AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene01456

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01456.t1 MTR_3g078653 100.000 204 0 0 1 204 1 204 8.57e-150 414
MS.gene01456.t1 MTR_2g014220 99.510 204 1 0 1 204 49 252 2.38e-149 415
MS.gene01456.t1 MTR_7g026915 94.915 59 3 0 1 59 1 59 3.81e-33 125
MS.gene01456.t1 MTR_7g026915 87.500 64 8 0 1 64 1 64 1.52e-31 120
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01456.t1 AT4G16720 88.235 204 24 0 1 204 1 204 8.64e-122 343
MS.gene01456.t1 AT4G17390 87.745 204 25 0 1 204 1 204 1.80e-121 342

Find 74 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTTCGAAGGGTATTGTATA+CGG 0.299480 2.2:-68688586 MS.gene01456:CDS
GGAGGAAGCTCGGTGGCCTC+AGG 0.313744 2.2:-68688489 MS.gene01456:CDS
TCCTGACAAAGCTCGCCGTT+TGG 0.353079 2.2:-68688888 MS.gene01456:CDS
TCAGGGTTCTCAATTCCTAC+TGG 0.363571 2.2:-68688471 MS.gene01456:CDS
ACAAGTATGTTTCTGAGTTA+TGG 0.369598 2.2:-68689009 MS.gene01456:CDS
CCTGACAAAGCTCGCCGTTT+GGG 0.382164 2.2:-68688887 MS.gene01456:CDS
GTCCTTCCCGCAGGGCAAAC+TGG 0.382984 2.2:-68688255 MS.gene01456:CDS
TTAGTGAGCCAGTTGATTCT+TGG 0.391426 2.2:+68688373 None:intergenic
TAGTGAGCCAGTTGATTCTT+GGG 0.399274 2.2:+68688374 None:intergenic
TGCGGGAAGGACGGGCTTTG+TGG 0.410020 2.2:+68688266 None:intergenic
TCTCTTCCAGTTTGCCCTGC+GGG 0.416755 2.2:+68688249 None:intergenic
AATGACCTCAAAATACTTGA+AGG 0.426532 2.2:+68688432 None:intergenic
AGCTCGCCGTTTGGGTTACA+AGG 0.427870 2.2:-68688879 MS.gene01456:CDS
CCCAAACGGCGAGCTTTGTC+AGG 0.428600 2.2:+68688887 None:intergenic
TATACAATACCCTTCGAAAC+AGG 0.440190 2.2:+68688589 None:intergenic
GTTTGCCCTGCGGGAAGGAC+GGG 0.445042 2.2:+68688258 None:intergenic
TTTGTCAGGACGAGTGGGTC+TGG 0.461552 2.2:+68688901 None:intergenic
AGTTTGCCCTGCGGGAAGGA+CGG 0.463498 2.2:+68688257 None:intergenic
TTGAGTAACTCCCTGGTTAG+TGG 0.468290 2.2:+68688558 None:intergenic
CTTCGTGGCCTCACTTCTGC+TGG 0.468828 2.2:-68688328 MS.gene01456:CDS
TCAGTTGCCGAGGAGCGTGC+TGG 0.471507 2.2:-68688511 MS.gene01456:CDS
TGAGTAACTCCCTGGTTAGT+GGG 0.482971 2.2:+68688559 None:intergenic
CTAATCCTGTCCACAAGCAT+AGG 0.483564 2.2:-68688354 MS.gene01456:CDS
CAGTTGCCGAGGAGCGTGCT+GGG 0.483968 2.2:-68688510 MS.gene01456:CDS
CAGGGTTCTCAATTCCTACT+GGG 0.490551 2.2:-68688470 MS.gene01456:CDS
TCATGCAGCGTGTGAGGTGT+TGG 0.501162 2.2:-68688958 MS.gene01456:CDS
ACAAAGCCCGTCCTTCCCGC+AGG 0.505243 2.2:-68688264 MS.gene01456:CDS
CATGCAGCGTGTGAGGTGTT+GGG 0.510206 2.2:-68688957 MS.gene01456:CDS
GAGCGTGCTGGGAGGAAGCT+CGG 0.519651 2.2:-68688499 MS.gene01456:CDS
TACGTAGAGGTGGTAGGAAG+AGG 0.522230 2.2:-68688612 MS.gene01456:CDS
TTCCAGTTTGCCCTGCGGGA+AGG 0.525009 2.2:+68688253 None:intergenic
TTACTCAACTGAAGTTTCAA+AGG 0.527187 2.2:-68688543 MS.gene01456:CDS
AACAGAGGTTTGAGTGGCAA+AGG 0.530737 2.2:-68688298 MS.gene01456:CDS
TTTCGAAGGGTATTGTATAC+GGG 0.532253 2.2:-68688585 MS.gene01456:CDS
CTTCCTCCCAGCACGCTCCT+CGG 0.535254 2.2:+68688504 None:intergenic
TTTGGGTTACAAGGCCAAGC+AGG 0.540516 2.2:-68688870 MS.gene01456:intron
AGTTCCCTATGCTTGTGGAC+AGG 0.542094 2.2:+68688349 None:intergenic
ATACGGGAAGCCCACTAACC+AGG 0.546286 2.2:-68688569 MS.gene01456:CDS
GCGAGCTTTGTCAGGACGAG+TGG 0.547527 2.2:+68688895 None:intergenic
CACCTCTACGTACCCTCACT+CGG 0.548557 2.2:+68688623 None:intergenic
AAGAATAGATGATACCTGCT+TGG 0.550130 2.2:+68688856 None:intergenic
GAAATGACCCAAGAATCAAC+TGG 0.550461 2.2:-68688381 MS.gene01456:CDS
TAGGAAGAGGCCTGTTTCGA+AGG 0.550472 2.2:-68688599 MS.gene01456:CDS
GAGGAAGCTCGGTGGCCTCA+GGG 0.552741 2.2:-68688488 MS.gene01456:CDS
ACTTCAGTTGAGTAACTCCC+TGG 0.559985 2.2:+68688551 None:intergenic
CACGAAGTTCCCTATGCTTG+TGG 0.560507 2.2:+68688344 None:intergenic
TAATCCTGTCCACAAGCATA+GGG 0.571077 2.2:-68688353 MS.gene01456:CDS
CAATTCCTACTGGGTCAATG+AGG 0.583661 2.2:-68688461 MS.gene01456:CDS
TTCTCTTCCAGTTTGCCCTG+CGG 0.587901 2.2:+68688248 None:intergenic
GATATGTTGTGTACCGAGTG+AGG 0.591649 2.2:-68688636 MS.gene01456:CDS
TGAGGGTACGTAGAGGTGGT+AGG 0.593507 2.2:-68688618 MS.gene01456:CDS
ACAGAGGTTTGAGTGGCAAA+GGG 0.593708 2.2:-68688297 MS.gene01456:CDS
GCTTGGCCTTGTAACCCAAA+CGG 0.594502 2.2:+68688873 None:intergenic
GAGCAAGAGATCAGTTGCCG+AGG 0.598712 2.2:-68688521 MS.gene01456:CDS
CACAAGCATAGGGAACTTCG+TGG 0.601845 2.2:-68688343 MS.gene01456:CDS
CAAAGCCCGTCCTTCCCGCA+GGG 0.606273 2.2:-68688263 MS.gene01456:CDS
AGGAAGAGGCCTGTTTCGAA+GGG 0.612480 2.2:-68688598 MS.gene01456:CDS
TACGGGAAGCCCACTAACCA+GGG 0.619308 2.2:-68688568 MS.gene01456:CDS
AGAATCCTCATTGACCCAGT+AGG 0.619890 2.2:+68688456 None:intergenic
CGAGCTTTGTCAGGACGAGT+GGG 0.623786 2.2:+68688896 None:intergenic
GGGTCTGGTGAGACGAACAA+TGG 0.629081 2.2:+68688916 None:intergenic
ACGATAACGACGGAGAGACA+AGG 0.632844 2.2:+68688219 None:intergenic
AAAGAAAACAGAGGTTTGAG+TGG 0.633735 2.2:-68688304 MS.gene01456:CDS
TGAGATTCATGCAGCGTGTG+AGG 0.638236 2.2:-68688964 MS.gene01456:CDS
AGTATGTTTCTGAGTTATGG+CGG 0.642445 2.2:-68689006 MS.gene01456:CDS
CGAGTGAGGGTACGTAGAGG+TGG 0.643734 2.2:-68688622 MS.gene01456:CDS
ATATGTTGTGTACCGAGTGA+GGG 0.647122 2.2:-68688635 MS.gene01456:CDS
TCTGCTGGAAAAGAAAACAG+AGG 0.661682 2.2:-68688313 MS.gene01456:CDS
GTTATGGCGGAAGAAGCAAT+CGG 0.676275 2.2:-68688993 MS.gene01456:CDS
TTGCCGAGGAGCGTGCTGGG+AGG 0.682144 2.2:-68688507 MS.gene01456:CDS
CGTGCTGGGAGGAAGCTCGG+TGG 0.684204 2.2:-68688496 MS.gene01456:CDS
AGTAAAATCAACGATAACGA+CGG 0.699472 2.2:+68688209 None:intergenic
TACCGAGTGAGGGTACGTAG+AGG 0.717794 2.2:-68688625 MS.gene01456:CDS
AGTAGGAATTGAGAACCCTG+AGG 0.790898 2.2:+68688473 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CATTAAGTGTGAAATAATTA+GGG + chr2.2:68688614-68688633 None:intergenic 20.0%
!!! AGTATTTGTTACATCATTTT+AGG - chr2.2:68688688-68688707 MS.gene01456:intron 20.0%
!!! GTATTTGTTACATCATTTTA+GGG - chr2.2:68688689-68688708 MS.gene01456:intron 20.0%
!!! GTTATTTGTGAATTTTGAAT+AGG - chr2.2:68688310-68688329 MS.gene01456:CDS 20.0%
! GCATTAAGTGTGAAATAATT+AGG + chr2.2:68688615-68688634 None:intergenic 25.0%
AATGACCTCAAAATACTTGA+AGG + chr2.2:68688918-68688937 None:intergenic 30.0%
TGAAATAATTAGGGTCTGTT+TGG + chr2.2:68688605-68688624 None:intergenic 30.0%
TTACTCAACTGAAGTTTCAA+AGG - chr2.2:68688804-68688823 MS.gene01456:intron 30.0%
TTTCACACTTAATGCTATGT+AGG - chr2.2:68688620-68688639 MS.gene01456:CDS 30.0%
! ACAAGTATGTTTCTGAGTTA+TGG - chr2.2:68688338-68688357 MS.gene01456:CDS 30.0%
! TTCTACCTTCAAGTATTTTG+AGG - chr2.2:68688910-68688929 MS.gene01456:CDS 30.0%
!!! CAAGTATTTTGAGGTCATTT+TGG - chr2.2:68688919-68688938 MS.gene01456:CDS 30.0%
AAAGAAAACAGAGGTTTGAG+TGG - chr2.2:68689043-68689062 MS.gene01456:intron 35.0%
AAGAATAGATGATACCTGCT+TGG + chr2.2:68688494-68688513 None:intergenic 35.0%
TAATTAGGGTCTGTTTGGAT+TGG + chr2.2:68688600-68688619 None:intergenic 35.0%
TATACAATACCCTTCGAAAC+AGG + chr2.2:68688761-68688780 None:intergenic 35.0%
! AGTATGTTTCTGAGTTATGG+CGG - chr2.2:68688341-68688360 MS.gene01456:CDS 35.0%
!! CTGTTTCTATTCATTCTCTC+TGG - chr2.2:68688244-68688263 MS.gene01456:CDS 35.0%
!! GTTTCGAAGGGTATTGTATA+CGG - chr2.2:68688761-68688780 MS.gene01456:intron 35.0%
!! TTTCGAAGGGTATTGTATAC+GGG - chr2.2:68688762-68688781 MS.gene01456:intron 35.0%
ATATGTTGTGTACCGAGTGA+GGG - chr2.2:68688712-68688731 MS.gene01456:intron 40.0%
GAAATGACCCAAGAATCAAC+TGG - chr2.2:68688966-68688985 MS.gene01456:CDS 40.0%
TAATCCTGTCCACAAGCATA+GGG - chr2.2:68688994-68689013 MS.gene01456:CDS 40.0%
TCTGCTGGAAAAGAAAACAG+AGG - chr2.2:68689034-68689053 MS.gene01456:intron 40.0%
! TAGTGAGCCAGTTGATTCTT+GGG + chr2.2:68688976-68688995 None:intergenic 40.0%
! TTAGTGAGCCAGTTGATTCT+TGG + chr2.2:68688977-68688996 None:intergenic 40.0%
! TTTCTTTTCCAGCAGAAGTG+AGG + chr2.2:68689030-68689049 None:intergenic 40.0%
AACAGAGGTTTGAGTGGCAA+AGG - chr2.2:68689049-68689068 MS.gene01456:intron 45.0%
ACAGAGGTTTGAGTGGCAAA+GGG - chr2.2:68689050-68689069 MS.gene01456:intron 45.0%
ACTTCAGTTGAGTAACTCCC+TGG + chr2.2:68688799-68688818 None:intergenic 45.0%
AGAATCCTCATTGACCCAGT+AGG + chr2.2:68688894-68688913 None:intergenic 45.0%
AGTAGGAATTGAGAACCCTG+AGG + chr2.2:68688877-68688896 None:intergenic 45.0%
CAATTCCTACTGGGTCAATG+AGG - chr2.2:68688886-68688905 MS.gene01456:CDS 45.0%
CAGGGTTCTCAATTCCTACT+GGG - chr2.2:68688877-68688896 MS.gene01456:CDS 45.0%
CTAATCCTGTCCACAAGCAT+AGG - chr2.2:68688993-68689012 MS.gene01456:CDS 45.0%
GAAACAGCAGCTGCAATAGA+TGG + chr2.2:68688231-68688250 None:intergenic 45.0%
GATATGTTGTGTACCGAGTG+AGG - chr2.2:68688711-68688730 MS.gene01456:intron 45.0%
TCAGGGTTCTCAATTCCTAC+TGG - chr2.2:68688876-68688895 MS.gene01456:CDS 45.0%
TGAGTAACTCCCTGGTTAGT+GGG + chr2.2:68688791-68688810 None:intergenic 45.0%
TTGAGTAACTCCCTGGTTAG+TGG + chr2.2:68688792-68688811 None:intergenic 45.0%
! GTTATGGCGGAAGAAGCAAT+CGG - chr2.2:68688354-68688373 MS.gene01456:CDS 45.0%
ACGATAACGACGGAGAGACA+AGG + chr2.2:68689131-68689150 None:intergenic 50.0%
AGGAAGAGGCCTGTTTCGAA+GGG - chr2.2:68688749-68688768 MS.gene01456:intron 50.0%
AGTTCCCTATGCTTGTGGAC+AGG + chr2.2:68689001-68689020 None:intergenic 50.0%
CACAAGCATAGGGAACTTCG+TGG - chr2.2:68689004-68689023 MS.gene01456:CDS 50.0%
CACGAAGTTCCCTATGCTTG+TGG + chr2.2:68689006-68689025 None:intergenic 50.0%
TACGTAGAGGTGGTAGGAAG+AGG - chr2.2:68688735-68688754 MS.gene01456:intron 50.0%
TAGGAAGAGGCCTGTTTCGA+AGG - chr2.2:68688748-68688767 MS.gene01456:intron 50.0%
TGAGATTCATGCAGCGTGTG+AGG - chr2.2:68688383-68688402 MS.gene01456:CDS 50.0%
TTCTCTTCCAGTTTGCCCTG+CGG + chr2.2:68689102-68689121 None:intergenic 50.0%
! TTTGGGTTACAAGGCCAAGC+AGG - chr2.2:68688477-68688496 MS.gene01456:CDS 50.0%
!! GCTTGGCCTTGTAACCCAAA+CGG + chr2.2:68688477-68688496 None:intergenic 50.0%
ATACGGGAAGCCCACTAACC+AGG - chr2.2:68688778-68688797 MS.gene01456:intron 55.0%
CACCTCTACGTACCCTCACT+CGG + chr2.2:68688727-68688746 None:intergenic 55.0%
CCTGACAAAGCTCGCCGTTT+GGG - chr2.2:68688460-68688479 MS.gene01456:CDS 55.0%
GAGCAAGAGATCAGTTGCCG+AGG - chr2.2:68688826-68688845 MS.gene01456:intron 55.0%
GGGTCTGGTGAGACGAACAA+TGG + chr2.2:68688434-68688453 None:intergenic 55.0%
TACGGGAAGCCCACTAACCA+GGG - chr2.2:68688779-68688798 MS.gene01456:intron 55.0%
TCATGCAGCGTGTGAGGTGT+TGG - chr2.2:68688389-68688408 MS.gene01456:CDS 55.0%
TCCTGACAAAGCTCGCCGTT+TGG - chr2.2:68688459-68688478 MS.gene01456:CDS 55.0%
TCTCTTCCAGTTTGCCCTGC+GGG + chr2.2:68689101-68689120 None:intergenic 55.0%
TTTGTCAGGACGAGTGGGTC+TGG + chr2.2:68688449-68688468 None:intergenic 55.0%
! AGCTCGCCGTTTGGGTTACA+AGG - chr2.2:68688468-68688487 MS.gene01456:CDS 55.0%
! CATGCAGCGTGTGAGGTGTT+GGG - chr2.2:68688390-68688409 MS.gene01456:CDS 55.0%
! CGAGCTTTGTCAGGACGAGT+GGG + chr2.2:68688454-68688473 None:intergenic 55.0%
! TACCGAGTGAGGGTACGTAG+AGG - chr2.2:68688722-68688741 MS.gene01456:intron 55.0%
! TGAGGGTACGTAGAGGTGGT+AGG - chr2.2:68688729-68688748 MS.gene01456:intron 55.0%
AGTTTGCCCTGCGGGAAGGA+CGG + chr2.2:68689093-68689112 None:intergenic 60.0%
CTTCGTGGCCTCACTTCTGC+TGG - chr2.2:68689019-68689038 MS.gene01456:intron 60.0%
TTCCAGTTTGCCCTGCGGGA+AGG + chr2.2:68689097-68689116 None:intergenic 60.0%
! CCCAAACGGCGAGCTTTGTC+AGG + chr2.2:68688463-68688482 None:intergenic 60.0%
! CGAGTGAGGGTACGTAGAGG+TGG - chr2.2:68688725-68688744 MS.gene01456:intron 60.0%
! GCGAGCTTTGTCAGGACGAG+TGG + chr2.2:68688455-68688474 None:intergenic 60.0%
ACAAAGCCCGTCCTTCCCGC+AGG - chr2.2:68689083-68689102 MS.gene01456:intron 65.0%
CAAAGCCCGTCCTTCCCGCA+GGG - chr2.2:68689084-68689103 MS.gene01456:intron 65.0%
CTTCCTCCCAGCACGCTCCT+CGG + chr2.2:68688846-68688865 None:intergenic 65.0%
GAGCGTGCTGGGAGGAAGCT+CGG - chr2.2:68688848-68688867 MS.gene01456:intron 65.0%
GTCCTTCCCGCAGGGCAAAC+TGG - chr2.2:68689092-68689111 MS.gene01456:intron 65.0%
GTTTGCCCTGCGGGAAGGAC+GGG + chr2.2:68689092-68689111 None:intergenic 65.0%
! CAGTTGCCGAGGAGCGTGCT+GGG - chr2.2:68688837-68688856 MS.gene01456:intron 65.0%
! GAGGAAGCTCGGTGGCCTCA+GGG - chr2.2:68688859-68688878 MS.gene01456:intron 65.0%
! TCAGTTGCCGAGGAGCGTGC+TGG - chr2.2:68688836-68688855 MS.gene01456:intron 65.0%
! TGCGGGAAGGACGGGCTTTG+TGG + chr2.2:68689084-68689103 None:intergenic 65.0%
CGTGCTGGGAGGAAGCTCGG+TGG - chr2.2:68688851-68688870 MS.gene01456:intron 70.0%
! GGAGGAAGCTCGGTGGCCTC+AGG - chr2.2:68688858-68688877 MS.gene01456:intron 70.0%
! TTGCCGAGGAGCGTGCTGGG+AGG - chr2.2:68688840-68688859 MS.gene01456:intron 70.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 68688216 68689153 68688216 ID=MS.gene01456
chr2.2 mRNA 68688216 68689153 68688216 ID=MS.gene01456.t1;Parent=MS.gene01456
chr2.2 exon 68689150 68689153 68689150 ID=MS.gene01456.t1.exon1;Parent=MS.gene01456.t1
chr2.2 CDS 68689150 68689153 68689150 ID=cds.MS.gene01456.t1;Parent=MS.gene01456.t1
chr2.2 exon 68688871 68689037 68688871 ID=MS.gene01456.t1.exon2;Parent=MS.gene01456.t1
chr2.2 CDS 68688871 68689037 68688871 ID=cds.MS.gene01456.t1;Parent=MS.gene01456.t1
chr2.2 exon 68688216 68688659 68688216 ID=MS.gene01456.t1.exon3;Parent=MS.gene01456.t1
chr2.2 CDS 68688216 68688659 68688216 ID=cds.MS.gene01456.t1;Parent=MS.gene01456.t1
Gene Sequence

>MS.gene01456

ATGGGTATGCATCCATCTATTGCAGCTGCTGTTTCTATTCATTCTCTCTGGATTTATGACAATGATCTTATCGAAATGTGATGTAATTGTTGTTGTTATTTGTGAATTTTGAATAGGTGCATACAAGTATGTTTCTGAGTTATGGCGGAAGAAGCAATCGGATGTGATGAGATTCATGCAGCGTGTGAGGTGTTGGGAGTATCGTCAACAATCTTCCATTGTTCGTCTCACCAGACCCACTCGTCCTGACAAAGCTCGCCGTTTGGGTTACAAGGCCAAGCAGGTATCATCTATTCTTTATTCATTTGTTTAACTTATGAATAATAGTACATTAAAGCTTGTTTATTTGCATACGTTGTTTTGCATAAGCTTAAGAATAAGCCAATCCAAACAGACCCTAATTATTTCACACTTAATGCTATGTAGGTTGTTTGTTTATTTACTTGTTAAGATGTGAACTTGATTGATGTATAGTATTTGTTACATCATTTTAGGGATATGTTGTGTACCGAGTGAGGGTACGTAGAGGTGGTAGGAAGAGGCCTGTTTCGAAGGGTATTGTATACGGGAAGCCCACTAACCAGGGAGTTACTCAACTGAAGTTTCAAAGGAGCAAGAGATCAGTTGCCGAGGAGCGTGCTGGGAGGAAGCTCGGTGGCCTCAGGGTTCTCAATTCCTACTGGGTCAATGAGGATTCTACCTTCAAGTATTTTGAGGTCATTTTGGTTGATGTTGCTCATAGTGCTATAAGAAATGACCCAAGAATCAACTGGCTCACTAATCCTGTCCACAAGCATAGGGAACTTCGTGGCCTCACTTCTGCTGGAAAAGAAAACAGAGGTTTGAGTGGCAAAGGGCATCGTTACCACAAAGCCCGTCCTTCCCGCAGGGCAAACTGGAAGAGAAACAACACCTTGTCTCTCCGTCGTTATCGTTGA
Protein sequence

>MS.gene01456.t1

MGAYKYVSELWRKKQSDVMRFMQRVRCWEYRQQSSIVRLTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVSKGIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLRVLNSYWVNEDSTFKYFEVILVDVAHSAIRNDPRINWLTNPVHKHRELRGLTSAGKENRGLSGKGHRYHKARPSRRANWKRNNTLSLRRYR