AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene030614


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene030614.t1 MTR_8g093770 100.000 143 0 0 1 143 1 143 1.51e-102 290
MS.gene030614.t1 MTR_5g012890 96.000 125 5 0 19 143 18 142 1.01e-86 249
MS.gene030614.t1 MTR_4g006830 88.889 144 15 1 1 143 1 144 2.91e-83 241
MS.gene030614.t1 MTR_5g012890 91.111 90 8 0 19 108 18 107 1.38e-56 172
MS.gene030614.t1 MTR_4g073510 66.667 54 17 1 1 53 1 54 3.27e-15 71.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene030614.t1 AT2G32060 76.000 125 29 1 19 143 21 144 1.29e-67 201
MS.gene030614.t1 AT2G32060 76.000 125 29 1 19 143 21 144 1.29e-67 201
MS.gene030614.t1 AT2G32060 76.000 125 29 1 19 143 21 144 1.29e-67 201
MS.gene030614.t1 AT1G15930 74.400 125 31 1 19 143 21 144 3.49e-64 192
MS.gene030614.t1 AT1G15930 74.400 125 31 1 19 143 21 144 3.49e-64 192

Find 33 sgRNAs with CRISPR-Local

Find 103 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCACCAACTTGACGTAATC+AGG 0.299059 4.3:-8092731 None:intergenic
TCTCCAAGGGTCTTTGCATT+TGG 0.313809 4.3:-8092794 None:intergenic
GTTGCTGCAGCTGGAATTCC+AGG 0.331115 4.3:+8092560 MS.gene030614:CDS
AATCAACTTGCAATTATGTC+TGG 0.359633 4.3:+8091943 None:intergenic
ATTCCAGCTGCAGCAACAAC+TGG 0.406602 4.3:-8092554 None:intergenic
TGCAAAGACCCTTGGAGAAT+GGG 0.412944 4.3:+8092799 MS.gene030614:CDS
ATAATATCCATTGGCTCCCC+TGG 0.419454 4.3:-8092578 None:intergenic
GAGCCAGTTGTTGCTGCAGC+TGG 0.425162 4.3:+8092551 MS.gene030614:CDS
TTGAGAAAGTCACGCGCTTA+TGG 0.428624 4.3:+8092620 MS.gene030614:CDS
GACACTGTGTTCAGCACAAA+GGG 0.447539 4.3:-8092756 None:intergenic
ATGCAAAGACCCTTGGAGAA+TGG 0.451113 4.3:+8092798 MS.gene030614:CDS
GGAAAAGCTAGGAAGGTAAC+TGG 0.463250 4.3:+8093520 MS.gene030614:CDS
TTGCTCCTGTGTGGTTGTCA+AGG 0.525394 4.3:+8093543 MS.gene030614:CDS
GTTCCAAATGCAAAGACCCT+TGG 0.532260 4.3:+8092791 MS.gene030614:CDS
TTGCTGCAGCTGGAATTCCA+GGG 0.537879 4.3:+8092561 MS.gene030614:CDS
ATCAACTTGCAATTATGTCT+GGG 0.539041 4.3:+8091944 None:intergenic
TTGTGCAAAATTGATTCAGA+AGG 0.565495 4.3:+8093499 MS.gene030614:CDS
ACTGCAGTCATAATATCCAT+TGG 0.568889 4.3:-8092587 None:intergenic
TGCTGCAGCTGGAATTCCAG+GGG 0.575795 4.3:+8092562 MS.gene030614:CDS
TTGATTCAGAAGGAAAAGCT+AGG 0.578774 4.3:+8093509 MS.gene030614:CDS
ACAGCTCTGTGTTCTTGCTG+AGG 0.587565 4.3:+8092697 MS.gene030614:CDS
CCAACCTGATTACGTCAAGT+TGG 0.591510 4.3:+8092727 MS.gene030614:CDS
TTACACCAGCCCATTCTCCA+AGG 0.592149 4.3:-8092808 None:intergenic
TTCAGAAGGAAAAGCTAGGA+AGG 0.596975 4.3:+8093513 MS.gene030614:CDS
TGGAATTCCAGGGGAGCCAA+TGG 0.602144 4.3:+8092571 MS.gene030614:CDS
AGAAAGTCACGCGCTTATGG+TGG 0.613205 4.3:+8092623 MS.gene030614:CDS
CCAACTTGACGTAATCAGGT+TGG 0.614249 4.3:-8092727 None:intergenic
AAGACCCTTGGAGAATGGGC+TGG 0.615483 4.3:+8092803 MS.gene030614:CDS
TGACACTGTGTTCAGCACAA+AGG 0.628583 4.3:-8092757 None:intergenic
GCTTATGGTGGTCTTGCACG+TGG 0.635715 4.3:+8092635 MS.gene030614:CDS
GGTAACTGGTTGCTCCTGTG+TGG 0.641819 4.3:+8093534 MS.gene030614:CDS
TACACCAGCCCATTCTCCAA+GGG 0.643748 4.3:-8092807 None:intergenic
ACATACCTTGACAACCACAC+AGG 0.682837 4.3:-8093548 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAAATTAAAAATTTAATTTG+TGG + chr4.3:8092250-8092269 MS.gene030614:intron 10.0%
!! AAATATATAATTGAGAATTG+TGG - chr4.3:8092889-8092908 None:intergenic 15.0%
!! CATATAGATTAAAATAAATG+AGG - chr4.3:8093371-8093390 None:intergenic 15.0%
!! TATAAAATGTTATTGCTTAT+TGG - chr4.3:8093032-8093051 None:intergenic 15.0%
!!! AATTACTTTAAAATAAGTGT+GGG + chr4.3:8092924-8092943 MS.gene030614:intron 15.0%
!!! TTAACTATTTTCATTTTTGT+AGG + chr4.3:8093627-8093646 MS.gene030614:intron 15.0%
!!! TTATAATAACTTTTTGATCT+GGG - chr4.3:8092338-8092357 None:intergenic 15.0%
!!! TTTATAATAACTTTTTGATC+TGG - chr4.3:8092339-8092358 None:intergenic 15.0%
!! ATTGATTATGAGGATAATTA+TGG + chr4.3:8092286-8092305 MS.gene030614:intron 20.0%
!! CAAAACCAATATAAAACAAA+AGG - chr4.3:8093281-8093300 None:intergenic 20.0%
!!! ATTTGCCTTTTGTTTTATAT+TGG + chr4.3:8093273-8093292 MS.gene030614:intron 20.0%
!!! GAATTACTTTAAAATAAGTG+TGG + chr4.3:8092923-8092942 MS.gene030614:intron 20.0%
!!! TTTTCATTTTTGTAGGATTT+CGG + chr4.3:8093634-8093653 MS.gene030614:intron 20.0%
! AATAGTTAAGCATACGTAAA+CGG - chr4.3:8093616-8093635 None:intergenic 25.0%
! CTATGTTTATAGTAATGCAA+GGG - chr4.3:8092837-8092856 None:intergenic 25.0%
! TCAAATATGTCATAAGGAAA+TGG - chr4.3:8092866-8092885 None:intergenic 25.0%
! TCTATGTTTATAGTAATGCA+AGG - chr4.3:8092838-8092857 None:intergenic 25.0%
!!! AGTACTGATATTGAAATAGT+TGG + chr4.3:8092131-8092150 MS.gene030614:intron 25.0%
AAATCCAGAAGTTATTGTCT+TGG + chr4.3:8093407-8093426 MS.gene030614:intron 30.0%
ATTTCTTATAGTTACTACCG+AGG - chr4.3:8092173-8092192 None:intergenic 30.0%
CGGTTTCATTAATTGCTTAT+TGG - chr4.3:8093005-8093024 None:intergenic 30.0%
GAATCCAAACATTTCTATTC+CGG - chr4.3:8093581-8093600 None:intergenic 30.0%
GACAATAACTTCTGGATTTA+AGG - chr4.3:8093406-8093425 None:intergenic 30.0%
TGTTGTTCAGTTATTGTTTC+TGG + chr4.3:8093205-8093224 MS.gene030614:intron 30.0%
TTGTGGTCAAATATGTCATA+AGG - chr4.3:8092872-8092891 None:intergenic 30.0%
TTTCTTATAGTTACTACCGA+GGG - chr4.3:8092172-8092191 None:intergenic 30.0%
! TGTGAGATTCTACTTGTTAA+AGG + chr4.3:8091996-8092015 MS.gene030614:intron 30.0%
! TTGTGCAAAATTGATTCAGA+AGG + chr4.3:8093499-8093518 MS.gene030614:CDS 30.0%
!! AACTTTTTGATCTGGGATTA+AGG - chr4.3:8092331-8092350 None:intergenic 30.0%
!! AAGGTTGTACACTATTTCTA+TGG - chr4.3:8093141-8093160 None:intergenic 30.0%
!! TGTACACTATTTCTATGGAT+TGG - chr4.3:8093136-8093155 None:intergenic 30.0%
AAGACCAAGACAATAACTTC+TGG - chr4.3:8093414-8093433 None:intergenic 35.0%
ACAAGTAGAATCTCACAAAC+AGG - chr4.3:8091993-8092012 None:intergenic 35.0%
ACTGCAGTCATAATATCCAT+TGG - chr4.3:8092590-8092609 None:intergenic 35.0%
ATGGTCAAATGAAGCTAATG+AGG + chr4.3:8092305-8092324 MS.gene030614:intron 35.0%
TCATCCGGAATAGAAATGTT+TGG + chr4.3:8093574-8093593 MS.gene030614:intron 35.0%
TCATTTCATGCATCACAGTT+AGG - chr4.3:8093090-8093109 None:intergenic 35.0%
TTGATTCAGAAGGAAAAGCT+AGG + chr4.3:8093509-8093528 MS.gene030614:CDS 35.0%
! AACTTCTGGATTTAAGGCAA+AGG - chr4.3:8093400-8093419 None:intergenic 35.0%
! AATTTTGCACAACTGCATGA+AGG - chr4.3:8093491-8093510 None:intergenic 35.0%
! CATTGCGATCATTGATTATG+AGG + chr4.3:8092276-8092295 MS.gene030614:intron 35.0%
! GTCAAGGTATGTTTTTCATC+CGG + chr4.3:8093559-8093578 MS.gene030614:intron 35.0%
! TGTTATTGCTTATTGGTGCT+CGG - chr4.3:8093025-8093044 None:intergenic 35.0%
!! ACACTATTTCTATGGATTGG+AGG - chr4.3:8093133-8093152 None:intergenic 35.0%
!! ATTGTTTCTGGTGTATTCCT+TGG + chr4.3:8093217-8093236 MS.gene030614:intron 35.0%
!! TTGTTTCTGGTGTATTCCTT+GGG + chr4.3:8093218-8093237 MS.gene030614:intron 35.0%
AAAAACTCAAGACGCACACA+TGG - chr4.3:8092458-8092477 None:intergenic 40.0%
AGTTAAGCATACGTAAACGG+AGG - chr4.3:8093613-8093632 None:intergenic 40.0%
CAACCTTTGAATGTCAAGAG+CGG + chr4.3:8093154-8093173 MS.gene030614:intron 40.0%
TTCACCAACTTGACGTAATC+AGG - chr4.3:8092734-8092753 None:intergenic 40.0%
TTCAGAAGGAAAAGCTAGGA+AGG + chr4.3:8093513-8093532 MS.gene030614:CDS 40.0%
TTTCATGCATCACAGTTAGG+AGG - chr4.3:8093087-8093106 None:intergenic 40.0%
! ATTTTTGTAGGATTTCGGCG+AGG + chr4.3:8093639-8093658 MS.gene030614:intron 40.0%
ACAGAGTTCAGAGAGGATAC+AGG - chr4.3:8093346-8093365 None:intergenic 45.0%
ACATACCTTGACAACCACAC+AGG - chr4.3:8093551-8093570 None:intergenic 45.0%
AGAGAGGATACAGGGTAAGA+GGG - chr4.3:8093337-8093356 None:intergenic 45.0%
ATCCTGACCCTAATCATGAG+AGG + chr4.3:8092977-8092996 MS.gene030614:intron 45.0%
ATGCAAAGACCCTTGGAGAA+TGG + chr4.3:8092798-8092817 MS.gene030614:CDS 45.0%
ATTGGCGCCTCTCATGATTA+GGG - chr4.3:8092987-8093006 None:intergenic 45.0%
CAGAGTTCAGAGAGGATACA+GGG - chr4.3:8093345-8093364 None:intergenic 45.0%
CCAACCTGATTACGTCAAGT+TGG + chr4.3:8092727-8092746 MS.gene030614:CDS 45.0%
CCAACTTGACGTAATCAGGT+TGG - chr4.3:8092730-8092749 None:intergenic 45.0%
CTGGTGTATTCCTTGGGTTT+GGG + chr4.3:8093224-8093243 MS.gene030614:intron 45.0%
GACACTGTGTTCAGCACAAA+GGG - chr4.3:8092759-8092778 None:intergenic 45.0%
GATCTGATAGTCATAGCCCT+CGG + chr4.3:8092153-8092172 MS.gene030614:intron 45.0%
GATTTGCACCACGATGTTGA+GGG - chr4.3:8092960-8092979 None:intergenic 45.0%
GGAAAAGCTAGGAAGGTAAC+TGG + chr4.3:8093520-8093539 MS.gene030614:CDS 45.0%
GTTCCAAATGCAAAGACCCT+TGG + chr4.3:8092791-8092810 MS.gene030614:CDS 45.0%
TATAGTCAGCGAGATTCACG+TGG - chr4.3:8092407-8092426 None:intergenic 45.0%
TATTGGCGCCTCTCATGATT+AGG - chr4.3:8092988-8093007 None:intergenic 45.0%
TCTCCAAGGGTCTTTGCATT+TGG - chr4.3:8092797-8092816 None:intergenic 45.0%
TCTGGTGTATTCCTTGGGTT+TGG + chr4.3:8093223-8093242 MS.gene030614:intron 45.0%
TGACACTGTGTTCAGCACAA+AGG - chr4.3:8092760-8092779 None:intergenic 45.0%
TGAGGTTACAGAGTTCAGAG+AGG - chr4.3:8093353-8093372 None:intergenic 45.0%
TGCAAAGACCCTTGGAGAAT+GGG + chr4.3:8092799-8092818 MS.gene030614:CDS 45.0%
TGGTGTATTCCTTGGGTTTG+GGG + chr4.3:8093225-8093244 MS.gene030614:intron 45.0%
TTGAGAAAGTCACGCGCTTA+TGG + chr4.3:8092620-8092639 MS.gene030614:CDS 45.0%
!! ATAATATCCATTGGCTCCCC+TGG - chr4.3:8092581-8092600 None:intergenic 45.0%
ACAGCTCTGTGTTCTTGCTG+AGG + chr4.3:8092697-8092716 MS.gene030614:CDS 50.0%
AGAAAGTCACGCGCTTATGG+TGG + chr4.3:8092623-8092642 MS.gene030614:CDS 50.0%
ATTCCAGCTGCAGCAACAAC+TGG - chr4.3:8092557-8092576 None:intergenic 50.0%
CAGAGAGGATACAGGGTAAG+AGG - chr4.3:8093338-8093357 None:intergenic 50.0%
CCACCGCTCTTGACATTCAA+AGG - chr4.3:8093160-8093179 None:intergenic 50.0%
CCTTTGAATGTCAAGAGCGG+TGG + chr4.3:8093157-8093176 MS.gene030614:intron 50.0%
GAGAGGATACAGGGTAAGAG+GGG - chr4.3:8093336-8093355 None:intergenic 50.0%
GGATTTGCACCACGATGTTG+AGG - chr4.3:8092961-8092980 None:intergenic 50.0%
TACACCAGCCCATTCTCCAA+GGG - chr4.3:8092810-8092829 None:intergenic 50.0%
TGACATCTCCCTCAACATCG+TGG + chr4.3:8092949-8092968 MS.gene030614:intron 50.0%
TGTATTCCTTGGGTTTGGGG+AGG + chr4.3:8093228-8093247 MS.gene030614:intron 50.0%
TTACACCAGCCCATTCTCCA+AGG - chr4.3:8092811-8092830 None:intergenic 50.0%
TTGCTCCTGTGTGGTTGTCA+AGG + chr4.3:8093543-8093562 MS.gene030614:CDS 50.0%
TTGCTGCAGCTGGAATTCCA+GGG + chr4.3:8092561-8092580 MS.gene030614:CDS 50.0%
AAGACCCTTGGAGAATGGGC+TGG + chr4.3:8092803-8092822 MS.gene030614:CDS 55.0%
CGCCTCTCATGATTAGGGTC+AGG - chr4.3:8092982-8093001 None:intergenic 55.0%
GGTAACTGGTTGCTCCTGTG+TGG + chr4.3:8093534-8093553 MS.gene030614:CDS 55.0%
GTTGCTGCAGCTGGAATTCC+AGG + chr4.3:8092560-8092579 MS.gene030614:CDS 55.0%
TGCTGCAGCTGGAATTCCAG+GGG + chr4.3:8092562-8092581 MS.gene030614:CDS 55.0%
TGGAATTCCAGGGGAGCCAA+TGG + chr4.3:8092571-8092590 MS.gene030614:CDS 55.0%
! GCTTATGGTGGTCTTGCACG+TGG + chr4.3:8092635-8092654 MS.gene030614:CDS 55.0%
AACCAGCCTCCCCAAACCCA+AGG - chr4.3:8093237-8093256 None:intergenic 60.0%
GAGCCAGTTGTTGCTGCAGC+TGG + chr4.3:8092551-8092570 MS.gene030614:CDS 60.0%
TTCCTTGGGTTTGGGGAGGC+TGG + chr4.3:8093232-8093251 MS.gene030614:intron 60.0%
! TGGGTTTGGGGAGGCTGGTT+CGG + chr4.3:8093237-8093256 MS.gene030614:intron 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 8091958 8093708 8091958 ID=MS.gene030614
chr4.3 mRNA 8091958 8093708 8091958 ID=MS.gene030614.t1;Parent=MS.gene030614
chr4.3 exon 8091958 8091965 8091958 ID=MS.gene030614.t1.exon1;Parent=MS.gene030614.t1
chr4.3 CDS 8091958 8091965 8091958 ID=cds.MS.gene030614.t1;Parent=MS.gene030614.t1
chr4.3 exon 8092529 8092826 8092529 ID=MS.gene030614.t1.exon2;Parent=MS.gene030614.t1
chr4.3 CDS 8092529 8092826 8092529 ID=cds.MS.gene030614.t1;Parent=MS.gene030614.t1
chr4.3 exon 8093499 8093564 8093499 ID=MS.gene030614.t1.exon3;Parent=MS.gene030614.t1
chr4.3 CDS 8093499 8093564 8093499 ID=cds.MS.gene030614.t1;Parent=MS.gene030614.t1
chr4.3 exon 8093649 8093708 8093649 ID=MS.gene030614.t1.exon4;Parent=MS.gene030614.t1
chr4.3 CDS 8093649 8093708 8093649 ID=cds.MS.gene030614.t1;Parent=MS.gene030614.t1
Gene Sequence

>MS.gene030614

ATGTCTGGGTATGTCTATTTTTGCTTAATTTACCTGTTTGTGAGATTCTACTTGTTAAAGGTCTATTCATTATCTTATTTTGCAATTTTTTGTTGAATCTATATAGTTTTATTTTCTTTCATGAACTGCGTTTGTAAACTTTCAAATGCATTATAGATTTGATTTTAATTTTAAGTACTGATATTGAAATAGTTGGATCTGATAGTCATAGCCCTCGGTAGTAACTATAAGAAATTTAGAACACAGATAACAGTTTAGTATTTATTTAATTTTCAAAACTATTTTTCAAAATGAAATTAAAAATTTAATTTGTGGTTGCATTGCGATCATTGATTATGAGGATAATTATGGTCAAATGAAGCTAATGAGGCCTTAATCCCAGATCAAAAAGTTATTATAAACTGCTGTGTATTAGTGTAGACACTTTTCTGTTTCTGTGATTTGAACCACGTGAATCTCGCTGACTATAGAGAAACTTTTTGTTGTGCAATGCTTATCCATGTGTGCGTCTTGAGTTTTTAAGATATTCATTGTTAATTTTCTGACTGTTGATAAACATTTTGTTGTTCAGAGAAGAAGAAGTTGTTGTAGCTGAGCCAGTTGTTGCTGCAGCTGGAATTCCAGGGGAGCCAATGGATATTATGACTGCAGTTCAGCTTGTGTTGAGAAAGTCACGCGCTTATGGTGGTCTTGCACGTGGTCTTCATGAAAGTGCTAAAGTGATTGAGAAGCATGCTGCACAGCTCTGTGTTCTTGCTGAGGATTGTGACCAACCTGATTACGTCAAGTTGGTGAAAGCCCTTTGTGCTGAACACAGTGTCAGTTTGTTGACTGTTCCAAATGCAAAGACCCTTGGAGAATGGGCTGGTGTAAGTGCCCTTGCATTACTATAAACATAGATCAATCCATTTCCTTATGACATATTTGACCACAATTCTCAATTATATATTTTTTGATAAATTCATGAATTACTTTAAAATAAGTGTGGGAGTGACATCTCCCTCAACATCGTGGTGCAAATCCTGACCCTAATCATGAGAGGCGCCAATAAGCAATTAATGAAACCGAGCACCAATAAGCAATAACATTTTATAAATTGCTTCTCTATAGATGTGACTTACTTAAACCTCCTAACTGTGATGCATGAAATGATAAATCTTTCTCATCAGACTCCTCCAATCCATAGAAATAGTGTACAACCTTTGAATGTCAAGAGCGGTGGACAGTTCTCAAATTTAGATTATGAATGTTGTTCAGTTATTGTTTCTGGTGTATTCCTTGGGTTTGGGGAGGCTGGTTCGGCAGCTTGTACTGTATTTGCCTTTTGTTTTATATTGGTTTTGTTTTTCTTTGTGATGTGTTTCTGTTTAGAGTACCCCTCTTACCCTGTATCCTCTCTGAACTCTGTAACCTCATTTATTTTAATCTATATGTTTATACCTTTGCCTTAAATCCAGAAGTTATTGTCTTGGTCTTTTTTTTATGCTTTCAAAATCTTATGTCATTCTTTTGTACTGATTTTGTGACGCACCTTCATGCAGTTGTGCAAAATTGATTCAGAAGGAAAAGCTAGGAAGGTAACTGGTTGCTCCTGTGTGGTTGTCAAGGTATGTTTTTCATCCGGAATAGAAATGTTTGGATTCTGTTTTCATCCTCCGTTTACGTATGCTTAACTATTTTCATTTTTGTAGGATTTCGGCGAGGAACATGAAGCATACAACGTTGTTCTTCAGCACGTGAAATCTAACTGA

Protein sequence

>MS.gene030614.t1

MSGEEEVVVAEPVVAAAGIPGEPMDIMTAVQLVLRKSRAYGGLARGLHESAKVIEKHAAQLCVLAEDCDQPDYVKLVKALCAEHSVSLLTVPNAKTLGEWAGLCKIDSEGKARKVTGCSCVVVKDFGEEHEAYNVVLQHVKSN