AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene053209


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053209.t1 MTR_4g007140 100.000 110 0 0 1 110 184 293 2.63e-75 224
MS.gene053209.t1 MTR_2g105090 87.273 110 14 0 1 110 181 290 2.30e-66 202
MS.gene053209.t1 MTR_2g105090 87.273 110 14 0 1 110 205 314 4.76e-66 201
MS.gene053209.t1 MTR_1g112170 55.455 110 49 0 1 110 171 280 3.48e-42 139
MS.gene053209.t1 MTR_1g112170 50.000 78 39 0 1 78 171 248 1.66e-22 88.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053209.t1 AT1G16880 80.000 110 22 0 1 110 181 290 1.84e-61 189
MS.gene053209.t1 AT5G04740 59.091 110 45 0 1 110 91 200 1.98e-46 148
MS.gene053209.t1 AT5G04740 59.091 110 45 0 1 110 192 301 3.10e-45 148

Find 24 sgRNAs with CRISPR-Local

Find 95 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGATTCATCACCTGCTCTTT+TGG 0.222017 4.3:-88264420 None:intergenic
TTAGCAATGGGAGCAGCTTT+TGG 0.275092 4.3:+88264387 None:intergenic
ATTGACATTGCTGTTGAATC+TGG 0.326851 4.3:+88265048 MS.gene053209:CDS
TGTTTGAACCTAGGGGCTCT+TGG 0.406397 4.3:+88265551 MS.gene053209:intron
AAACTGGATTCCTCAGTTGC+CGG 0.443051 4.3:-88266097 None:intergenic
AGATTAAAGTTACCTGCTGC+AGG 0.475170 4.3:-88265623 None:intergenic
CGAATGCATTACCTTCGATC+TGG 0.482009 4.3:-88264808 None:intergenic
AATCAGCAAGCCCCTGCAGC+AGG 0.483771 4.3:+88265611 MS.gene053209:CDS
GTGGAGACAGCTGATCGGCC+TGG 0.489025 4.3:+88264991 MS.gene053209:CDS
GAGATATTTCTTGAGGCGTC+CGG 0.523812 4.3:+88266078 MS.gene053209:CDS
AAGTTTCATGTTAGCTACAA+AGG 0.527152 4.3:+88265582 MS.gene053209:CDS
CACATAAACATATCCGATGA+TGG 0.529758 4.3:+88264784 MS.gene053209:CDS
CCTTCGATCTGGACCATCAT+CGG 0.546047 4.3:-88264797 None:intergenic
ATTAAAGTTACCTGCTGCAG+GGG 0.562709 4.3:-88265621 None:intergenic
ACAAGATCGACAAGTAATCC+AGG 0.566828 4.3:-88265009 None:intergenic
CAAGAAATATCTCAAGCTGT+TGG 0.569442 4.3:-88266068 None:intergenic
CTTGAGGCGTCCGGCAACTG+AGG 0.581879 4.3:+88266087 MS.gene053209:CDS
AATTGTCATTCAGGTTGATG+TGG 0.589579 4.3:+88264750 MS.gene053209:intron
GATTAAAGTTACCTGCTGCA+GGG 0.589784 4.3:-88265622 None:intergenic
ACTTCTACCTCCAAAAGAGC+AGG 0.595122 4.3:+88264410 MS.gene053209:CDS
CCGATGATGGTCCAGATCGA+AGG 0.598336 4.3:+88264797 MS.gene053209:CDS
ACAGCTTGAGATATTTCTTG+AGG 0.602665 4.3:+88266071 MS.gene053209:CDS
TCTATGTGGAGACAGCTGAT+CGG 0.632715 4.3:+88264986 MS.gene053209:CDS
ATCTGGAGAATTTGACACTG+AGG 0.685475 4.3:+88265065 MS.gene053209:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATCTTGATTTTTTATCATTT+AGG - chr4.3:88265912-88265931 None:intergenic 15.0%
!!! TTCTGTAATGTATATTTTAT+TGG - chr4.3:88264568-88264587 None:intergenic 15.0%
!! ATATGTTTGGTAAATTGTAA+TGG - chr4.3:88265889-88265908 None:intergenic 20.0%
!! TCTGTAAATTGAAAAGATAA+GGG + chr4.3:88264506-88264525 MS.gene053209:intron 20.0%
!! TGTTAAAGTCATGATATATA+AGG + chr4.3:88264883-88264902 MS.gene053209:intron 20.0%
!! TTCTGTAAATTGAAAAGATA+AGG + chr4.3:88264505-88264524 MS.gene053209:intron 20.0%
!!! TTTATCATTTAGGATATGTT+TGG - chr4.3:88265902-88265921 None:intergenic 20.0%
! ATACATTACAGAAGACATTA+TGG + chr4.3:88264575-88264594 MS.gene053209:intron 25.0%
! ATACTCATGCTTTCTAATTT+CGG + chr4.3:88264916-88264935 MS.gene053209:intron 25.0%
! ATGATTAAAGTAGATTTGTC+TGG + chr4.3:88265750-88265769 MS.gene053209:intron 25.0%
! CTATAAACTATACGCTATAA+GGG - chr4.3:88265843-88265862 None:intergenic 25.0%
! GATTGTTAGAATAGAAAATC+TGG - chr4.3:88265468-88265487 None:intergenic 25.0%
! TCCTACTATTCAATGAATTA+GGG - chr4.3:88265406-88265425 None:intergenic 25.0%
! TGAGCTTCAAAAAAAAAGAA+GGG + chr4.3:88265499-88265518 MS.gene053209:intron 25.0%
! TTATTGGTGAAAAATGAAAC+AGG - chr4.3:88264552-88264571 None:intergenic 25.0%
! TTCCTACTATTCAATGAATT+AGG - chr4.3:88265407-88265426 None:intergenic 25.0%
! TTCTTTCTATTTGTGATAGA+GGG - chr4.3:88264718-88264737 None:intergenic 25.0%
! TTGAGCTTCAAAAAAAAAGA+AGG + chr4.3:88265498-88265517 MS.gene053209:intron 25.0%
! TTTCTTTCTATTTGTGATAG+AGG - chr4.3:88264719-88264738 None:intergenic 25.0%
!!! ATTTTGTAGTTTGTTCTATG+TGG + chr4.3:88264972-88264991 MS.gene053209:intron 25.0%
!!! GATACATTCATTTTGAGTAA+TGG - chr4.3:88265157-88265176 None:intergenic 25.0%
AACTCATAGTACATTGAAGT+AGG + chr4.3:88265940-88265959 MS.gene053209:intron 30.0%
AAGTAGATTTGTCTGGTAAA+CGG + chr4.3:88265757-88265776 MS.gene053209:intron 30.0%
AAGTTTCATGTTAGCTACAA+AGG + chr4.3:88265582-88265601 MS.gene053209:CDS 30.0%
ACCCTAATTCATTGAATAGT+AGG + chr4.3:88265402-88265421 MS.gene053209:intron 30.0%
GAATGTATCAATGTTGAGTA+TGG + chr4.3:88265168-88265187 MS.gene053209:intron 30.0%
GAGCTTCAAAAAAAAAGAAG+GGG + chr4.3:88265500-88265519 MS.gene053209:intron 30.0%
GCTATAAACTATACGCTATA+AGG - chr4.3:88265844-88265863 None:intergenic 30.0%
TGATGAATCTCTTTACTTCT+CGG + chr4.3:88264433-88264452 MS.gene053209:intron 30.0%
TGTTATTCGTTGTAAGCTAA+TGG - chr4.3:88265712-88265731 None:intergenic 30.0%
TTCATTACCAATTGTCATTC+AGG + chr4.3:88264741-88264760 MS.gene053209:intron 30.0%
TTTAATCGTCAAGTACTCTT+TGG + chr4.3:88265676-88265695 MS.gene053209:intron 30.0%
! TGTGAATTTTTCATTCTCTC+TGG + chr4.3:88264470-88264489 MS.gene053209:intron 30.0%
!! AAAAAGCTTTGTTTGAACCT+AGG + chr4.3:88265542-88265561 MS.gene053209:intron 30.0%
!! AAAAGCTTTGTTTGAACCTA+GGG + chr4.3:88265543-88265562 MS.gene053209:intron 30.0%
!!! ACAAAGCTTTTTCATCAGAT+TGG - chr4.3:88265534-88265553 None:intergenic 30.0%
ACAGCTTGAGATATTTCTTG+AGG + chr4.3:88266071-88266090 MS.gene053209:CDS 35.0%
ACATCAACCTGAATGACAAT+TGG - chr4.3:88264751-88264770 None:intergenic 35.0%
ATTTGTCTGGTAAACGGTAA+TGG + chr4.3:88265763-88265782 MS.gene053209:intron 35.0%
CAAGAAATATCTCAAGCTGT+TGG - chr4.3:88266071-88266090 None:intergenic 35.0%
CACATAAACATATCCGATGA+TGG + chr4.3:88264784-88264803 MS.gene053209:CDS 35.0%
CTTCATATTTACCATGTTGC+AGG + chr4.3:88266039-88266058 MS.gene053209:intron 35.0%
TTGTTGGGTTACAACTATGA+GGG + chr4.3:88265277-88265296 MS.gene053209:intron 35.0%
TTTCTATTTGTGATAGAGGG+AGG - chr4.3:88264715-88264734 None:intergenic 35.0%
TTTGTTGGGTTACAACTATG+AGG + chr4.3:88265276-88265295 MS.gene053209:intron 35.0%
! ATTGACATTGCTGTTGAATC+TGG + chr4.3:88265048-88265067 MS.gene053209:CDS 35.0%
!! AAAGCTTTGTTTGAACCTAG+GGG + chr4.3:88265544-88265563 MS.gene053209:intron 35.0%
!! AATTGTCATTCAGGTTGATG+TGG + chr4.3:88264750-88264769 MS.gene053209:intron 35.0%
ACAAGATCGACAAGTAATCC+AGG - chr4.3:88265012-88265031 None:intergenic 40.0%
AGATTAAAGTTACCTGCTGC+AGG - chr4.3:88265626-88265645 None:intergenic 40.0%
ATCTGGAGAATTTGACACTG+AGG + chr4.3:88265065-88265084 MS.gene053209:CDS 40.0%
ATTAAAGTTACCTGCTGCAG+GGG - chr4.3:88265624-88265643 None:intergenic 40.0%
GATTAAAGTTACCTGCTGCA+GGG - chr4.3:88265625-88265644 None:intergenic 40.0%
GCGTGGCTTATTCATTTGTT+GGG + chr4.3:88265262-88265281 MS.gene053209:intron 40.0%
GCTCATAATCGCTGATAAGA+GGG + chr4.3:88265190-88265209 MS.gene053209:intron 40.0%
GTACATTGAAGTAGGCAAGT+AGG + chr4.3:88265948-88265967 MS.gene053209:intron 40.0%
TTACGGATAAGCTTGTGAAC+TGG + chr4.3:88265337-88265356 MS.gene053209:intron 40.0%
! AAACCTTCTAAGTTCTGACG+TGG + chr4.3:88265131-88265150 MS.gene053209:intron 40.0%
! AGATTCATCACCTGCTCTTT+TGG - chr4.3:88264423-88264442 None:intergenic 40.0%
AAACTGGATTCCTCAGTTGC+CGG - chr4.3:88266100-88266119 None:intergenic 45.0%
ACTTCTACCTCCAAAAGAGC+AGG + chr4.3:88264410-88264429 MS.gene053209:CDS 45.0%
ATGAATAAGCCACGCCCAAA+CGG - chr4.3:88265257-88265276 None:intergenic 45.0%
CACTAGATGCTTGCGCAATA+AGG - chr4.3:88265975-88265994 None:intergenic 45.0%
CGAATGCATTACCTTCGATC+TGG - chr4.3:88264811-88264830 None:intergenic 45.0%
CTTATTGCGCAAGCATCTAG+TGG + chr4.3:88265973-88265992 MS.gene053209:intron 45.0%
GGCGTGGCTTATTCATTTGT+TGG + chr4.3:88265261-88265280 MS.gene053209:intron 45.0%
GGCTCATAATCGCTGATAAG+AGG + chr4.3:88265189-88265208 MS.gene053209:intron 45.0%
GGTTACAACTATGAGGGCTA+GGG + chr4.3:88265283-88265302 MS.gene053209:intron 45.0%
GTTACAACTATGAGGGCTAG+GGG + chr4.3:88265284-88265303 MS.gene053209:intron 45.0%
TCTATGTGGAGACAGCTGAT+CGG + chr4.3:88264986-88265005 MS.gene053209:CDS 45.0%
TTATCCGTAAACCGTAACGC+AGG - chr4.3:88265327-88265346 None:intergenic 45.0%
! GAGATATTTCTTGAGGCGTC+CGG + chr4.3:88266078-88266097 MS.gene053209:CDS 45.0%
! TTCATCACCTGCTCTTTTGG+AGG - chr4.3:88264420-88264439 None:intergenic 45.0%
!! AATGAAAGCGCCTTCCGTTT+GGG + chr4.3:88265240-88265259 MS.gene053209:intron 45.0%
!! TAATGAAAGCGCCTTCCGTT+TGG + chr4.3:88265239-88265258 MS.gene053209:intron 45.0%
CCTTCGATCTGGACCATCAT+CGG - chr4.3:88264800-88264819 None:intergenic 50.0%
GGGTTACAACTATGAGGGCT+AGG + chr4.3:88265282-88265301 MS.gene053209:intron 50.0%
GTTGGCAAGAACCTGCAACA+TGG - chr4.3:88266053-88266072 None:intergenic 50.0%
TGGCCACGTCAGAACTTAGA+AGG - chr4.3:88265137-88265156 None:intergenic 50.0%
TGTTTGAACCTAGGGGCTCT+TGG + chr4.3:88265551-88265570 MS.gene053209:intron 50.0%
AACTATGAGGGCTAGGGGTG+AGG + chr4.3:88265289-88265308 MS.gene053209:intron 55.0%
ACTATGAGGGCTAGGGGTGA+GGG + chr4.3:88265290-88265309 MS.gene053209:intron 55.0%
ATAAGCCACGCCCAAACGGA+AGG - chr4.3:88265253-88265272 None:intergenic 55.0%
GCCACCTGCGTTACGGTTTA+CGG + chr4.3:88265320-88265339 MS.gene053209:intron 55.0%
TCCGTAAACCGTAACGCAGG+TGG - chr4.3:88265324-88265343 None:intergenic 55.0%
TGCTTTAGCCAAGAGCCCCT+AGG - chr4.3:88265562-88265581 None:intergenic 55.0%
! CCGATGATGGTCCAGATCGA+AGG + chr4.3:88264797-88264816 MS.gene053209:CDS 55.0%
AATCAGCAAGCCCCTGCAGC+AGG + chr4.3:88265611-88265630 MS.gene053209:CDS 60.0%
CTATGAGGGCTAGGGGTGAG+GGG + chr4.3:88265291-88265310 MS.gene053209:intron 60.0%
TATGAGGGCTAGGGGTGAGG+GGG + chr4.3:88265292-88265311 MS.gene053209:intron 60.0%
AAGCGCCTTCCGTTTGGGCG+TGG + chr4.3:88265245-88265264 MS.gene053209:intron 65.0%
ATGAGGGCTAGGGGTGAGGG+GGG + chr4.3:88265293-88265312 MS.gene053209:intron 65.0%
GGGCTTCGCCACCTGCGTTA+CGG + chr4.3:88265313-88265332 MS.gene053209:intron 65.0%
GTGGAGACAGCTGATCGGCC+TGG + chr4.3:88264991-88265010 MS.gene053209:CDS 65.0%
! CTTGAGGCGTCCGGCAACTG+AGG + chr4.3:88266087-88266106 MS.gene053209:CDS 65.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 88264393 88266123 88264393 ID=MS.gene053209
chr4.3 mRNA 88264393 88266123 88264393 ID=MS.gene053209.t1;Parent=MS.gene053209
chr4.3 exon 88264393 88264431 88264393 ID=MS.gene053209.t1.exon1;Parent=MS.gene053209.t1
chr4.3 CDS 88264393 88264431 88264393 ID=cds.MS.gene053209.t1;Parent=MS.gene053209.t1
chr4.3 exon 88264763 88264818 88264763 ID=MS.gene053209.t1.exon2;Parent=MS.gene053209.t1
chr4.3 CDS 88264763 88264818 88264763 ID=cds.MS.gene053209.t1;Parent=MS.gene053209.t1
chr4.3 exon 88264981 88265086 88264981 ID=MS.gene053209.t1.exon3;Parent=MS.gene053209.t1
chr4.3 CDS 88264981 88265086 88264981 ID=cds.MS.gene053209.t1;Parent=MS.gene053209.t1
chr4.3 exon 88265564 88265632 88265564 ID=MS.gene053209.t1.exon4;Parent=MS.gene053209.t1
chr4.3 CDS 88265564 88265632 88265564 ID=cds.MS.gene053209.t1;Parent=MS.gene053209.t1
chr4.3 exon 88266061 88266123 88266061 ID=MS.gene053209.t1.exon5;Parent=MS.gene053209.t1
chr4.3 CDS 88266061 88266123 88266061 ID=cds.MS.gene053209.t1;Parent=MS.gene053209.t1
Gene Sequence

>MS.gene053209

ATGGGAGCAGCTTTTGGACTTCTACCTCCAAAAGAGCAGGTGATGAATCTCTTTACTTCTCGGTTTCAGTTATAACTTGTGAATTTTTCATTCTCTCTGGTAACACATAGAGTTCTGTAAATTGAAAAGATAAGGGTACGTTTACTTCAGATGTTTCCTGTTTCATTTTTCACCAATAAAATATACATTACAGAAGACATTATGGAAGTTTTTAAAATTGAATTTTGAAAATCTATTGAATATTTCTGAAAAATCTATTAAATGACAAAATATTGTTGTCGACGTTTCAAGAAATGTATTCTCTCTAGTTAGCTTTTATCCTCCCTCTATCACAAATAGAAAGAAAAGTTCATTACCAATTGTCATTCAGGTTGATGTGGACATTGCAACTCACATAAACATATCCGATGATGGTCCAGATCGAAGGTAATGCATTCGTTTGTTTCTTGCGTAGCAGTACAGATATTATCATCGAATCAAGAAATGACATTGTTAAAGTCATGATATATAAGGTCTTAGAAGAATACTCATGCTTTCTAATTTCGGTTATATTTGTATGTTGTTAATTATTTGTTTTCAATTTTGTAGTTTGTTCTATGTGGAGACAGCTGATCGGCCTGGATTACTTGTCGATCTTGTAAAAAGTATTACTGACATTGACATTGCTGTTGAATCTGGAGAATTTGACACTGAGGTATACAGATATCATTATACAACTTATGCTCAAACTAAATAAATAAACCTTCTAAGTTCTGACGTGGCCATTACTCAAAATGAATGTATCAATGTTGAGTATGGCTCATAATCGCTGATAAGAGGGCAGACGCTCGAGCATAGCTGAAAGTGTAATGAAAGCGCCTTCCGTTTGGGCGTGGCTTATTCATTTGTTGGGTTACAACTATGAGGGCTAGGGGTGAGGGGGGCTTCGCCACCTGCGTTACGGTTTACGGATAAGCTTGTGAACTGGATCATAGATTCATAGTATTTGAGCAAAACTTTGTACTCTCTAACCCTAATTCATTGAATAGTAGGAAAATACGAAGTCACTCTGATGCGTTTTCTTACGTTAGAACCAGATTTTCTATTCTAACAATCAATTTAATTATTGAGCTTCAAAAAAAAAGAAGGGGATTTTGTACCAATCTGATGAAAAAGCTTTGTTTGAACCTAGGGGCTCTTGGCTAAAGCAAAGTTTCATGTTAGCTACAAAGGCAAAGCAATCAGCAAGCCCCTGCAGCAGGTAACTTTAATCTTCTAATTTTTCATTTTTGAAAGAAAAAAGCTTTAATCGTCAAGTACTCTTTGGTAAGATCAAACCATTAGCTTACAACGAATAACATATAGCGTATAAACTCGAATGATTAAAGTAGATTTGTCTGGTAAACGGTAATGGTCTCTTTCACAAGTATAAATCATTTTTTCACTAGCTTATATCGTATCATTTTTACCCTTATAGCGTATAGTTTATAGCTTATAGCTAGCTTATTCATTGTCCATTACAATTTACCAAACATATCCTAAATGATAAAAAATCAAGATTGTATCATAACTCATAGTACATTGAAGTAGGCAAGTAGGTCCTTATTGCGCAAGCATCTAGTGGTGAACTTTACATGATGTCAGAAAGAGTTTCTGAACTGATTTTACTTCATATTTACCATGTTGCAGGTTCTTGCCAACAGCTTGAGATATTTCTTGAGGCGTCCGGCAACTGAGGAATCCAGTTTTTGA

Protein sequence

>MS.gene053209.t1

MGAAFGLLPPKEQVDVDIATHINISDDGPDRSLFYVETADRPGLLVDLVKSITDIDIAVESGEFDTEGLLAKAKFHVSYKGKAISKPLQQVLANSLRYFLRRPATEESSF