AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene43109


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 50 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTGATGGTGGATGGTTTA+TGG 0.205537 7.2:-77188751 MS.gene43109:CDS
TTTCATGTTACTGATCAAAA+TGG 0.211096 7.2:-77188574 MS.gene43109:CDS
CAGAACAACAACTTTGATAA+AGG 0.291767 7.2:-77188961 MS.gene43109:intron
GTCATTCATGTTCTTGCAAT+TGG 0.312088 7.2:-77187324 MS.gene43109:CDS
CCGCTACCACATTGCATTTG+AGG 0.353645 7.2:+77187791 None:intergenic
GTTGATGATTGCATCGATAA+AGG 0.360000 7.2:-77187481 MS.gene43109:CDS
AATAGTAACTTCGGTCGATC+TGG 0.375903 7.2:+77187433 None:intergenic
CATACAACGATCGAGTTAAC+AGG 0.410366 7.2:-77187862 MS.gene43109:CDS
TGAAGGAACAGAAGCATATC+AGG 0.414309 7.2:-77187350 MS.gene43109:CDS
AAGACTTCTGAAAGCAATCC+TGG 0.415942 7.2:+77187829 None:intergenic
TCGAGTTAACAGGACGAGAT+AGG 0.422142 7.2:-77187852 MS.gene43109:CDS
ATGTGGTAGCGGCTGAAGTC+TGG 0.426365 7.2:-77187780 MS.gene43109:CDS
TTCATGTTACTGATCAAAAT+GGG 0.434204 7.2:-77188573 MS.gene43109:CDS
TACATCACCGACGACACAAC+AGG 0.443441 7.2:-77187727 MS.gene43109:CDS
TTAATCTTGGCAAGGCGGTC+AGG 0.450576 7.2:+77187688 None:intergenic
GATCGGAAGCTACGGACTCT+TGG 0.452011 7.2:+77187922 None:intergenic
TGTAGCTGATAGAATTCAAC+AGG 0.458713 7.2:-77188530 MS.gene43109:intron
TCAATTGATGTATGCTGATC+GGG 0.471630 7.2:-77187569 MS.gene43109:CDS
CGGGATTATGACATATATGA+TGG 0.473270 7.2:-77187550 MS.gene43109:CDS
AAGCAGAAGATGCTTAATCT+TGG 0.477322 7.2:+77187675 None:intergenic
ATATTTCATCTGATGGTGGA+TGG 0.481369 7.2:-77188758 MS.gene43109:CDS
TAATAAACGTGGTAGTTTGT+TGG 0.488332 7.2:-77188829 MS.gene43109:CDS
AGAGCTTATATTTCATCTGA+TGG 0.514352 7.2:-77188765 MS.gene43109:CDS
TTTGTTCGACTCACAAGGAT+AGG 0.516487 7.2:-77187600 MS.gene43109:CDS
GATATACCGTCGTGAATTTG+AGG 0.531940 7.2:-77187459 MS.gene43109:CDS
CGGCAATCCTGTTGTGTCGT+CGG 0.534641 7.2:+77187720 None:intergenic
TTCTCACGGATCGGAAGCTA+CGG 0.542549 7.2:+77187914 None:intergenic
CTTCAGCATTGACAGTTCCA+TGG 0.546213 7.2:+77187368 None:intergenic
CCTCAAATGCAATGTGGTAG+CGG 0.554458 7.2:-77187791 MS.gene43109:CDS
CTGGACACACAATTCAAGAA+TGG 0.562636 7.2:-77187761 MS.gene43109:CDS
GTTCGACTCACAAGGATAGG+AGG 0.577855 7.2:-77187597 MS.gene43109:CDS
ATCAATTGATGTATGCTGAT+CGG 0.588153 7.2:-77187570 MS.gene43109:CDS
ATCTGTCGGTGTTCAAGCTG+CGG 0.596760 7.2:-77187890 MS.gene43109:CDS
TTAACAGGACGAGATAGGCC+AGG 0.610170 7.2:-77187847 MS.gene43109:CDS
CATGGAACTGTCAATGCTGA+AGG 0.610676 7.2:-77187367 MS.gene43109:CDS
CGACAGATCTTCTCACGGAT+CGG 0.618439 7.2:+77187905 None:intergenic
GCTTATATTTCATCTGATGG+TGG 0.619057 7.2:-77188762 MS.gene43109:CDS
AGGCGGTCAGGATTGTCGAT+CGG 0.626180 7.2:+77187700 None:intergenic
GATGGTGGATGGTTTATGGA+TGG 0.634152 7.2:-77188747 MS.gene43109:intron
GAAGATGCTTAATCTTGGCA+AGG 0.637572 7.2:+77187680 None:intergenic
AACACCGACAGATCTTCTCA+CGG 0.646279 7.2:+77187900 None:intergenic
CGATCCGTGAGAAGATCTGT+CGG 0.650412 7.2:-77187904 MS.gene43109:CDS
ACGGTATCGAATAGTAACTT+CGG 0.652560 7.2:+77187424 None:intergenic
CATGTCTGTGATAGTACACA+CGG 0.656721 7.2:+77187405 None:intergenic
CTTCTGCTTTATGTGCTGAG+AGG 0.660385 7.2:-77187661 MS.gene43109:CDS
ATGCAGTATGTTGTGTACCA+TGG 0.674170 7.2:-77187385 MS.gene43109:CDS
GATGCTTAATCTTGGCAAGG+CGG 0.685591 7.2:+77187683 None:intergenic
GTTGATAGTGCTAATAAACG+TGG 0.727553 7.2:-77188840 MS.gene43109:CDS
TGCTGACCTCAAATGCAATG+TGG 0.737650 7.2:-77187797 MS.gene43109:CDS
TGGACACCTCAAATTCACGA+CGG 0.751563 7.2:+77187453 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGATATTTTCTTATTTTAT+CGG - chr7.2:77187862-77187881 MS.gene43109:CDS 10.0%
!! AAATGAAGAATTATTGTAAA+TGG + chr7.2:77187565-77187584 None:intergenic 15.0%
!!! ATTTGTTATGATTGTAATTT+AGG - chr7.2:77187812-77187831 MS.gene43109:CDS 15.0%
!!! TTTGAAATTTAAACCTTATA+AGG - chr7.2:77187335-77187354 MS.gene43109:CDS 15.0%
!! AATCTTTGATGAATTTCAAA+AGG - chr7.2:77187362-77187381 MS.gene43109:CDS 20.0%
!! ATCTTTGATGAATTTCAAAA+GGG - chr7.2:77187363-77187382 MS.gene43109:CDS 20.0%
!! TAGAGTAATATAAACTATCA+TGG + chr7.2:77188053-77188072 None:intergenic 20.0%
!! TCAAAGATTATAACCTTATA+AGG + chr7.2:77187351-77187370 None:intergenic 20.0%
!!! CTTTTATATTGTGGTAAAAT+CGG + chr7.2:77188013-77188032 None:intergenic 20.0%
!!! TCAATTTTCATCATACTATT+TGG - chr7.2:77188100-77188119 MS.gene43109:intron 20.0%
!!! TGTTTACTAATAACACTTTT+TGG - chr7.2:77188305-77188324 MS.gene43109:intron 20.0%
! GAAGAATTATTGTAAATGGT+AGG + chr7.2:77187561-77187580 None:intergenic 25.0%
! GTTATTAGTAAACAAAGTTC+TGG + chr7.2:77188299-77188318 None:intergenic 25.0%
! TAGATCTGTGTAATATTCAT+CGG - chr7.2:77187769-77187788 MS.gene43109:CDS 25.0%
! TTCATGTTACTGATCAAAAT+GGG - chr7.2:77187700-77187719 MS.gene43109:CDS 25.0%
! TTTCATGTTACTGATCAAAA+TGG - chr7.2:77187699-77187718 MS.gene43109:CDS 25.0%
!! TGTGATCAACTTTTATATTG+TGG + chr7.2:77188022-77188041 None:intergenic 25.0%
!! TTTTCATGTGAATTTTGTGT+AGG - chr7.2:77187411-77187430 MS.gene43109:CDS 25.0%
!!! AACTAGTACTTTTTTTCTTG+AGG - chr7.2:77188260-77188279 MS.gene43109:intron 25.0%
!!! AAGAAAAAAAGTACTAGTTC+TGG + chr7.2:77188259-77188278 None:intergenic 25.0%
AGAGCTTATATTTCATCTGA+TGG - chr7.2:77187508-77187527 MS.gene43109:CDS 30.0%
ATCAATTGATGTATGCTGAT+CGG - chr7.2:77188703-77188722 MS.gene43109:intron 30.0%
ATCATCCTATTCCAATCAAA+AGG + chr7.2:77188139-77188158 None:intergenic 30.0%
CAGAACAACAACTTTGATAA+AGG - chr7.2:77187312-77187331 MS.gene43109:CDS 30.0%
! TAATAAACGTGGTAGTTTGT+TGG - chr7.2:77187444-77187463 MS.gene43109:CDS 30.0%
! TTTAGTCATTGCCTTTTGAT+TGG - chr7.2:77188125-77188144 MS.gene43109:intron 30.0%
AAGCAGAAGATGCTTAATCT+TGG + chr7.2:77188601-77188620 None:intergenic 35.0%
AAGCATATTTCCATGATTCC+CGG - chr7.2:77187916-77187935 MS.gene43109:CDS 35.0%
CGGGATTATGACATATATGA+TGG - chr7.2:77188723-77188742 MS.gene43109:intron 35.0%
GCTTATATTTCATCTGATGG+TGG - chr7.2:77187511-77187530 MS.gene43109:CDS 35.0%
GTCATTCATGTTCTTGCAAT+TGG - chr7.2:77188949-77188968 MS.gene43109:intron 35.0%
TCAATTGATGTATGCTGATC+GGG - chr7.2:77188704-77188723 MS.gene43109:intron 35.0%
TGTAGCTGATAGAATTCAAC+AGG - chr7.2:77187743-77187762 MS.gene43109:CDS 35.0%
! ACGGTATCGAATAGTAACTT+CGG + chr7.2:77188852-77188871 None:intergenic 35.0%
!! ATATTTCATCTGATGGTGGA+TGG - chr7.2:77187515-77187534 MS.gene43109:CDS 35.0%
!! CATTGCCTTTTGATTGGAAT+AGG - chr7.2:77188131-77188150 MS.gene43109:intron 35.0%
!! GTTGATAGTGCTAATAAACG+TGG - chr7.2:77187433-77187452 MS.gene43109:CDS 35.0%
!! GTTGATGATTGCATCGATAA+AGG - chr7.2:77188792-77188811 MS.gene43109:CDS 35.0%
AATAGTAACTTCGGTCGATC+TGG + chr7.2:77188843-77188862 None:intergenic 40.0%
ATGCAGTATGTTGTGTACCA+TGG - chr7.2:77188888-77188907 MS.gene43109:intron 40.0%
CAGCAATAAATCGGTCTCAA+AGG - chr7.2:77187946-77187965 MS.gene43109:intron 40.0%
CATACAACGATCGAGTTAAC+AGG - chr7.2:77188411-77188430 MS.gene43109:intron 40.0%
CATGTCTGTGATAGTACACA+CGG + chr7.2:77188871-77188890 None:intergenic 40.0%
CTGGACACACAATTCAAGAA+TGG - chr7.2:77188512-77188531 MS.gene43109:intron 40.0%
GAAGATGCTTAATCTTGGCA+AGG + chr7.2:77188596-77188615 None:intergenic 40.0%
GATATACCGTCGTGAATTTG+AGG - chr7.2:77188814-77188833 MS.gene43109:CDS 40.0%
TGTGGTAAAATCGGCAAATG+TGG + chr7.2:77188004-77188023 None:intergenic 40.0%
TTTGTTCGACTCACAAGGAT+AGG - chr7.2:77188673-77188692 MS.gene43109:intron 40.0%
! AAGACTTCTGAAAGCAATCC+TGG + chr7.2:77188447-77188466 None:intergenic 40.0%
! GTTTTCTTGTTCCAGTCACT+CGG - chr7.2:77188327-77188346 MS.gene43109:intron 40.0%
! TGAAGGAACAGAAGCATATC+AGG - chr7.2:77188923-77188942 MS.gene43109:intron 40.0%
!! ATCTGATGGTGGATGGTTTA+TGG - chr7.2:77187522-77187541 MS.gene43109:CDS 40.0%
!! TTCGTTTTGTTCGACTCACA+AGG - chr7.2:77188668-77188687 MS.gene43109:intron 40.0%
AACACCGACAGATCTTCTCA+CGG + chr7.2:77188376-77188395 None:intergenic 45.0%
CATGGAACTGTCAATGCTGA+AGG - chr7.2:77188906-77188925 MS.gene43109:intron 45.0%
CCTCAAATGCAATGTGGTAG+CGG - chr7.2:77188482-77188501 MS.gene43109:intron 45.0%
CGACATCACAACCACAATTG+CGG - chr7.2:77187978-77187997 MS.gene43109:intron 45.0%
CTTCTGCTTTATGTGCTGAG+AGG - chr7.2:77188612-77188631 MS.gene43109:intron 45.0%
GATGCTTAATCTTGGCAAGG+CGG + chr7.2:77188593-77188612 None:intergenic 45.0%
TCGAGTTAACAGGACGAGAT+AGG - chr7.2:77188421-77188440 MS.gene43109:intron 45.0%
TGCTGACCTCAAATGCAATG+TGG - chr7.2:77188476-77188495 MS.gene43109:intron 45.0%
TGGACACCTCAAATTCACGA+CGG + chr7.2:77188823-77188842 None:intergenic 45.0%
!! CTTCAGCATTGACAGTTCCA+TGG + chr7.2:77188908-77188927 None:intergenic 45.0%
!! GATGGTGGATGGTTTATGGA+TGG - chr7.2:77187526-77187545 MS.gene43109:CDS 45.0%
!! AAAAAATATTAAAAAAACAA+TGG + chr7.2:77187608-77187627 None:intergenic 5.0%
CCGCTACCACATTGCATTTG+AGG + chr7.2:77188485-77188504 None:intergenic 50.0%
CGACAGATCTTCTCACGGAT+CGG + chr7.2:77188371-77188390 None:intergenic 50.0%
CGATCCGTGAGAAGATCTGT+CGG - chr7.2:77188369-77188388 MS.gene43109:intron 50.0%
GTTCGACTCACAAGGATAGG+AGG - chr7.2:77188676-77188695 MS.gene43109:intron 50.0%
TACATCACCGACGACACAAC+AGG - chr7.2:77188546-77188565 MS.gene43109:CDS 50.0%
TTAACAGGACGAGATAGGCC+AGG - chr7.2:77188426-77188445 MS.gene43109:intron 50.0%
TTAATCTTGGCAAGGCGGTC+AGG + chr7.2:77188588-77188607 None:intergenic 50.0%
TTCTCACGGATCGGAAGCTA+CGG + chr7.2:77188362-77188381 None:intergenic 50.0%
! AGACCGATTTATTGCTGCCG+CGG + chr7.2:77187943-77187962 None:intergenic 50.0%
! ATCTGTCGGTGTTCAAGCTG+CGG - chr7.2:77188383-77188402 MS.gene43109:intron 50.0%
AGGCGGTCAGGATTGTCGAT+CGG + chr7.2:77188576-77188595 None:intergenic 55.0%
ATTTATTGCTGCCGCGGACC+GGG + chr7.2:77187937-77187956 None:intergenic 55.0%
CGGCAATCCTGTTGTGTCGT+CGG + chr7.2:77188556-77188575 None:intergenic 55.0%
GATCGGAAGCTACGGACTCT+TGG + chr7.2:77188354-77188373 None:intergenic 55.0%
GATTTATTGCTGCCGCGGAC+CGG + chr7.2:77187938-77187957 None:intergenic 55.0%
GGCAAATGTGGCCGCAATTG+TGG + chr7.2:77187992-77188011 None:intergenic 55.0%
GGTCCGCGGCAGCAATAAAT+CGG - chr7.2:77187937-77187956 MS.gene43109:intron 55.0%
TTTCCATGATTCCCGGTCCG+CGG - chr7.2:77187923-77187942 MS.gene43109:CDS 55.0%
!! ATGTGGTAGCGGCTGAAGTC+TGG - chr7.2:77188493-77188512 MS.gene43109:intron 55.0%
GGACTCTTGGACCGAGTGAC+TGG + chr7.2:77188341-77188360 None:intergenic 60.0%
CTGCCGCGGACCGGGAATCA+TGG + chr7.2:77187929-77187948 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 77187288 77189007 77187288 ID=MS.gene43109
chr7.2 mRNA 77187288 77189007 77187288 ID=MS.gene43109.t1;Parent=MS.gene43109
chr7.2 exon 77188962 77189007 77188962 ID=MS.gene43109.t1.exon1;Parent=MS.gene43109.t1
chr7.2 CDS 77188962 77189007 77188962 ID=cds.MS.gene43109.t1;Parent=MS.gene43109.t1
chr7.2 exon 77188748 77188862 77188748 ID=MS.gene43109.t1.exon2;Parent=MS.gene43109.t1
chr7.2 CDS 77188748 77188862 77188748 ID=cds.MS.gene43109.t1;Parent=MS.gene43109.t1
chr7.2 exon 77188531 77188598 77188531 ID=MS.gene43109.t1.exon3;Parent=MS.gene43109.t1
chr7.2 CDS 77188531 77188598 77188531 ID=cds.MS.gene43109.t1;Parent=MS.gene43109.t1
chr7.2 exon 77187288 77187953 77187288 ID=MS.gene43109.t1.exon4;Parent=MS.gene43109.t1
chr7.2 CDS 77187288 77187953 77187288 ID=cds.MS.gene43109.t1;Parent=MS.gene43109.t1
Gene Sequence

>MS.gene43109

AGTAACTGTGGATAATACTTCAAGCAGAACAACAACTTTGATAAAGGTTTGAAATTTAAACCTTATAAGGTTATAATCTTTGATGAATTTCAAAAGGGTCGTTTTAGTTTAGTATATAAATAATTTTCATGTGAATTTTGTGTAGGTTGATAGTGCTAATAAACGTGGTAGTTTGTTGGAAGTTGTTCAAGTTCTTACTGATATGAATCTCATTGTTAGAAGAGCTTATATTTCATCTGATGGTGGATGGTTTATGGATGGTATGCTATACCTACCATTTACAATAATTCTTCATTTTTTCATCAACTAATTAGTCACCATTGTTTTTTTAATATTTTTTGATAAAAATATTAATCTTGTTTTTCATGTGTTTTTTTTTTTTTTTTTGTTTACATTTTTTATTTTTCAGTTTTTCATGTTACTGATCAAAATGGGAAAAAGATTCTTCAAGAAGATGTAGCTGATAGAATTCAACAGGTAATAGATCTGTGTAATATTCATCGGACATTAGTTTTTGATTTTACATTTGTTATGATTGTAATTTAGGTGTGAAATTAAGATTTTAAGTAAGTAATTGATATTTTCTTATTTTATCGGTATATAAAGCGTATCGAATTATGAGTAATCAAAGCATATTTCCATGATTCCCGGTCCGCGGCAGCAATAAATCGGTCTCAAAGGTCTCTGCAACGACATCACAACCACAATTGCGGCCACATTTGCCGATTTTACCACAATATAAAAGTTGATCACAATTTAAAACCATGATAGTTTATATTACTCTAGCTTGAAATCAATGCTCATATAATTTTTCAATTTTCATCATACTATTTGGCTTTTAGTCATTGCCTTTTGATTGGAATAGGATGATTTTGTTAATGATCTTTCACTAAATGCATGATTTTGTTTATGATCTTTCTTTTCAATAAAGTAATTCAACAACTAGATTGAAAAAGAACAAGACAAAACCAGAACTAGTACTTTTTTTCTTGAGGTACTTTGTTTGTTCCAGAACTTTGTTTACTAATAACACTTTTTGGTTTTCTTGTTCCAGTCACTCGGTCCAAGAGTCCGTAGCTTCCGATCCGTGAGAAGATCTGTCGGTGTTCAAGCTGCGGCAGAACATACAACGATCGAGTTAACAGGACGAGATAGGCCAGGATTGCTTTCAGAAGTCTTTGCAATTCTTGCTGACCTCAAATGCAATGTGGTAGCGGCTGAAGTCTGGACACACAATTCAAGAATGGCGTCTGTCGTTTACATCACCGACGACACAACAGGATTGCCGATCGACAATCCTGACCGCCTTGCCAAGATTAAGCATCTTCTGCTTTATGTGCTGAGAGGAGACATTGACAAGAAGAATGCAAACACTGCTGTTTCGTTTTGTTCGACTCACAAGGATAGGAGGCTGCATCAATTGATGTATGCTGATCGGGATTATGACATATATGATGGAGATTATTCTTGCTCAACAAATGAAAGAAGCAAGCTCAATGTAACTGTTGATGATTGCATCGATAAAGGATATACCGTCGTGAATTTGAGGTGTCCAGATCGACCGAAGTTACTATTCGATACCGTGTGTACTATCACAGACATGCAGTATGTTGTGTACCATGGAACTGTCAATGCTGAAGGAACAGAAGCATATCAGGTTTGTCATTCATGTTCTTGCAATTGGAATCTAGTAAATTTAATACTTGTCTATTTGTCCTGA

Protein sequence

>MS.gene43109.t1

SNCGUYFKQNNNFDKGUUCUUTWUFVGSCSSSYUYESHCUKSLYFIUWWMVYGCFSCYUSKWEKDSSRRCSUUNSTVTRSKSPULPIREKICRCSSCGRTYNDRVNRTRUARIAFRSLCNSCUPQMQCGSGUSLDTQFKNGVCRLHHRRHNRIADRQSUPPCQDUASSALCAERRHUQEECKHCCFVLFDSQGUEAASIDVCUSGLUHIUWRLFLLNKUKKQAQCNCUULHRURIYRREFEVSRSTEVTIRYRVYYHRHAVCCVPWNCQCURNRSISGLSFMFLQLESSKFNTCLFVL