AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene068936

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068936.t1 MTR_2g045630 83.582 201 18 2 1 201 92 277 6.00e-114 326
MS.gene068936.t1 MTR_2g045670 74.257 202 28 2 1 202 104 281 2.89e-95 279
MS.gene068936.t1 MTR_2g045700 74.752 202 27 2 1 202 94 271 4.70e-93 273
MS.gene068936.t1 MTR_1g034500 68.473 203 39 3 1 202 129 307 1.84e-82 247
MS.gene068936.t1 MTR_8g077950 45.000 80 44 0 117 196 258 337 4.16e-16 75.5
MS.gene068936.t1 MTR_8g077950 45.000 80 44 0 117 196 260 339 4.30e-16 75.5
MS.gene068936.t1 MTR_8g077950 45.000 80 44 0 117 196 200 279 4.89e-16 74.7
MS.gene068936.t1 MTR_8g028150 41.176 68 40 0 117 184 280 347 9.23e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068936.t1 AT4G36730 40.000 80 48 0 117 196 222 301 2.35e-13 67.8
MS.gene068936.t1 AT4G36730 40.000 80 48 0 117 196 220 299 2.39e-13 67.8

Find 31 sgRNAs with CRISPR-Local

Find 95 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATATCTTCTTCATACTTAA+AGG 0.172932 2.1:+45512495 None:intergenic
GTTCCATCCCTATCATATTT+TGG 0.188178 2.1:+45512850 None:intergenic
CACTCTTAAGGATGAAAATT+TGG 0.215284 2.1:-45511665 MS.gene068936:CDS
TCTGGGATGGCTCAGAATTT+AGG 0.229957 2.1:-45512294 MS.gene068936:CDS
AGACGGGTTTCCATATTTAT+TGG 0.261362 2.1:+45512879 None:intergenic
AAGATATCTAACATGATTAT+TGG 0.278744 2.1:-45512480 MS.gene068936:CDS
ACTGGGGAATCCAATAAATA+TGG 0.294546 2.1:-45512889 MS.gene068936:CDS
CTGGGATGGCTCAGAATTTA+GGG 0.315292 2.1:-45512293 MS.gene068936:CDS
GCTCAGCGAGCGTTTGTGTT+AGG 0.327287 2.1:+45511641 None:intergenic
GAACAAACTGTACCTCATTA+TGG 0.344928 2.1:+45512828 None:intergenic
CTTCTGCACCAAAATATGAT+AGG 0.359166 2.1:-45512858 MS.gene068936:CDS
TACTTTGTAGAAAATCCATC+TGG 0.371434 2.1:-45512312 MS.gene068936:CDS
GAAGAGCTCGTTAAGGAGTA+TGG 0.378867 2.1:-45510943 MS.gene068936:CDS
TTGCTGCACTGCACTCATAA+AGG 0.401928 2.1:+45512753 None:intergenic
TCAAAAGATAAACACTCTTA+AGG 0.422261 2.1:-45511677 MS.gene068936:CDS
AAGATCAAAGATAAAGAAAC+AGG 0.437513 2.1:-45511923 MS.gene068936:intron
AATAGATCCGCAATTGATTC+TGG 0.439062 2.1:+45510919 None:intergenic
TTCTGCACCAAAATATGATA+GGG 0.545791 2.1:-45512857 MS.gene068936:CDS
CAATGAAAACGATTCTATTG+AGG 0.546332 2.1:-45511593 MS.gene068936:intron
TCTAACATGATTATTGGTGA+TGG 0.558881 2.1:-45512474 MS.gene068936:intron
GGAAGCAAGAGATCAACAGA+TGG 0.570698 2.1:-45512728 MS.gene068936:CDS
AAATTCTGAGCCATCCCAGA+TGG 0.579881 2.1:+45512297 None:intergenic
GGAACAGGAAGAGCTCGTTA+AGG 0.581436 2.1:-45510950 MS.gene068936:intron
GCACCAAAATATGATAGGGA+TGG 0.584620 2.1:-45512853 MS.gene068936:CDS
TATGAGTGCAGTGCAGCAAG+TGG 0.608454 2.1:-45512749 MS.gene068936:CDS
TGTAGAAAATCCATCTGGGA+TGG 0.612430 2.1:-45512307 MS.gene068936:CDS
GAATTTAGGGACAGTCGTCA+AGG 0.625189 2.1:-45512280 MS.gene068936:CDS
CACATGAACTGCAGTTGATG+TGG 0.629119 2.1:-45512355 MS.gene068936:intron
ACTTTGTAGAAAATCCATCT+GGG 0.631448 2.1:-45512311 MS.gene068936:CDS
ATAGGGATGGAACCATAATG+AGG 0.644156 2.1:-45512840 MS.gene068936:CDS
GTATGGACCAGAATCAATTG+CGG 0.711023 2.1:-45510926 MS.gene068936:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATTAATTTTTATATAAATG+TGG - chr2.1:45511120-45511139 MS.gene068936:intron 10.0%
!!! AATTATTTATTTTCCAAGAT+TGG - chr2.1:45512729-45512748 MS.gene068936:CDS 15.0%
!! AAAATTGAACAAGTAAGAAA+GGG + chr2.1:45512240-45512259 None:intergenic 20.0%
!! AAGATATCTAACATGATTAT+TGG - chr2.1:45511312-45511331 MS.gene068936:intron 20.0%
!! AATAGAATCGTTTACATTAA+TGG + chr2.1:45512614-45512633 None:intergenic 20.0%
!! ATATAATTTGAATGTTCAGA+AGG - chr2.1:45511400-45511419 MS.gene068936:intron 20.0%
!! CAAAAGAAATTCAACTAAAT+AGG + chr2.1:45511789-45511808 None:intergenic 20.0%
!! GTACATGTTATATAAAATGT+CGG - chr2.1:45511235-45511254 MS.gene068936:intron 20.0%
!! TAAAATTGAACAAGTAAGAA+AGG + chr2.1:45512241-45512260 None:intergenic 20.0%
!! TTGCTAATTTGATTGTAATT+TGG - chr2.1:45512815-45512834 MS.gene068936:intron 20.0%
!!! TTGTTTCTCATACAAATATT+AGG + chr2.1:45512547-45512566 None:intergenic 20.0%
! AAACTTAGCAACATTAAGAA+GGG + chr2.1:45511735-45511754 None:intergenic 25.0%
! AAGATCAAAGATAAAGAAAC+AGG - chr2.1:45511869-45511888 MS.gene068936:intron 25.0%
! AATCAAATTAGCAACAATCT+TGG + chr2.1:45512809-45512828 None:intergenic 25.0%
! ACATCTTTATAAACCAATCT+TGG + chr2.1:45512745-45512764 None:intergenic 25.0%
! CTAATTTGATTGTAATTTGG+TGG - chr2.1:45512818-45512837 MS.gene068936:intron 25.0%
! GATATCTTCTTCATACTTAA+AGG + chr2.1:45511300-45511319 None:intergenic 25.0%
! TAAACTTAGCAACATTAAGA+AGG + chr2.1:45511736-45511755 None:intergenic 25.0%
! TCAAAAGATAAACACTCTTA+AGG - chr2.1:45512115-45512134 MS.gene068936:intron 25.0%
! TGATGCTCAACTAAAAAATA+TGG - chr2.1:45511557-45511576 MS.gene068936:intron 25.0%
!! AATGGACATCTTATGATTTT+TGG + chr2.1:45512596-45512615 None:intergenic 25.0%
!! GATTCAAAAGAGATTTTACA+GGG + chr2.1:45511655-45511674 None:intergenic 25.0%
!! TGATTCAAAAGAGATTTTAC+AGG + chr2.1:45511656-45511675 None:intergenic 25.0%
!! TTAGTTGAATTTCTTTTGAC+AGG - chr2.1:45511791-45511810 MS.gene068936:intron 25.0%
!!! TAGAAAGTTTGTTACAAAGA+GGG + chr2.1:45512640-45512659 None:intergenic 25.0%
!!! TTAGAAAGTTTGTTACAAAG+AGG + chr2.1:45512641-45512660 None:intergenic 25.0%
!!! TTGTTCATATCATTTTTCCA+AGG - chr2.1:45511004-45511023 MS.gene068936:intron 25.0%
AAAGAAAAAGACTGTCAAAC+AGG - chr2.1:45511835-45511854 MS.gene068936:intron 30.0%
ACTTTGTAGAAAATCCATCT+GGG - chr2.1:45511481-45511500 MS.gene068936:intron 30.0%
CAATGAAAACGATTCTATTG+AGG - chr2.1:45512199-45512218 MS.gene068936:intron 30.0%
CACTCTTAAGGATGAAAATT+TGG - chr2.1:45512127-45512146 MS.gene068936:intron 30.0%
CTAACTTCTTAAGATAACAG+TGG + chr2.1:45511168-45511187 None:intergenic 30.0%
CTATGAATTGGACAATGATT+TGG - chr2.1:45511950-45511969 MS.gene068936:CDS 30.0%
CTTAAGAAGTTAGAACACTT+AGG - chr2.1:45511175-45511194 MS.gene068936:intron 30.0%
GTATTGAGATGTCTATGAAT+TGG - chr2.1:45511938-45511957 MS.gene068936:CDS 30.0%
TACTTTGTAGAAAATCCATC+TGG - chr2.1:45511480-45511499 MS.gene068936:intron 30.0%
TCTAACATGATTATTGGTGA+TGG - chr2.1:45511318-45511337 MS.gene068936:intron 30.0%
TCTTCATATTCTTTCTGACA+AGG + chr2.1:45512089-45512108 None:intergenic 30.0%
TTCTGCACCAAAATATGATA+GGG - chr2.1:45510935-45510954 MS.gene068936:CDS 30.0%
! AATTACATCCTTTCTTTTGC+AGG - chr2.1:45511269-45511288 MS.gene068936:intron 30.0%
! ACTCATAAAGGATTTTGTTC+AGG + chr2.1:45511030-45511049 None:intergenic 30.0%
! AGAAGTAGCATTTTCCTATT+AGG + chr2.1:45512337-45512356 None:intergenic 30.0%
! ATTTGATTGTAATTTGGTGG+TGG - chr2.1:45512821-45512840 MS.gene068936:intron 30.0%
! CTCAATAGAATCGTTTTCAT+TGG + chr2.1:45512201-45512220 None:intergenic 30.0%
! GGATTTTCTACAAAGTAACA+AGG + chr2.1:45511477-45511496 None:intergenic 30.0%
!! CACAGTTGGCAAATTTTAAT+TGG - chr2.1:45512388-45512407 MS.gene068936:intron 30.0%
!!! AGAATTTTTCAAGACACAGT+TGG - chr2.1:45512374-45512393 MS.gene068936:intron 30.0%
ACTGGGGAATCCAATAAATA+TGG - chr2.1:45510903-45510922 MS.gene068936:CDS 35.0%
ATTCCATCCTGTTTCCTAAT+AGG - chr2.1:45512320-45512339 MS.gene068936:CDS 35.0%
CTTCTGCACCAAAATATGAT+AGG - chr2.1:45510934-45510953 MS.gene068936:CDS 35.0%
GAACAAACTGTACCTCATTA+TGG + chr2.1:45510967-45510986 None:intergenic 35.0%
GTCATTTAACAAGATGAACC+TGG + chr2.1:45512709-45512728 None:intergenic 35.0%
TAATTCTCCGTATTGTGTTG+TGG - chr2.1:45512765-45512784 MS.gene068936:CDS 35.0%
TTGAGAACCACAACACAATA+CGG + chr2.1:45512775-45512794 None:intergenic 35.0%
TTTCCTATTAGGAAACAGGA+TGG + chr2.1:45512326-45512345 None:intergenic 35.0%
! AATAGATCCGCAATTGATTC+TGG + chr2.1:45512876-45512895 None:intergenic 35.0%
! ACAGTTTGTTCTTGTTCTTC+TGG - chr2.1:45510976-45510995 MS.gene068936:intron 35.0%
! AGACGGGTTTCCATATTTAT+TGG + chr2.1:45510916-45510935 None:intergenic 35.0%
! CAAAAGAGATTTTACAGGGT+TGG + chr2.1:45511651-45511670 None:intergenic 35.0%
! GCATTTTCCTATTAGGAAAC+AGG + chr2.1:45512330-45512349 None:intergenic 35.0%
! GTTCCATCCCTATCATATTT+TGG + chr2.1:45510945-45510964 None:intergenic 35.0%
! TGAATTGGACAATGATTTGG+TGG - chr2.1:45511953-45511972 MS.gene068936:CDS 35.0%
!!! TCATATTTTGGTGCAGAAGA+CGG + chr2.1:45510933-45510952 None:intergenic 35.0%
AACCTGGCTACATTCATGTT+AGG + chr2.1:45512693-45512712 None:intergenic 40.0%
AGGAGAATCCTGCAAAAGAA+AGG + chr2.1:45511280-45511299 None:intergenic 40.0%
ATAGGGATGGAACCATAATG+AGG - chr2.1:45510952-45510971 MS.gene068936:intron 40.0%
ATGCGCTTTCGTAGCATAAA+TGG - chr2.1:45511594-45511613 MS.gene068936:CDS 40.0%
CTATTTGCCACAATTCAAGG+AGG + chr2.1:45512450-45512469 None:intergenic 40.0%
GAAGAGCAATGCTATATCTC+TGG + chr2.1:45512525-45512544 None:intergenic 40.0%
GCACCAAAATATGATAGGGA+TGG - chr2.1:45510939-45510958 MS.gene068936:CDS 40.0%
GCACTATTTGCCACAATTCA+AGG + chr2.1:45512453-45512472 None:intergenic 40.0%
GGCAAATAGTGCATTGTGAT+TGG - chr2.1:45512461-45512480 MS.gene068936:intron 40.0%
GTATGGACCAGAATCAATTG+CGG - chr2.1:45512866-45512885 MS.gene068936:CDS 40.0%
TACCTAACATGAATGTAGCC+AGG - chr2.1:45512688-45512707 MS.gene068936:intron 40.0%
TGTAGAAAATCCATCTGGGA+TGG - chr2.1:45511485-45511504 MS.gene068936:intron 40.0%
TGTGGCTGAAAAATAGGAAG+TGG + chr2.1:45512427-45512446 None:intergenic 40.0%
! AAAGGATTTTGTTCAGGCCT+TGG + chr2.1:45511024-45511043 None:intergenic 40.0%
!! TTGTAATTTGGTGGTGGAAC+AGG - chr2.1:45512827-45512846 MS.gene068936:intron 40.0%
!!! CATATTTTGGTGCAGAAGAC+GGG + chr2.1:45510932-45510951 None:intergenic 40.0%
AAATTCTGAGCCATCCCAGA+TGG + chr2.1:45511498-45511517 None:intergenic 45.0%
CTGGGATGGCTCAGAATTTA+GGG - chr2.1:45511499-45511518 MS.gene068936:intron 45.0%
GAAGAGCTCGTTAAGGAGTA+TGG - chr2.1:45512849-45512868 MS.gene068936:CDS 45.0%
GAATTTAGGGACAGTCGTCA+AGG - chr2.1:45511512-45511531 MS.gene068936:intron 45.0%
GGAAGCAAGAGATCAACAGA+TGG - chr2.1:45511064-45511083 MS.gene068936:intron 45.0%
GGTACATGCTTGACCATGAT+CGG - chr2.1:45511890-45511909 MS.gene068936:intron 45.0%
TTGCTGCACTGCACTCATAA+AGG + chr2.1:45511042-45511061 None:intergenic 45.0%
! AGGAGGTGTGGCTGAAAAAT+AGG + chr2.1:45512433-45512452 None:intergenic 45.0%
! ATGTTGCAATGCACCGATCA+TGG + chr2.1:45511906-45511925 None:intergenic 45.0%
! CACATGAACTGCAGTTGATG+TGG - chr2.1:45511437-45511456 MS.gene068936:intron 45.0%
! TCTGGGATGGCTCAGAATTT+AGG - chr2.1:45511498-45511517 MS.gene068936:intron 45.0%
AGCCACACCTCCTTGAATTG+TGG - chr2.1:45512440-45512459 MS.gene068936:intron 50.0%
GGAACAGGAAGAGCTCGTTA+AGG - chr2.1:45512842-45512861 MS.gene068936:CDS 50.0%
TATGAGTGCAGTGCAGCAAG+TGG - chr2.1:45511043-45511062 MS.gene068936:intron 50.0%
TGCCACAATTCAAGGAGGTG+TGG + chr2.1:45512445-45512464 None:intergenic 50.0%
GCTCAGCGAGCGTTTGTGTT+AGG + chr2.1:45512154-45512173 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 45510900 45512914 45510900 ID=MS.gene068936
chr2.1 mRNA 45510900 45512914 45510900 ID=MS.gene068936.t1;Parent=MS.gene068936
chr2.1 exon 45512836 45512914 45512836 ID=MS.gene068936.t1.exon1;Parent=MS.gene068936.t1
chr2.1 CDS 45512836 45512914 45512836 ID=cds.MS.gene068936.t1;Parent=MS.gene068936.t1
chr2.1 exon 45512706 45512788 45512706 ID=MS.gene068936.t1.exon2;Parent=MS.gene068936.t1
chr2.1 CDS 45512706 45512788 45512706 ID=cds.MS.gene068936.t1;Parent=MS.gene068936.t1
chr2.1 exon 45512475 45512523 45512475 ID=MS.gene068936.t1.exon3;Parent=MS.gene068936.t1
chr2.1 CDS 45512475 45512523 45512475 ID=cds.MS.gene068936.t1;Parent=MS.gene068936.t1
chr2.1 exon 45512236 45512363 45512236 ID=MS.gene068936.t1.exon4;Parent=MS.gene068936.t1
chr2.1 CDS 45512236 45512363 45512236 ID=cds.MS.gene068936.t1;Parent=MS.gene068936.t1
chr2.1 exon 45511924 45512001 45511924 ID=MS.gene068936.t1.exon5;Parent=MS.gene068936.t1
chr2.1 CDS 45511924 45512001 45511924 ID=cds.MS.gene068936.t1;Parent=MS.gene068936.t1
chr2.1 exon 45511594 45511719 45511594 ID=MS.gene068936.t1.exon6;Parent=MS.gene068936.t1
chr2.1 CDS 45511594 45511719 45511594 ID=cds.MS.gene068936.t1;Parent=MS.gene068936.t1
chr2.1 exon 45510900 45510965 45510900 ID=MS.gene068936.t1.exon7;Parent=MS.gene068936.t1
chr2.1 CDS 45510900 45510965 45510900 ID=cds.MS.gene068936.t1;Parent=MS.gene068936.t1
Gene Sequence

>MS.gene068936

ATGACTGGGGAATCCAATAAATATGGAAACCCGTCTTCTGCACCAAAATATGATAGGGATGGAACCATAATGAGGTACAGTTTGTTCTTGTTCTTCTGGTAAACTTGTTCATATCATTTTTCCAAGGCCTGAACAAAATCCTTTATGAGTGCAGTGCAGCAAGTGGAAGCAAGAGATCAACAGATGGAGATCAAGATGATAGTAACAAAGTATGTTTATCGATTAATTTTTATATAAATGTGGTTGATGAATGTATTGTTTTCTGCCACTGTTATCTTAAGAAGTTAGAACACTTAGGAAATGAGTAGTTTATTAAAGCTTTAAAATTTTCTTTAGTACATGTTATATAAAATGTCGGCAAAAATGTCTAATTACATCCTTTCTTTTGCAGGATTCTCCTTTAAGTATGAAGAAGATATCTAACATGATTATTGGTGATGGTAAGATTATTGATTTTTCTTTTGATTATTTTATAATAAGACTTCATGCTTTATTTTGATATATAATTTGAATGTTCAGAAGGTGACTAATACAAAACACATGAACTGCAGTTGATGTGGCTAACAGTCTCGCACCTTGTTACTTTGTAGAAAATCCATCTGGGATGGCTCAGAATTTAGGGACAGTCGTCAAGGAATCTGACACTGACATTGATGTTGATGCTCAACTAAAAAATATGGTATTATAAAGTTTTATGCGCTTTCGTAGCATAAATGGAAAGTTTTTTTTTTTTTTTTTTGTGAATTAGCCAACCCTGTAAAATCTCTTTTGAATCATTATGATGTGCACATAGTTATAATCAGTTTTCGTGCATACATTTCAGAAAGTAAATCCCTTCTTAATGTTGCTAAGTTTAGTTGCATTTCTTGCACAATGTCTAGCAAAACCTATTTAGTTGAATTTCTTTTGACAGGAAGCTGATGAAATAAGAAAAGAAAGAAAAAGACTGTCAAACAGGAAATCAGCTCAAAGATCAAAGATAAAGAAACAGGTACATGCTTGACCATGATCGGTGCATTGCAACATTTATAAATAGTTGTATTGAGATGTCTATGAATTGGACAATGATTTGGTGGCATATGATTAAAATGTAAAAAGAAAAAGATGATCTGATTATCTAACTTCTGATGTGTTTGTTTGATGATCTATTTAACTTGTATTTCATTTGATGTTATCATTATTTGTGCCTTGTCAGAAAGAATATGAAGAGCAATGTCAAAAGATAAACACTCTTAAGGATGAAAATTTGGTCCTAACACAAACGCTCGCTGAGCTTTCAGAGAAATGTCTCGAGCTCACCAATGAAAACGATTCTATTGAGGTCAATCATTTTAACTCCCTTTCTTACTTGTTCAATTTTATATCATTCAATTAACAAGATACTTGTTTGATTTGAGAAATATTTTTTTCAATTAAAAAAATTCCATCCTGTTTCCTAATAGGAAAATGCTACTTCTCAAGAAAAATAGCTTCAAGAATTTTTCAAGACACAGTTGGCAAATTTTAATTGGATGATTTATTTGTCCACTTCCTATTTTTCAGCCACACCTCCTTGAATTGTGGCAAATAGTGCATTGTGATTGGCTACTCTTTATTCTTGAAGAATTCTTGATGTTATTTTTCCAGAGATATAGCATTGCTCTTCCTAATATTTGTATGAGAAACAATTAAATAAACTAAGATTCTTATGAATCCAAAAATCATAAGATGTCCATTAATGTAAACGATTCTATTGATCCCTCTTTGTAACAAACTTTCTAATAAACTAGTGCAACAAATAATCTAAGTTACCTAACATGAATGTAGCCAGGTTCATCTTGTTAAATGACAATTATTTATTTTCCAAGATTGGTTTATAAAGATGTTAATTCTCCGTATTGTGTTGTGGTTCTCAATGCTCTATTTTCCAAGATTGTTGCTAATTTGATTGTAATTTGGTGGTGGAACAGGAAGAGCTCGTTAAGGAGTATGGACCAGAATCAATTGCGGATCTATTGCATATGAATCCTACTTGA
Protein sequence

>MS.gene068936.t1

MTGESNKYGNPSSAPKYDRDGTIMRYSLNKILYECSAASGSKRSTDGDQDDSNKDSPLSMKKISNMIIGDVDVANSLAPCYFVENPSGMAQNLGTVVKESDTDIDVDAQLKNMEADEIRKERKRLSNRKSAQRSKIKKQKEYEEQCQKINTLKDENLVLTQTLAELSEKCLELTNENDSIEEELVKEYGPESIADLLHMNPT