AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene027891

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene027891.t1 MTR_5g030180 98.113 106 2 0 1 106 23 128 1.51e-75 219
MS.gene027891.t1 MTR_5g030180 98.113 106 2 0 1 106 10 115 1.75e-75 218
MS.gene027891.t1 MTR_7g116750 85.981 107 14 1 1 106 10 116 1.85e-65 193
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene027891.t1 AT4G07950 44.444 90 47 2 17 106 19 105 1.99e-24 89.4
MS.gene027891.t1 AT1G01210 42.222 90 49 2 17 106 19 105 6.68e-23 85.5
MS.gene027891.t1 AT1G01210 42.222 90 49 2 17 106 19 105 6.68e-23 85.5
MS.gene027891.t1 AT1G01210 42.222 90 49 2 17 106 19 105 6.68e-23 85.5

Find 28 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTGAGGATGGCGACAATT+TGG 0.237510 5.4:+20423503 None:intergenic
TTCTCGATTGAGCAAATATA+TGG 0.241781 5.4:+20424706 None:intergenic
ATCTCATGATGGGAGATAAT+AGG 0.295531 5.4:+20424535 None:intergenic
CTTGAGGATGGCGACAATTT+GGG 0.324696 5.4:+20423504 None:intergenic
AAATTTGTCGTGACTCGAAT+TGG 0.331864 5.4:+20424759 None:intergenic
CACTCGTAAAATATTGTTGC+AGG 0.338187 5.4:+20423443 None:intergenic
AGAGAAGACAAATGCTGGTT+AGG 0.408988 5.4:-20424570 MS.gene027891:CDS
AAAGTAGTACCGTCGGCTTT+TGG 0.414427 5.4:+20424499 None:intergenic
TCTCATGATGGGAGATAATA+GGG 0.429313 5.4:+20424536 None:intergenic
TATTCTTGTTGATCTCATGA+TGG 0.460772 5.4:+20424524 None:intergenic
CATCTCACTCCTTCCACTTG+TGG 0.461178 5.4:+20423402 None:intergenic
AATTTGTCGTGACTCGAATT+GGG 0.488382 5.4:+20424760 None:intergenic
GACAAATGCTGGTTAGGAAA+GGG 0.497928 5.4:-20424564 MS.gene027891:CDS
ATTCTTGTTGATCTCATGAT+GGG 0.514246 5.4:+20424525 None:intergenic
GATTAAGAGAAGACAAATGC+TGG 0.517033 5.4:-20424575 MS.gene027891:CDS
TATTTGCTCAATCGAGAAAG+AGG 0.528655 5.4:-20424701 MS.gene027891:intron
GTGAGGCAATAAAACCTTGT+GGG 0.529652 5.4:+20424733 None:intergenic
AGACAAATGCTGGTTAGGAA+AGG 0.564511 5.4:-20424565 MS.gene027891:CDS
ATGAAAAGTGTGGCCACAAG+TGG 0.599470 5.4:-20423415 MS.gene027891:CDS
GGATGGCGACAATTTGGGCA+TGG 0.605399 5.4:+20423509 None:intergenic
AGCAAATATATGGACAAGTG+AGG 0.632197 5.4:+20424716 None:intergenic
AAAGTGTGGCCACAAGTGGA+AGG 0.641576 5.4:-20423411 MS.gene027891:CDS
ACGACAAATTTCATCCCACA+AGG 0.644788 5.4:-20424747 MS.gene027891:CDS
AAGAATAAACCAAAAGCCGA+CGG 0.660260 5.4:-20424508 MS.gene027891:intron
AGTGAGGCAATAAAACCTTG+TGG 0.661965 5.4:+20424732 None:intergenic
TGTGATAACTAGCTTGAGGA+TGG 0.663098 5.4:+20423492 None:intergenic
TGCATGTGATAACTAGCTTG+AGG 0.701040 5.4:+20423488 None:intergenic
GAGTGCTTGAATGAAAAGTG+TGG 0.765667 5.4:-20423425 MS.gene027891:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAAACCTTTAAAATATATT+GGG + chr5.4:20424054-20424073 None:intergenic 10.0%
!!! TTTAAACCTTTAAAATATAT+TGG + chr5.4:20424055-20424074 None:intergenic 10.0%
!! AAAAATGGAAATAATGATAA+AGG + chr5.4:20424607-20424626 None:intergenic 15.0%
!! TGTGAAATAATTATATCAAT+TGG - chr5.4:20423815-20423834 MS.gene027891:intron 15.0%
!! AAAAGAAAACATGATGAAAT+GGG + chr5.4:20423575-20423594 None:intergenic 20.0%
!! ACACAAAATTTGATATGTAT+TGG + chr5.4:20424167-20424186 None:intergenic 20.0%
!! AGAAAAGGAAGATATAAAAA+TGG + chr5.4:20424622-20424641 None:intergenic 20.0%
!! TAAAAGAAAACATGATGAAA+TGG + chr5.4:20423576-20423595 None:intergenic 20.0%
!! TTGTGAATTAACATTGTTTA+TGG - chr5.4:20424515-20424534 MS.gene027891:CDS 20.0%
!!! CTTTTCTTTTACATGATTTA+CGG - chr5.4:20424403-20424422 MS.gene027891:intron 20.0%
!!! TTTTGTGTGATTTGTTTTTA+AGG - chr5.4:20424179-20424198 MS.gene027891:intron 20.0%
! AAGGAAATAACAAAGAAACA+AGG + chr5.4:20424588-20424607 None:intergenic 25.0%
! ATAAACCAATACAATCAGTT+CGG + chr5.4:20423841-20423860 None:intergenic 25.0%
! ATTTGATTATCCAAGTAAAC+AGG + chr5.4:20423768-20423787 None:intergenic 25.0%
! CTTTAGTCAATAAGATAAGA+GGG + chr5.4:20423930-20423949 None:intergenic 25.0%
! TAAACTTCAAAGTTCCTATT+AGG + chr5.4:20424333-20424352 None:intergenic 25.0%
! TCGTGAATTAACATTGTTTA+TGG - chr5.4:20424440-20424459 MS.gene027891:intron 25.0%
! TCTTTAGTCAATAAGATAAG+AGG + chr5.4:20423931-20423950 None:intergenic 25.0%
! TGAATGTAATCTAATGCAAA+GGG - chr5.4:20423964-20423983 MS.gene027891:intron 25.0%
! TTGAATGTAATCTAATGCAA+AGG - chr5.4:20423963-20423982 MS.gene027891:intron 25.0%
! TTTAGTCAATAAGATAAGAG+GGG + chr5.4:20423929-20423948 None:intergenic 25.0%
!! AAAATTTGATATGTATTGGC+AGG + chr5.4:20424163-20424182 None:intergenic 25.0%
!! CATGTTTTCTTTTACTTTAC+AGG - chr5.4:20423582-20423601 MS.gene027891:intron 25.0%
!!! AACTGATTGTATTGGTTTAT+TGG - chr5.4:20423841-20423860 MS.gene027891:intron 25.0%
!!! ATATATGGTAAAAGTATTGC+TGG + chr5.4:20424111-20424130 None:intergenic 25.0%
!!! ATTTACGAGCTTTAAGAATT+AGG - chr5.4:20424219-20424238 MS.gene027891:intron 25.0%
!!! GGCTCTAAAGATAAATATTT+CGG - chr5.4:20423899-20423918 MS.gene027891:intron 25.0%
!!! TTATGGTTTTGTTATTTGAG+CGG - chr5.4:20424457-20424476 MS.gene027891:intron 25.0%
!!! TTTACGAGCTTTAAGAATTA+GGG - chr5.4:20424220-20424239 MS.gene027891:intron 25.0%
ATCTAATGCAAAGGGATAAA+TGG - chr5.4:20423972-20423991 MS.gene027891:intron 30.0%
ATTACATTCAACTCAAGAGA+AGG + chr5.4:20423954-20423973 None:intergenic 30.0%
ATTCTTGTTGATCTCATGAT+GGG + chr5.4:20423662-20423681 None:intergenic 30.0%
TAAAAGAAAAGTAGTACCGT+CGG + chr5.4:20423695-20423714 None:intergenic 30.0%
TATTCTTGTTGATCTCATGA+TGG + chr5.4:20423663-20423682 None:intergenic 30.0%
TCTAATGCAAAGGGATAAAT+GGG - chr5.4:20423973-20423992 MS.gene027891:intron 30.0%
TCTCAGACAGCTTATATATA+TGG + chr5.4:20424126-20424145 None:intergenic 30.0%
TTCTCGATTGAGCAAATATA+TGG + chr5.4:20423481-20423500 None:intergenic 30.0%
TTGGATTATCAACTCCTAAT+AGG - chr5.4:20424291-20424310 MS.gene027891:intron 30.0%
!! GGTCACCCAATATATTTTAA+AGG - chr5.4:20424046-20424065 MS.gene027891:intron 30.0%
!! TAACTGGTTGGTAATAGAAA+TGG + chr5.4:20423540-20423559 None:intergenic 30.0%
!! TGTATTGGTTTATTGGTCAT+TGG - chr5.4:20423848-20423867 MS.gene027891:intron 30.0%
!!! ACGATCTGTTTTTAGTGATT+GGG - chr5.4:20423878-20423897 MS.gene027891:intron 30.0%
!!! TACGATCTGTTTTTAGTGAT+TGG - chr5.4:20423877-20423896 MS.gene027891:intron 30.0%
!!! TATTTTTTCTAGCACTGTTG+AGG - chr5.4:20424025-20424044 MS.gene027891:intron 30.0%
AAATTTGTCGTGACTCGAAT+TGG + chr5.4:20423428-20423447 None:intergenic 35.0%
AAGAATAAACCAAAAGCCGA+CGG - chr5.4:20423676-20423695 MS.gene027891:intron 35.0%
AATTAGGGAAGTAGAAGTTG+TGG - chr5.4:20424235-20424254 MS.gene027891:intron 35.0%
AATTTGTCGTGACTCGAATT+GGG + chr5.4:20423427-20423446 None:intergenic 35.0%
AGCAAATATATGGACAAGTG+AGG + chr5.4:20423471-20423490 None:intergenic 35.0%
AGCAAGACAAACTTTGTACA+AGG + chr5.4:20424360-20424379 None:intergenic 35.0%
CACTCGTAAAATATTGTTGC+AGG + chr5.4:20424744-20424763 None:intergenic 35.0%
CTAATGCAAAGGGATAAATG+GGG - chr5.4:20423974-20423993 MS.gene027891:intron 35.0%
GATTAAGAGAAGACAAATGC+TGG - chr5.4:20423609-20423628 MS.gene027891:intron 35.0%
TATTTGCTCAATCGAGAAAG+AGG - chr5.4:20423483-20423502 MS.gene027891:CDS 35.0%
TGAGTTTGCATGTTTCAGTT+TGG - chr5.4:20424272-20424291 MS.gene027891:intron 35.0%
TTGAATTGAAGGTAACTGGT+TGG + chr5.4:20423552-20423571 None:intergenic 35.0%
TTGACTCAACAGTTCCTATT+AGG + chr5.4:20424308-20424327 None:intergenic 35.0%
! AAGTATTGCTGGCTAAGATT+TGG + chr5.4:20424100-20424119 None:intergenic 35.0%
! ATCTCATGATGGGAGATAAT+AGG + chr5.4:20423652-20423671 None:intergenic 35.0%
! CATTCTTCTTTAGCTCATTG+TGG - chr5.4:20423741-20423760 MS.gene027891:intron 35.0%
! TCTCATGATGGGAGATAATA+GGG + chr5.4:20423651-20423670 None:intergenic 35.0%
!! GATGAAATGGGTTGAATTGA+AGG + chr5.4:20423563-20423582 None:intergenic 35.0%
ACGACAAATTTCATCCCACA+AGG - chr5.4:20423437-20423456 MS.gene027891:CDS 40.0%
AGTGAGGCAATAAAACCTTG+TGG + chr5.4:20423455-20423474 None:intergenic 40.0%
ATTGGCCGAACTGATTGTAT+TGG - chr5.4:20423833-20423852 MS.gene027891:intron 40.0%
CTAGGAGGGAAAAAAAGAAG+AGG + chr5.4:20424653-20424672 None:intergenic 40.0%
CTGTTGAGTCAACTCCTAAT+AGG - chr5.4:20424316-20424335 MS.gene027891:intron 40.0%
GAAGAGGAATGAGTGAGAAA+AGG + chr5.4:20424637-20424656 None:intergenic 40.0%
GAGTGCTTGAATGAAAAGTG+TGG - chr5.4:20424759-20424778 MS.gene027891:CDS 40.0%
GTGAGGCAATAAAACCTTGT+GGG + chr5.4:20423454-20423473 None:intergenic 40.0%
TCATTGTGGACCTGTTTACT+TGG - chr5.4:20423755-20423774 MS.gene027891:intron 40.0%
! AGACAAATGCTGGTTAGGAA+AGG - chr5.4:20423619-20423638 MS.gene027891:intron 40.0%
! AGAGAAGACAAATGCTGGTT+AGG - chr5.4:20423614-20423633 MS.gene027891:intron 40.0%
! GACAAATGCTGGTTAGGAAA+GGG - chr5.4:20423620-20423639 MS.gene027891:intron 40.0%
! TGCATGTGATAACTAGCTTG+AGG + chr5.4:20424699-20424718 None:intergenic 40.0%
! TGGGGCTTTAGTTTAGTGTA+AGG - chr5.4:20423992-20424011 MS.gene027891:intron 40.0%
! TGGGTTGAATTGAAGGTAAC+TGG + chr5.4:20423556-20423575 None:intergenic 40.0%
! TGTGATAACTAGCTTGAGGA+TGG + chr5.4:20424695-20424714 None:intergenic 40.0%
AATTTGGGCATGGTACTAGG+AGG + chr5.4:20424668-20424687 None:intergenic 45.0%
ATTTGGGCATGGTACTAGGA+GGG + chr5.4:20424667-20424686 None:intergenic 45.0%
CTTGAGGATGGCGACAATTT+GGG + chr5.4:20424683-20424702 None:intergenic 45.0%
GACAATTTGGGCATGGTACT+AGG + chr5.4:20424671-20424690 None:intergenic 45.0%
GCTCAAACCAAGACAAACAG+TGG + chr5.4:20424488-20424507 None:intergenic 45.0%
GGGAAGTAGAAGTTGTGGTA+TGG - chr5.4:20424240-20424259 MS.gene027891:intron 45.0%
GGTTCAACCACTGTTTGTCT+TGG - chr5.4:20424478-20424497 MS.gene027891:intron 45.0%
! ATGAAAAGTGTGGCCACAAG+TGG - chr5.4:20424769-20424788 MS.gene027891:CDS 45.0%
!!! AAAGTAGTACCGTCGGCTTT+TGG + chr5.4:20423688-20423707 None:intergenic 45.0%
!! TGAAAAAATAAAATAAAAAT+AGG + chr5.4:20424548-20424567 None:intergenic 5.0%
AAAGTGTGGCCACAAGTGGA+AGG - chr5.4:20424773-20424792 MS.gene027891:CDS 50.0%
GCTTGAGGATGGCGACAATT+TGG + chr5.4:20424684-20424703 None:intergenic 50.0%
GGATGGCGACAATTTGGGCA+TGG + chr5.4:20424678-20424697 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 20423406 20424800 20423406 ID=MS.gene027891
chr5.4 mRNA 20423406 20424800 20423406 ID=MS.gene027891.t1;Parent=MS.gene027891
chr5.4 exon 20424702 20424800 20424702 ID=MS.gene027891.t1.exon1;Parent=MS.gene027891.t1
chr5.4 CDS 20424702 20424800 20424702 ID=cds.MS.gene027891.t1;Parent=MS.gene027891.t1
chr5.4 exon 20424509 20424602 20424509 ID=MS.gene027891.t1.exon2;Parent=MS.gene027891.t1
chr5.4 CDS 20424509 20424602 20424509 ID=cds.MS.gene027891.t1;Parent=MS.gene027891.t1
chr5.4 exon 20423406 20423533 20423406 ID=MS.gene027891.t1.exon3;Parent=MS.gene027891.t1
chr5.4 CDS 20423406 20423533 20423406 ID=cds.MS.gene027891.t1;Parent=MS.gene027891.t1
Gene Sequence

>MS.gene027891

ATGCTGATGCTTGAACTACCCAATTCGAGTCACGACAAATTTCATCCCACAAGGTTTTATTGCCTCACTTGTCCATATATTTGCTCAATCGAGAAAGAGGTATGTTATGTTATGTACTCTTCTTCTATTTTCCATTTCTATTACCAACCAGTTACCTTCAATTCAACCCATTTCATCATGTTTTCTTTTACTTTACAGGTTAAGATTAAGAGAAGACAAATGCTGGTTAGGAAAGGGATTGACCCTATTATCTCCCATCATGAGATCAACAAGAATAAACCAAAAGCCGACGGTACTACTTTTCTTTTACTTTTCTCGCAACAATTTTTGTCAATCATTCTTCTTTAGCTCATTGTGGACCTGTTTACTTGGATAATCAAATATCAATCAATACTAGTTTATTGTTATTTGTGAAATAATTATATCAATTGGCCGAACTGATTGTATTGGTTTATTGGTCATTGGAGATGATACGATCTGTTTTTAGTGATTGGGCTCTAAAGATAAATATTTCGGATTACCCCTCTTATCTTATTGACTAAAGACCTTCTCTTGAGTTGAATGTAATCTAATGCAAAGGGATAAATGGGGCTTTAGTTTAGTGTAAGGCAAGCTTGTTTATTTTTTCTAGCACTGTTGAGGTCACCCAATATATTTTAAAGGTTTAAACTTTAAATGTCAAAATGTGAAGCCAAATCTTAGCCAGCAATACTTTTACCATATATATAAGCTGTCTGAGATAGCTTAATTTATACCTGCCAATACATATCAAATTTTGTGTGATTTGTTTTTAAGGACGTTGTGCTCAGCTATATTTACGAGCTTTAAGAATTAGGGAAGTAGAAGTTGTGGTATGGTTTTGTTTGTGAGTTTGCATGTTTCAGTTTGGATTATCAACTCCTAATAGGAACTGTTGAGTCAACTCCTAATAGGAACTTTGAAGTTTATTTTCCTTGTACAAAGTTTGTCTTGCTTTTCATCATGCAATTTCATTATGCTTTTCTTTTACATGATTTACGGTTTGAGCAGTTGAATCGTGAATTAACATTGTTTATGGTTTTGTTATTTGAGCGGTTCAACCACTGTTTGTCTTGGTTTGAGCAGTTGAATTGTGAATTAACATTGTTTATGGTTGCAATCCTATTTTTATTTTATTTTTTCATAAAGTGATTATGCAATCCTTGTTTCTTTGTTATTTCCTTTATCATTATTTCCATTTTTATATCTTCCTTTTCTCACTCATTCCTCTTCTTTTTTTCCCTCCTAGTACCATGCCCAAATTGTCGCCATCCTCAAGCTAGTTATCACATGCAACAGACTCGATCAGCTGATGAACCTGCAACAATATTTTACGAGTGCTTGAATGAAAAGTGTGGCCACAAGTGGAAGGAGTGA
Protein sequence

>MS.gene027891.t1

MLMLELPNSSHDKFHPTRFYCLTCPYICSIEKEVKIKRRQMLVRKGIDPIISHHEINKNKPKADVPCPNCRHPQASYHMQQTRSADEPATIFYECLNEKCGHKWKE