDS
AAAATCATCATGATAGGAAG+AGG 0.535692 4.3:+87807101 None:intergenic
ACATTCTGCAACATGGTGGA+AGG 0.539324 4.3:+87807289 None:intergenic
TGATCTCATCCAGGATGATA+GGG 0.550931 4.3:+87807158 None:intergenic
TAGTAACATATCCTAAGGAC+GGG 0.551671 4.3:-87807685 MS.gene65425:CDS
TCCTTCAACATTCTGCAACA+TGG 0.556193 4.3:+87807282 None:intergenic
CATTCTGCAACATGGTGGAA+GGG 0.560478 4.3:+87807290 None:intergenic
AGTATGAGCAAGAGGTGTGA+TGG 0.566077 4.3:+87807219 None:intergenic
GATGGTCATTGTTGATGCTA+AGG 0.581330 4.3:-87807648 MS.gene65425:intron
TCCAGGATGATAGGGTGGAT+AGG 0.585429 4.3:+87807166 None:intergenic
CAAGAGGTGTGATGGCAGCA+GGG 0.589536 4.3:+87807227 None:intergenic
GCAGAGGTAGTATGAGCAAG+AGG 0.599567 4.3:+87807211 None:intergenic
ATAGTAACATATCCTAAGGA+CGG 0.602531 4.3:-87807686 MS.gene65425:CDS
CGGGAAGGAACATTTGGAGA+TGG 0.612772 4.3:-87807666 MS.gene65425:CDS
TGTTGAAGGAGGCAAGAACT+GGG 0.613431 4.3:-87807269 MS.gene65425:CDS
AACATATCCTAAGGACGGGA+AGG 0.619664 4.3:-87807681 MS.gene65425:CDS
CAGGATGATAGGGTGGATAG+GGG 0.620934 4.3:+87807168 None:intergenic
AAGAGGTGTGATGGCAGCAG+GGG 0.623171 4.3:+87807228 None:intergenic
TTCAACATTCTGCAACATGG+TGG 0.658953 4.3:+87807285 None:intergenic
TCTCATCCAGGATGATAGGG+TGG 0.663515 4.3:+87807161 None:intergenic
ACTTGAACCAATCTTAGCAG+AGG 0.665354 4.3:+87807195 None:intergenic
ATGTTGCAGAATGTTGAAGG+AGG 0.685850 4.3:-87807280 MS.gene65425:CDS
TATGATTTAGGACACAAATG+TGG 0.703373 4.3:-87807483 MS.gene65425:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGAAAAAAGATTATAATT+AGG - chr4.3:87807667-87807686 MS.gene65425:CDS 10.0%
!! TATATTAGATCTTAAAAAAT+TGG + chr4.3:87807576-87807595 None:intergenic 10.0%
!!! AAAAGTAATTAATTCTTTTT+TGG - chr4.3:87807161-87807180 MS.gene65425:CDS 10.0%
!!! ATATTTTATGTATAAAACAA+TGG - chr4.3:87807456-87807475 MS.gene65425:intron 10.0%
!!! TACATAAAGATTTTTTTTAA+AGG + chr4.3:87807488-87807507 None:intergenic 10.0%
!! AAAAAAATCTTTATGTATTG+AGG - chr4.3:87807491-87807510 MS.gene65425:intron 15.0%
!! AACAAAATCACATTTATCAA+AGG + chr4.3:87807782-87807801 None:intergenic 20.0%
!! ACAATATACAATAGTAATAC+AGG + chr4.3:87807425-87807444 None:intergenic 20.0%
!! ACATATGTTTAAACATATCA+AGG + chr4.3:87808662-87808681 None:intergenic 20.0%
!! ATGTTATTATGCAGTTATTT+AGG + chr4.3:87808290-87808309 None:intergenic 20.0%
!! CAAACTTATAACATGTTAAA+TGG - chr4.3:87808243-87808262 MS.gene65425:intron 20.0%
!! TAAAAAAAAATAGCAGTTGA+TGG + chr4.3:87808328-87808347 None:intergenic 20.0%
!!! TTAATTCTTTTTTGGCTTTT+AGG - chr4.3:87807169-87807188 MS.gene65425:CDS 20.0%
!!! TTTGATAAATGTGATTTTGT+TGG - chr4.3:87807781-87807800 MS.gene65425:intron 20.0%
! AAAATCTTTATGTATTGAGG+TGG - chr4.3:87807494-87807513 MS.gene65425:intron 25.0%
! AAGATGTCATAAATTAGTCA+AGG + chr4.3:87808449-87808468 None:intergenic 25.0%
! CACATTTATCAAAGGAAAAA+AGG + chr4.3:87807774-87807793 None:intergenic 25.0%
! GATATGTTCTGCAAATTTAT+TGG - chr4.3:87807381-87807400 MS.gene65425:intron 25.0%
! TAAGATAGTAACATATCCTA+AGG - chr4.3:87808346-87808365 MS.gene65425:intron 25.0%
! TCAATTAAGATGATCTACAT+TGG - chr4.3:87808619-87808638 MS.gene65425:intron 25.0%
!! AAAAAACTCTTACTCTAAGA+TGG - chr4.3:87808908-87808927 MS.gene65425:intron 25.0%
!! AATTTGTAGTGTTTTCAACT+AGG - chr4.3:87808038-87808057 MS.gene65425:intron 25.0%
!! TTTAGGATATGTACATATGA+AGG + chr4.3:87808273-87808292 None:intergenic 25.0%
!!! ATTGGTAATGTTGTTTTGAA+CGG + chr4.3:87807714-87807733 None:intergenic 25.0%
!!! CAACAAATCAAATGGTTTTA+AGG + chr4.3:87807851-87807870 None:intergenic 25.0%
ACATGCATCAACAAATCAAA+TGG + chr4.3:87807859-87807878 None:intergenic 30.0%
AGATGACAATGCTATGATTT+AGG - chr4.3:87808541-87808560 MS.gene65425:intron 30.0%
ATAGTAACATATCCTAAGGA+CGG - chr4.3:87808350-87808369 MS.gene65425:intron 30.0%
CATACCTTTGTGAAGATAAA+AGG + chr4.3:87808165-87808184 None:intergenic 30.0%
GATGCATGTTTGAAAGAATT+AGG - chr4.3:87807870-87807889 MS.gene65425:intron 30.0%
GTGTGTTTGTTTGCTTATTA+GGG - chr4.3:87808473-87808492 MS.gene65425:intron 30.0%
TCAAGGAAATAATCAGTTGT+AGG + chr4.3:87808432-87808451 None:intergenic 30.0%
TGTGTGTTTGTTTGCTTATT+AGG - chr4.3:87808472-87808491 MS.gene65425:intron 30.0%
TTCTTGTGAGGAAACATAAT+TGG + chr4.3:87807732-87807751 None:intergenic 30.0%
! ATATCATGTAAGCTCTCTTT+TGG + chr4.3:87807897-87807916 None:intergenic 30.0%
! CTACATTGGTTATTTATCTG+CGG - chr4.3:87808633-87808652 MS.gene65425:intron 30.0%
! TACTCCTTTTATCTTCACAA+AGG - chr4.3:87808158-87808177 MS.gene65425:intron 30.0%
! TATGATTTAGGACACAAATG+TGG - chr4.3:87808553-87808572 MS.gene65425:intron 30.0%
! TTTTCTGTCCAATAAACCAA+GGG + chr4.3:87807280-87807299 None:intergenic 30.0%
! TTTTTCTGTCCAATAAACCA+AGG + chr4.3:87807281-87807300 None:intergenic 30.0%
!!! CGGATATTTTTTTTCATGTG+CGG + chr4.3:87807694-87807713 None:intergenic 30.0%
!!! TTAGAGTAAGAGTTTTTTGC+AGG + chr4.3:87808906-87808925 None:intergenic 30.0%
AAAGCTTTCCCTTGGTTTAT+TGG - chr4.3:87807269-87807288 MS.gene65425:CDS 35.0%
AATAAAGGCGAGTACAAAGT+TGG - chr4.3:87807126-87807145 MS.gene65425:CDS 35.0%
AGAGAGCTTACATGATATGT+AGG - chr4.3:87807899-87807918 MS.gene65425:CDS 35.0%
ATAAAGGCGAGTACAAAGTT+GGG - chr4.3:87807127-87807146 MS.gene65425:CDS 35.0%
ATCATAGCATTGTCATCTTG+TGG + chr4.3:87808539-87808558 None:intergenic 35.0%
TAAGAACATGATCTGTCACT+TGG - chr4.3:87808711-87808730 MS.gene65425:intron 35.0%
TAGTAACATATCCTAAGGAC+GGG - chr4.3:87808351-87808370 MS.gene65425:intron 35.0%
TTGTATCTGTTGTTCTTGTG+AGG + chr4.3:87807744-87807763 None:intergenic 35.0%
! GAAGAAGCACGAGAAAATAA+AGG - chr4.3:87807111-87807130 MS.gene65425:CDS 35.0%
!! CAGTTGATGGATATGTACTT+AGG + chr4.3:87808315-87808334 None:intergenic 35.0%
ACCATGTTGCAGAATGTTGA+AGG - chr4.3:87808753-87808772 MS.gene65425:intron 40.0%
ACTTGAACCAATCTTAGCAG+AGG + chr4.3:87808844-87808863 None:intergenic 40.0%
ATGTTGCAGAATGTTGAAGG+AGG - chr4.3:87808756-87808775 MS.gene65425:intron 40.0%
CATACTACCTCTGCTAAGAT+TGG - chr4.3:87808834-87808853 MS.gene65425:intron 40.0%
GATGGTCATTGTTGATGCTA+AGG - chr4.3:87808388-87808407 MS.gene65425:intron 40.0%
GTTGTAGTACTCCATGAATG+AGG - chr4.3:87807932-87807951 MS.gene65425:intron 40.0%
TAAAGGCGAGTACAAAGTTG+GGG - chr4.3:87807128-87807147 MS.gene65425:CDS 40.0%
TCCATGAATGAGGTCGAAAA+TGG - chr4.3:87807942-87807961 MS.gene65425:intron 40.0%
TCCTTCAACATTCTGCAACA+TGG + chr4.3:87808757-87808776 None:intergenic 40.0%
TGATCTCATCCAGGATGATA+GGG + chr4.3:87808881-87808900 None:intergenic 40.0%
TGTCTTTGAACAACAAGTGC+AGG - chr4.3:87808128-87808147 MS.gene65425:intron 40.0%
TTCAACATTCTGCAACATGG+TGG + chr4.3:87808754-87808773 None:intergenic 40.0%
! ACCATTTTCGACCTCATTCA+TGG + chr4.3:87807946-87807965 None:intergenic 40.0%
AAATGTTCCTTCCCGTCCTT+AGG + chr4.3:87808365-87808384 None:intergenic 45.0%
AACATATCCTAAGGACGGGA+AGG - chr4.3:87808355-87808374 MS.gene65425:intron 45.0%
ATGTTGAAGGAGGCAAGAAC+TGG - chr4.3:87808766-87808785 MS.gene65425:intron 45.0%
GTGATCTCATCCAGGATGAT+AGG + chr4.3:87808882-87808901 None:intergenic 45.0%
GTTCTTGCAAAGCTTTCCCT+TGG - chr4.3:87807261-87807280 MS.gene65425:CDS 45.0%
TAAGGACGGGAAGGAACATT+TGG - chr4.3:87808364-87808383 MS.gene65425:intron 45.0%
TGTTGAAGGAGGCAAGAACT+GGG - chr4.3:87808767-87808786 MS.gene65425:intron 45.0%
! ACATTCTGCAACATGGTGGA+AGG + chr4.3:87808750-87808769 None:intergenic 45.0%
! AGTATGAGCAAGAGGTGTGA+TGG + chr4.3:87808820-87808839 None:intergenic 45.0%
! ATTCTGCAACATGGTGGAAG+GGG + chr4.3:87808748-87808767 None:intergenic 45.0%
! CATTCTGCAACATGGTGGAA+GGG + chr4.3:87808749-87808768 None:intergenic 45.0%
AAGTTGCAGATGCAGCACAC+TGG + chr4.3:87808686-87808705 None:intergenic 50.0%
CAGGATGATAGGGTGGATAG+GGG + chr4.3:87808871-87808890 None:intergenic 50.0%
CCAGGATGATAGGGTGGATA+GGG + chr4.3:87808872-87808891 None:intergenic 50.0%
CGGGAAGGAACATTTGGAGA+TGG - chr4.3:87808370-87808389 MS.gene65425:intron 50.0%
GCAGAGGTAGTATGAGCAAG+AGG + chr4.3:87808828-87808847 None:intergenic 50.0%
TCCAGGATGATAGGGTGGAT+AGG + chr4.3:87808873-87808892 None:intergenic 50.0%
TCTCATCCAGGATGATAGGG+TGG + chr4.3:87808878-87808897 None:intergenic 50.0%
TTGCAGGAGTGATCTCATCC+AGG + chr4.3:87808890-87808909 None:intergenic 50.0%
CCCTATCCACCCTATCATCC+TGG - chr4.3:87808869-87808888 MS.gene65425:intron 55.0%
TGATGGCAGCAGGGGTAAGT+TGG + chr4.3:87808803-87808822 None:intergenic 55.0%
! AAGAGGTGTGATGGCAGCAG+GGG + chr4.3:87808811-87808830 None:intergenic 55.0%
! CAAGAGGTGTGATGGCAGCA+GGG + chr4.3:87808812-87808831 None:intergenic 55.0%
! GCAAGAGGTGTGATGGCAGC+AGG + chr4.3:87808813-87808832 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 87807108 87808950 87807108 ID=MS.gene65425
chr4.3 mRNA 87807108 87808950 87807108 ID=MS.gene65425.t1;Parent=MS.gene65425
chr4.3 exon 87808922 87808950 87808922 ID=MS.gene65425.t1.exon1;Parent=MS.gene65425.t1
chr4.3 CDS 87808922 87808950 87808922 ID=cds.MS.gene65425.t1;Parent=MS.gene65425.t1
chr4.3 exon 87807879 87807939 87807879 ID=MS.gene65425.t1.exon2;Parent=MS.gene65425.t1
chr4.3 CDS 87807879 87807939 87807879 ID=cds.MS.gene65425.t1;Parent=MS.gene65425.t1
chr4.3 exon 87807649 87807708 87807649 ID=MS.gene65425.t1.exon3;Parent=MS.gene65425.t1
chr4.3 CDS 87807649 87807708 87807649 ID=cds.MS.gene65425.t1;Parent=MS.gene65425.t1
chr4.3 exon 87807457 87807495 87807457 ID=MS.gene65425.t1.exon4;Parent=MS.gene65425.t1
chr4.3 CDS 87807457 87807495 87807457 ID=cds.MS.gene65425.t1;Parent=MS.gene65425.t1
chr4.3 exon 87807108 87807320 87807108 ID=MS.gene65425.t1.exon5;Parent=MS.gene65425.t1
chr4.3 CDS 87807108 87807320 87807108 ID=cds.MS.gene65425.t1;Parent=MS.gene65425.t1
Gene Sequence

>MS.gene65425

ATGGAAGAAGCACGAGAAAATAAAGGCGAGTACAAAGTTGGGGTAGAGAGAGTAAAAGTAATTAATTCTTTTTTGGCTTTTAGGAAAAGTGAAGAAAATTCGTCATTTTCTTTTTTATCATAAATGCAATCAAAACTTCTAATACTTATGTATGTTCTTGCAAAGCTTTCCCTTGGTTTATTGGACAGAAAAACAGACAACAATTATATATTGTGCAAAAAAATATATATTAAATAATATATATACAGAAAGTTGATGAATTTTTTTATGCGAGATATGTTCTGCAAATTTATTGGTCAATTAAATAATATAAGCCTGTATTACTATTGTATATTGTGCAAAAAATATATATTTTATGTATAAAACAATGGTCAGTGCCTTTAAAAAAAATCTTTATGTATTGAGGTGGTTGAGTTTTAATCTTTTAAATATTTCTATTATTATGCTAAACAAAATTCTTAAAAACCAATTTTTTAAGATCTAATATAGATATAACAAACTGTATTTAACATAAGCTTCATCAAGAGTATTTGTTCACTTTCATTTGTAAACTTTCATGATAGAAAAAAGATTATAATTAGGTCCGCACATGAAAAAAAATATCCGTTCAAAACAACATTACCAATTATGTTTCCTCACAAGAACAACAGATACAAATCAATGCCTTTTTTCCTTTGATAAATGTGATTTTGTTGGCTGTATCAAATAAGAGTTGATGAAGATATGAATATATAATCTGACCTTAAAACCATTTGATTTGTTGATGCATGTTTGAAAGAATTAGGTCCAAAAGAGAGCTTACATGATATGTAGGTTCAAGATCTGTTGTAGTACTCCATGAATGAGGTCGAAAATGGTGATTTAAATGTCAATTTGACGATTTTGAAAAAAAATCTGCACAACAGAAGAAAATAAATGATGATGTCATAAAATTTGTAGTGTTTTCAACTAGGTTTACTTTTTCTTCAACATATTTCTAACTTTCATTTTATTTTCATCTCTCTTTTGCAGAAAAATTGATGTCTTTGAACAACAAGTGCAGGTAAATGATACTCCTTTTATCTTCACAAAGGTATGAATATGTAATGAACTCATTTTTTTGTTGTGCATTCTCTTTATTATTTGTTATCTCTATCAAACTTATAACATGTTAAATGGAGCTCCTTCATATGTACATATCCTAAATAACTGCATAATAACATATCCTAAGTACATATCCATCAACTGCTATTTTTTTTTAAGATAGTAACATATCCTAAGGACGGGAAGGAACATTTGGAGATGGTCATTGTTGATGCTAAGGTCTAATTATATACTGATTCCTACAACTGATTATTTCCTTGACTAATTTATGACATCTTAATTGTGTGTTTGTTTGCTTATTAGGGTGATGATATACAAGTTGCTGTTCTATACTAGCAGCATGCACCACAAGATGACAATGCTATGATTTAGGACACAAATGTGGAGAGTGATGATGTTACTATCTCAGTTGTAAGTTGATTAATTATTCAATTAAGATGATCTACATTGGTTATTTATCTGCGGTAACCTTGATATGTTTAAACATATGTGCCAGTGTGCTGCATCTGCAACTTCTGAATAAGAACATGATCTGTCACTTGGTCAGATGCAAACCCCTTCCACCATGTTGCAGAATGTTGAAGGAGGCAAGAACTGGGACTCACTCAGCCAACTTACCCCTGCTGCCATCACACCTCTTGCTCATACTACCTCTGCTAAGATTGGTTCAAGTGCTACCCCTATCCACCCTATCATCCTGGATGAGATCACTCCTGCAAAAAACTCTTACTCTAAGATGGTTAACCTCTTCCTATCATGA
Protein sequence

>MS.gene65425.t1

MEEARENKGEKIDVFEQQVQVNDTPFIFTKIVTYPKDGKEHLEMVIVDAKDTNVESDDVTISVMQTPSTMLQNVEGGKNWDSLSQLTPAAITPLAHTTSAKIGSSATPIHPIILDEITPAKNSYSKMVNLFLS