AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene030304

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene030304.t1 MTR_6g091630 100.000 121 0 0 1 121 1 121 7.55e-85 243
MS.gene030304.t1 MTR_8g101980 97.521 121 3 0 1 121 1 121 8.29e-83 238
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene030304.t1 AT5G56710 84.211 114 18 0 8 121 6 119 3.45e-67 198
MS.gene030304.t1 AT4G26230 83.333 114 19 0 8 121 6 119 1.30e-66 197
MS.gene030304.t1 AT2G19740 81.667 120 21 1 2 121 1 119 4.59e-66 196
MS.gene030304.t1 AT5G56710 58.772 114 13 1 8 121 6 85 6.30e-38 123

Find 36 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGATCTCCTTGATAGCTTT+TGG 0.199036 6.2:+88792698 None:intergenic
ATTCCTAAAGAAGAGTTAAA+AGG 0.277484 6.2:-88792494 MS.gene030304:CDS
TAAAGAAGAGTTAAAAGGTT+TGG 0.305277 6.2:-88792489 MS.gene030304:CDS
TCAAGCTGAACAAGGCTATC+TGG 0.323250 6.2:-88792628 MS.gene030304:CDS
AAAGAAGAGTTAAAAGGTTT+GGG 0.335880 6.2:-88792488 MS.gene030304:CDS
GAAGTGTACCAAGGAGGATC+AGG 0.398880 6.2:-88792592 MS.gene030304:CDS
TTGGTACACTTCTGATTCCC+TGG 0.413987 6.2:+88792603 None:intergenic
AAGATTGAAATTACCATCCA+TGG 0.468912 6.2:+88794637 None:intergenic
GAAGGCACCAAAAGCTATCA+AGG 0.472855 6.2:-88792705 MS.gene030304:CDS
GAACAAGGCTATCTGGAGCC+AGG 0.480113 6.2:-88792621 MS.gene030304:CDS
ATGGTGGAGAAGGGTGCAGC+AGG 0.507040 6.2:-88794714 MS.gene030304:CDS
ATGCGTACCCTGATCCTCCT+TGG 0.524657 6.2:+88792584 None:intergenic
GAGACGCTTGTGGAGATTGA+TGG 0.526766 6.2:+88794659 None:intergenic
AAGGGAGTATAACTCTTCCT+TGG 0.536523 6.2:+88792532 None:intergenic
GAAGCTGAAAATGGTGGAGA+AGG 0.536786 6.2:-88794724 None:intergenic
TCTAACATCGTTAGTGCCCA+TGG 0.538776 6.2:+88792658 None:intergenic
ATCTTCATCATCAATGACCT+TGG 0.551546 6.2:+88792463 None:intergenic
AAACAGCACCTTCAAGAAGA+AGG 0.555549 6.2:-88792723 MS.gene030304:intron
AATCTCCACAAGCGTCTCCA+TGG 0.563199 6.2:-88794654 MS.gene030304:CDS
TCCACAAGCGTCTCCATGGA+TGG 0.567901 6.2:-88794650 MS.gene030304:intron
TGCAGCAGGTAGAAAAGAAG+AGG 0.581022 6.2:-88794700 MS.gene030304:CDS
AAAAGAAGAGGTGGTTACAC+GGG 0.584738 6.2:-88794688 MS.gene030304:CDS
GAAAAGAAGAGGTGGTTACA+CGG 0.586191 6.2:-88794689 MS.gene030304:CDS
ACCATCCATGGAGACGCTTG+TGG 0.589153 6.2:+88794649 None:intergenic
GAATTTCAACGACAGTGACA+AGG 0.604839 6.2:+88792513 None:intergenic
AAGCTGAAAATGGTGGAGAA+GGG 0.607163 6.2:-88794723 None:intergenic
GAATGACGACGAAGATGCCA+AGG 0.608749 6.2:-88792549 MS.gene030304:CDS
AACAAGGCTATCTGGAGCCA+GGG 0.614836 6.2:-88792620 MS.gene030304:CDS
AAGTGTACCAAGGAGGATCA+GGG 0.622533 6.2:-88792591 MS.gene030304:CDS
AGTTGATGTCAAGCTGAACA+AGG 0.626602 6.2:-88792636 MS.gene030304:CDS
GTTAAAAGGTTTGGGCACCA+AGG 0.626806 6.2:-88792480 MS.gene030304:CDS
AGCAGGTAGAAAAGAAGAGG+TGG 0.632837 6.2:-88794697 MS.gene030304:CDS
AATTTCAACGACAGTGACAA+GGG 0.644182 6.2:+88792514 None:intergenic
GGGTACGCATTGCTCGCAAG+AGG 0.652748 6.2:-88792571 MS.gene030304:CDS
AGGGAATCAGAAGTGTACCA+AGG 0.682823 6.2:-88792601 MS.gene030304:CDS
GAATCAGAAGTGTACCAAGG+AGG 0.739011 6.2:-88792598 MS.gene030304:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTCATGATTTGAAAAAT+CGG - chr6.2:88794243-88794262 MS.gene030304:intron 15.0%
!! AGCACTTATAATATTATAAG+CGG + chr6.2:88793626-88793645 None:intergenic 20.0%
!! ATTAAACTGTTAATCAAAAC+AGG + chr6.2:88793600-88793619 None:intergenic 20.0%
!! TTAAACTGTTAATCAAAACA+GGG + chr6.2:88793599-88793618 None:intergenic 20.0%
!! TTATGACGAGATAAAAATAA+AGG - chr6.2:88792800-88792819 MS.gene030304:intron 20.0%
!! TTATGTAACACAACAATTAT+GGG + chr6.2:88793052-88793071 None:intergenic 20.0%
!! TTGATATTCATATTGTGAAT+TGG + chr6.2:88794273-88794292 None:intergenic 20.0%
!!! AAGCTATTTTTATAAGCTAA+GGG - chr6.2:88792845-88792864 MS.gene030304:intron 20.0%
!!! CTGTGTTTATTAGATAATTT+TGG - chr6.2:88792944-88792963 MS.gene030304:intron 20.0%
!!! TAAGCTATTTTTATAAGCTA+AGG - chr6.2:88792844-88792863 MS.gene030304:intron 20.0%
! AAAAATAAGCCAATCTAAAC+AGG + chr6.2:88792871-88792890 None:intergenic 25.0%
! AAAGAAGAGTTAAAAGGTTT+GGG - chr6.2:88794686-88794705 MS.gene030304:CDS 25.0%
! AAATATGTATGCTGTTCATT+TGG - chr6.2:88794078-88794097 MS.gene030304:intron 25.0%
! AATGAACAGCATACATATTT+AGG + chr6.2:88794078-88794097 None:intergenic 25.0%
! ACTAAGTTATTTATCCATAC+AGG + chr6.2:88792722-88792741 None:intergenic 25.0%
! ATGAACAGCATACATATTTA+GGG + chr6.2:88794077-88794096 None:intergenic 25.0%
! ATGAATTCAAAAACAGCTTA+TGG + chr6.2:88793968-88793987 None:intergenic 25.0%
! ATTCCTAAAGAAGAGTTAAA+AGG - chr6.2:88794680-88794699 MS.gene030304:CDS 25.0%
! CTAAGTTATTTATCCATACA+GGG + chr6.2:88792721-88792740 None:intergenic 25.0%
! CTTATGTAACACAACAATTA+TGG + chr6.2:88793053-88793072 None:intergenic 25.0%
! GTGAGTAAATTAATAGTTTG+TGG - chr6.2:88794100-88794119 MS.gene030304:intron 25.0%
! TAAAGAAGAGTTAAAAGGTT+TGG - chr6.2:88794685-88794704 MS.gene030304:CDS 25.0%
! TATGAAAATAAGCTGAATAC+AGG + chr6.2:88793457-88793476 None:intergenic 25.0%
! TATGTAACACAACAATTATG+GGG + chr6.2:88793051-88793070 None:intergenic 25.0%
! TTTCATGATCTAACTACATT+AGG - chr6.2:88793573-88793592 MS.gene030304:intron 25.0%
!! AGTGATGAAATTGATGATTA+TGG + chr6.2:88793542-88793561 None:intergenic 25.0%
!! ATACATATTTAGGGTTTGTT+TGG + chr6.2:88794068-88794087 None:intergenic 25.0%
!! CTCAAATAAGCTATTTCAAA+AGG - chr6.2:88793811-88793830 MS.gene030304:intron 25.0%
!! TCAATTTTGTAGATCTACTA+GGG - chr6.2:88793326-88793345 MS.gene030304:intron 25.0%
!! TTCAATTTTGTAGATCTACT+AGG - chr6.2:88793325-88793344 MS.gene030304:intron 25.0%
!!! AAACCTTTTAACTCTTCTTT+AGG + chr6.2:88794686-88794705 None:intergenic 25.0%
!!! GCTGTTTTAAAAAAACATCA+TGG + chr6.2:88793486-88793505 None:intergenic 25.0%
!!! TAATATGAATTGAGTTGAGT+TGG - chr6.2:88794126-88794145 MS.gene030304:intron 25.0%
!!! TCCTGTAATATTGTTTTAGT+TGG - chr6.2:88793299-88793318 MS.gene030304:intron 25.0%
!!! TGCTAATTTCTGTTTTTGTT+TGG - chr6.2:88794409-88794428 MS.gene030304:intron 25.0%
AAGATTGAAATTACCATCCA+TGG + chr6.2:88792540-88792559 None:intergenic 30.0%
ATGTAACACAACAATTATGG+GGG + chr6.2:88793050-88793069 None:intergenic 30.0%
ATTCTCTAATGGCATAACAT+TGG + chr6.2:88793791-88793810 None:intergenic 30.0%
GCCAACTAAAACAATATTAC+AGG + chr6.2:88793303-88793322 None:intergenic 30.0%
TAGGATCTGTTTGGATAAAT+AGG - chr6.2:88793092-88793111 MS.gene030304:intron 30.0%
TGCATAATTGGATCTGTTTA+TGG - chr6.2:88794359-88794378 MS.gene030304:intron 30.0%
TGTCATCAACTGTTTCAATA+AGG + chr6.2:88793425-88793444 None:intergenic 30.0%
! AAAATTTGCTCAAAAAGCCA+TGG - chr6.2:88794499-88794518 MS.gene030304:intron 30.0%
! AAATTTGCTCAAAAAGCCAT+GGG - chr6.2:88794500-88794519 MS.gene030304:intron 30.0%
! GCTTATTTGAGATTCTCTAA+TGG + chr6.2:88793802-88793821 None:intergenic 30.0%
! TATTTAGGGTTTGTTTGGAT+AGG + chr6.2:88794063-88794082 None:intergenic 30.0%
! TCAGTTTTCTGTGTTTACAT+TGG - chr6.2:88793245-88793264 MS.gene030304:intron 30.0%
!! CGTTTCAAATTTGTTGATCT+AGG - chr6.2:88793073-88793092 MS.gene030304:intron 30.0%
!!! TGTTTTTTATAAGCGACTCT+TGG - chr6.2:88793691-88793710 MS.gene030304:intron 30.0%
AATTTCAACGACAGTGACAA+GGG + chr6.2:88794663-88794682 None:intergenic 35.0%
ATCTTCATCATCAATGACCT+TGG + chr6.2:88794714-88794733 None:intergenic 35.0%
GCTATGCGTAATTGCATAAT+TGG - chr6.2:88794347-88794366 MS.gene030304:intron 35.0%
TGTCATTGTTCATAAGTTGC+TGG + chr6.2:88794009-88794028 None:intergenic 35.0%
! TTGTTGATCTAGGATCTGTT+TGG - chr6.2:88793083-88793102 MS.gene030304:intron 35.0%
AAAAGAAGAGGTGGTTACAC+GGG - chr6.2:88792486-88792505 MS.gene030304:CDS 40.0%
AAACAGCACCTTCAAGAAGA+AGG - chr6.2:88794451-88794470 MS.gene030304:intron 40.0%
AACACAACAATTATGGGGGA+AGG + chr6.2:88793046-88793065 None:intergenic 40.0%
CTATAGATCTAGACCCTGTA+TGG - chr6.2:88792705-88792724 MS.gene030304:CDS 40.0%
CTATTTGCATAAGCTCCTGT+TGG - chr6.2:88793386-88793405 MS.gene030304:intron 40.0%
GAAAAGAAGAGGTGGTTACA+CGG - chr6.2:88792485-88792504 MS.gene030304:CDS 40.0%
GAATTTCAACGACAGTGACA+AGG + chr6.2:88794664-88794683 None:intergenic 40.0%
! AAGGGAGTATAACTCTTCCT+TGG + chr6.2:88794645-88794664 None:intergenic 40.0%
! AGTTGATGTCAAGCTGAACA+AGG - chr6.2:88794538-88794557 MS.gene030304:intron 40.0%
! ATCTACTAGGGTGTTAGGAT+CGG - chr6.2:88793338-88793357 MS.gene030304:intron 40.0%
! TGTAGATCTACTAGGGTGTT+AGG - chr6.2:88793333-88793352 MS.gene030304:intron 40.0%
! TTCATAAGTTGCTGGCTGTT+TGG + chr6.2:88794001-88794020 None:intergenic 40.0%
!! CTGATCTCCTTGATAGCTTT+TGG + chr6.2:88794479-88794498 None:intergenic 40.0%
!!! TTTTGGTGCCTTCTTCTTGA+AGG + chr6.2:88794462-88794481 None:intergenic 40.0%
AAGCTCCTGTTGGACTGTTT+GGG - chr6.2:88793396-88793415 MS.gene030304:intron 45.0%
AAGTGTACCAAGGAGGATCA+GGG - chr6.2:88794583-88794602 MS.gene030304:intron 45.0%
AGCAGGTAGAAAAGAAGAGG+TGG - chr6.2:88792477-88792496 MS.gene030304:CDS 45.0%
AGCTAAGGGCCTGTTTAGAT+TGG - chr6.2:88792859-88792878 MS.gene030304:intron 45.0%
GTTAAAAGGTTTGGGCACCA+AGG - chr6.2:88794694-88794713 MS.gene030304:CDS 45.0%
TAAGCTCCTGTTGGACTGTT+TGG - chr6.2:88793395-88793414 MS.gene030304:intron 45.0%
TCAAGCTGAACAAGGCTATC+TGG - chr6.2:88794546-88794565 MS.gene030304:intron 45.0%
TCTAACATCGTTAGTGCCCA+TGG + chr6.2:88794519-88794538 None:intergenic 45.0%
TGCAGCAGGTAGAAAAGAAG+AGG - chr6.2:88792474-88792493 MS.gene030304:CDS 45.0%
TTGGTACACTTCTGATTCCC+TGG + chr6.2:88794574-88794593 None:intergenic 45.0%
! AGGGAATCAGAAGTGTACCA+AGG - chr6.2:88794573-88794592 MS.gene030304:intron 45.0%
! GAATCAGAAGTGTACCAAGG+AGG - chr6.2:88794576-88794595 MS.gene030304:intron 45.0%
! TCGCACTGTTTTGTGTGTTG+TGG - chr6.2:88794161-88794180 MS.gene030304:intron 45.0%
!! GAAGGCACCAAAAGCTATCA+AGG - chr6.2:88794469-88794488 MS.gene030304:intron 45.0%
!! TTAATTAAAATTAAAATCAT+GGG + chr6.2:88792675-88792694 None:intergenic 5.0%
!! TTTAATTAAAATTAAAATCA+TGG + chr6.2:88792676-88792695 None:intergenic 5.0%
AATCTCCACAAGCGTCTCCA+TGG - chr6.2:88792520-88792539 MS.gene030304:CDS 50.0%
AGCGACTCTTGGAGAGCTTA+TGG - chr6.2:88793702-88793721 MS.gene030304:intron 50.0%
GAAGTGTACCAAGGAGGATC+AGG - chr6.2:88794582-88794601 MS.gene030304:intron 50.0%
GAATGACGACGAAGATGCCA+AGG - chr6.2:88794625-88794644 MS.gene030304:intron 50.0%
GAGACGCTTGTGGAGATTGA+TGG + chr6.2:88792518-88792537 None:intergenic 50.0%
! AACAAGGCTATCTGGAGCCA+GGG - chr6.2:88794554-88794573 MS.gene030304:intron 50.0%
! CTAGGGTGTTAGGATCGGTT+TGG - chr6.2:88793343-88793362 MS.gene030304:intron 50.0%
ACCATCCATGGAGACGCTTG+TGG + chr6.2:88792528-88792547 None:intergenic 55.0%
ATGCGTACCCTGATCCTCCT+TGG + chr6.2:88794593-88794612 None:intergenic 55.0%
GGTCTCCCAAACAGTCCAAC+AGG + chr6.2:88793404-88793423 None:intergenic 55.0%
TCCACAAGCGTCTCCATGGA+TGG - chr6.2:88792524-88792543 MS.gene030304:CDS 55.0%
! GAACAAGGCTATCTGGAGCC+AGG - chr6.2:88794553-88794572 MS.gene030304:intron 55.0%
GGGTACGCATTGCTCGCAAG+AGG - chr6.2:88794603-88794622 MS.gene030304:intron 60.0%
! ATGGTGGAGAAGGGTGCAGC+AGG - chr6.2:88792460-88792479 MS.gene030304:CDS 60.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 88792460 88794736 88792460 ID=MS.gene030304
chr6.2 mRNA 88792460 88794736 88792460 ID=MS.gene030304.t1;Parent=MS.gene030304
chr6.2 exon 88794651 88794736 88794651 ID=MS.gene030304.t1.exon1;Parent=MS.gene030304.t1
chr6.2 CDS 88794651 88794736 88794651 ID=cds.MS.gene030304.t1;Parent=MS.gene030304.t1
chr6.2 exon 88792460 88792739 88792460 ID=MS.gene030304.t1.exon2;Parent=MS.gene030304.t1
chr6.2 CDS 88792460 88792739 88792460 ID=cds.MS.gene030304.t1;Parent=MS.gene030304.t1
Gene Sequence

>MS.gene030304

ATGGTGGAGAAGGGTGCAGCAGGTAGAAAAGAAGAGGTGGTTACACGGGAGTATACCATCAATCTCCACAAGCGTCTCCATGGATGGTAATTTCAATCTTTCGATTATTTGCTTCTCATGATTCAACTCTCTGTTTTTCATTGCAAATATTGATTCATCATTTTTGTTGTTAATTTCATGATTTAACTGCTAATCAGTAATTTTCTCACTTGCCCATGATTTTAATTTTAATTAAAGTTCAATTTCTATAGATCTAGACCCTGTATGGATAAATAACTTAGTTTGCAGCTTATATTGTAAAGTTAAATTGTTCTTATAAGCGCTTAGTTGTAAGCTATTTTTATGACGAGATAAAAATAAAGGTTAATTGTTTTTTGTTAGTTATAAGCTATTTTTATAAGCTAAGGGCCTGTTTAGATTGGCTTATTTTTGAGCTTATGAATGCTAATAAGTAAGCTTTTATGTTAATTTAATAAGCTATACACTGTGTTTATTAGATAATTTTGGAGAGTTTATGAAAAATAGTTGAAAACAACTTGTGCAATAGATGCTCAAATAAGCTTGTTATTCAGTAATTTTCTCACCTTCCCCCATAATTGTTGTGTTACATAAGCGTTTCAAATTTGTTGATCTAGGATCTGTTTGGATAAATAGGCTAATTTGCAGTGTTTACTGTAAGTACTTATCATGATAAATGCTACTTTTGTTAAACTATGTTAGATAACATATGAAAAGAAGCTGATAACACGTAATAACATGTCACGAGTAATTTTGACTTTTGTGATTCAGTTTTCTGTGTTTACATTGGAAATTACAACTTATCAGTAATTTTCTCACTTTCCTGTAATATTGTTTTAGTTGGCATTTCAATTTTGTAGATCTACTAGGGTGTTAGGATCGGTTTGGATCGACTTATTTATGCTTATCTATTTGCATAAGCTCCTGTTGGACTGTTTGGGAGACCTTATTGAAACAGTTGATGACATTTTCATAACCTGTATTCAGCTTATTTTCATAATCTCTCCATGATGTTTTTTTAAAACAGCTTATAACTACTAATCAGTAATTTTCTCACTTTTCCATAATCATCAATTTCATCACTTTAATTGTTAATTTCATGATCTAACTACATTAGGCCCTGTTTTGATTAACAGTTTAATTTGCCGCTTATAATATTATAAGTGCTTAGTTATAAGCTATTTTTATAACAAAAGATAAAATAAATTTAAATTGTTTTTTATAAGCGACTCTTGGAGAGCTTATGGAAATAAGCTGAAACAACTTATGCACAAAGTCATAAGCTGTTTTAATAAGCTCTTACAGTCATTCCAATGTTATGCCATTAGAGAATCTCAAATAAGCTATTTCAAAAGGCTCTAAGTATTTATGCTGTTCATTTGATGTTAATGAGTAAATTATTATAGTTTGTGAACAATGTCATTAGCTGTTTGTGTATGTTATCTGCGAGAACTTATAAAATAGCTGAAAGCAGCTTATGAACAATGCCATAAGCTGTTTTTGAATTCATATATGTTTTTCCAAACAGCCAGCAACTTATGAACAATGACAAAATTTATGTGAGTAAATAAGCTCAAATAAGCCTATCCAAACAAACCCTAAATATGTATGCTGTTCATTTGGTGAGTAAATTAATAGTTTGTGGTTTTAATATGAATTGAGTTGAGTTGGAATGCATCTGAATCGCACTGTTTTGTGTGTTGTGGACTCTCAGTTTTTTAGTCATATTGATTTTTGACTTGTTTCTTTTTTACTGTGTATCTTATTATTCATGATTTGAAAAATCGGTATGCCAATTCACAATATGAATATCAATATAAGCTCTGTTTCGTTGCTTTGAGATCAAGTTATTTTTTGTAGATGATTCATGCTATGCGTAATTGCATAATTGGATCTGTTTATGGTTTCTGTAATTGTATAACTAGATCTCTTGCTAATTTCTGTTTTTGTTTGGTATTTTTTTGTATGTAAAAAAACAGCACCTTCAAGAAGAAGGCACCAAAAGCTATCAAGGAGATCAGAAAATTTGCTCAAAAAGCCATGGGCACTAACGATGTTAGAGTTGATGTCAAGCTGAACAAGGCTATCTGGAGCCAGGGAATCAGAAGTGTACCAAGGAGGATCAGGGTACGCATTGCTCGCAAGAGGAATGACGACGAAGATGCCAAGGAAGAGTTATACTCCCTTGTCACTGTCGTTGAAATTCCTAAAGAAGAGTTAAAAGGTTTGGGCACCAAGGTCATTGATGATGAAGATTGA
Protein sequence

>MS.gene030304.t1

MVEKGAAGRKEEVVTREYTINLHKRLHGCTFKKKAPKAIKEIRKFAQKAMGTNDVRVDVKLNKAIWSQGIRSVPRRIRVRIARKRNDDEDAKEELYSLVTVVEIPKEELKGLGTKVIDDED