AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene98608

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene98608.t1 MTR_4g052040 94.318 176 10 0 1 176 1 176 1.05e-113 320
MS.gene98608.t1 MTR_4g052060 67.956 181 46 4 1 176 1 174 5.83e-78 230
MS.gene98608.t1 MTR_5g079710 46.386 166 77 5 4 168 6 160 2.82e-40 137
MS.gene98608.t1 MTR_7g105790 34.759 187 104 4 1 176 1 180 2.70e-25 97.1
MS.gene98608.t1 MTR_0907s0020 60.870 69 27 0 101 169 104 172 4.01e-24 93.6
MS.gene98608.t1 MTR_5g075210 53.030 66 31 0 97 162 278 343 9.98e-15 70.9
MS.gene98608.t1 MTR_8g103520 42.857 77 44 0 92 168 217 293 5.11e-14 68.6
MS.gene98608.t1 MTR_7g072875 45.070 71 39 0 90 160 210 280 1.15e-13 67.8
MS.gene98608.t1 MTR_4g028930 49.180 61 31 0 100 160 315 375 1.43e-13 67.8
MS.gene98608.t1 MTR_7g072630 45.070 71 39 0 90 160 272 342 1.65e-13 67.8
MS.gene98608.t1 MTR_2g018030 40.000 65 39 0 96 160 274 338 2.99e-11 61.2
MS.gene98608.t1 MTR_3g111780 46.835 79 42 0 86 164 185 263 3.98e-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.gene98608.t1 AT3G52525 61.667 60 23 0 100 159 67 126 5.72e-21 84.7
MS.gene98608.t1 AT2G36026 55.738 61 27 0 104 164 91 151 1.24e-17 76.6
MS.gene98608.t1 AT5G19650 50.000 66 33 0 99 164 154 219 5.03e-15 70.5
MS.gene98608.t1 AT5G22240 44.595 74 39 1 100 171 97 170 3.73e-14 67.8
MS.gene98608.t1 AT1G06920 39.759 83 50 0 82 164 226 308 1.21e-13 67.8
MS.gene98608.t1 AT2G18500 46.875 64 34 0 97 160 224 287 2.17e-13 67.0
MS.gene98608.t1 AT5G58360 44.118 68 38 0 93 160 218 285 2.30e-13 67.0
MS.gene98608.t1 AT2G30400 46.875 64 34 0 97 160 250 313 9.20e-13 65.5
MS.gene98608.t1 AT5G01840 51.724 58 28 0 103 160 202 259 2.25e-12 63.9
MS.gene98608.t1 AT4G18830 46.552 58 31 0 102 159 285 342 5.32e-11 60.5

Find 34 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTCATTAGTGGGCTTTGTT+TGG 0.342399 4.2:+50134717 None:intergenic
GCAGTGCTACCAACCTTGTC+CGG 0.389497 4.2:+50134499 None:intergenic
CATATGTCATGAAGCTTTCC+CGG 0.390173 4.2:-50134518 MS.gene98608:CDS
CTCAATTCCAGTTGTTATCA+TGG 0.390489 4.2:-50134565 MS.gene98608:CDS
TTTCTCCACCACGACGTTCT+CGG 0.395337 4.2:-50134770 MS.gene98608:CDS
TTCATTAGTGGGCTTTGTTT+GGG 0.402789 4.2:+50134718 None:intergenic
GATAACACCATGATAACAAC+TGG 0.403158 4.2:+50134558 None:intergenic
GATCACAAACCCAAGTAGTA+AGG 0.415466 4.2:-50134857 MS.gene98608:CDS
GGTTCTTCAACTACAACTTC+AGG 0.425708 4.2:-50134835 MS.gene98608:CDS
ACAACTTCAGGTGAAGGATA+TGG 0.425803 4.2:-50134823 MS.gene98608:CDS
GTTGAAGAACCCTTACTACT+TGG 0.435315 4.2:+50134847 None:intergenic
ACCGCCACCGTGTTCATTAG+TGG 0.446501 4.2:+50134706 None:intergenic
CTATCGTCGATGCTACAAAC+GGG 0.480286 4.2:+50134799 None:intergenic
CGAGCCAAAGCCAACTCAAA+AGG 0.488426 4.2:-50134902 MS.gene98608:CDS
TTCACATCAAATGGAAGTTG+TGG 0.499142 4.2:-50134955 MS.gene98608:CDS
ATGATCTTCAAGATCTTCTC+CGG 0.511298 4.2:-50134600 MS.gene98608:CDS
ACTATCGTCGATGCTACAAA+CGG 0.524855 4.2:+50134798 None:intergenic
CCGCCACCGTGTTCATTAGT+GGG 0.525048 4.2:+50134707 None:intergenic
TTGAAGAACCCTTACTACTT+GGG 0.531511 4.2:+50134848 None:intergenic
TCATGAAGCTTTCCCGGACA+AGG 0.542749 4.2:-50134512 MS.gene98608:CDS
CAGTGCTACCAACCTTGTCC+GGG 0.561453 4.2:+50134500 None:intergenic
GAACACGGTGGCGGTAGAGA+AGG 0.563314 4.2:-50134698 MS.gene98608:CDS
GAATGTTTGAAATCATGATA+CGG 0.577874 4.2:+50134664 None:intergenic
TCAACTACAACTTCAGGTGA+AGG 0.579124 4.2:-50134829 MS.gene98608:CDS
GAAGCTTTCCCGGACAAGGT+TGG 0.580453 4.2:-50134508 MS.gene98608:CDS
ATCACAAACCCAAGTAGTAA+GGG 0.581401 4.2:-50134856 MS.gene98608:CDS
CCCACTAATGAACACGGTGG+CGG 0.643057 4.2:-50134707 MS.gene98608:CDS
AATTGAGATGAAGAAAACAC+CGG 0.659676 4.2:+50134581 None:intergenic
AACATCCGAGAACGTCGTGG+TGG 0.663722 4.2:+50134765 None:intergenic
GGCGGTAGAGAAGGACTCTG+AGG 0.686815 4.2:-50134689 MS.gene98608:CDS
GCTAACATCCGAGAACGTCG+TGG 0.690883 4.2:+50134762 None:intergenic
ACAAAGCCCACTAATGAACA+CGG 0.697529 4.2:-50134713 MS.gene98608:CDS
TATCGTCGATGCTACAAACG+GGG 0.740115 4.2:+50134800 None:intergenic
AAGCCCACTAATGAACACGG+TGG 0.804493 4.2:-50134710 MS.gene98608:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTTGATTAATAGAAAATT+TGG + chr4.2:50134595-50134614 None:intergenic 15.0%
!! ATGTGAAAAATGTTCTTATA+AGG + chr4.2:50134503-50134522 None:intergenic 20.0%
!! AGAACATTTTTCACATCAAA+TGG - chr4.2:50134507-50134526 MS.gene98608:CDS 25.0%
!! GAATGTTTGAAATCATGATA+CGG + chr4.2:50134810-50134829 None:intergenic 25.0%
!! TCTTATAAGGTTTTTCTTGT+TGG + chr4.2:50134490-50134509 None:intergenic 25.0%
AATTGAGATGAAGAAAACAC+CGG + chr4.2:50134893-50134912 None:intergenic 30.0%
ATCACAAACCCAAGTAGTAA+GGG - chr4.2:50134615-50134634 MS.gene98608:CDS 35.0%
ATGATCTTCAAGATCTTCTC+CGG - chr4.2:50134871-50134890 MS.gene98608:CDS 35.0%
CTCAATTCCAGTTGTTATCA+TGG - chr4.2:50134906-50134925 MS.gene98608:CDS 35.0%
GATAACACCATGATAACAAC+TGG + chr4.2:50134916-50134935 None:intergenic 35.0%
TTCACATCAAATGGAAGTTG+TGG - chr4.2:50134516-50134535 MS.gene98608:CDS 35.0%
TTGAAGAACCCTTACTACTT+GGG + chr4.2:50134626-50134645 None:intergenic 35.0%
!! GAAAATTTGGCCTTTTGAGT+TGG + chr4.2:50134582-50134601 None:intergenic 35.0%
!! TTCATTAGTGGGCTTTGTTT+GGG + chr4.2:50134756-50134775 None:intergenic 35.0%
ACAAAGCCCACTAATGAACA+CGG - chr4.2:50134758-50134777 MS.gene98608:CDS 40.0%
ACAACTTCAGGTGAAGGATA+TGG - chr4.2:50134648-50134667 MS.gene98608:CDS 40.0%
ACTATCGTCGATGCTACAAA+CGG + chr4.2:50134676-50134695 None:intergenic 40.0%
CATATGTCATGAAGCTTTCC+CGG - chr4.2:50134953-50134972 MS.gene98608:CDS 40.0%
GATCACAAACCCAAGTAGTA+AGG - chr4.2:50134614-50134633 MS.gene98608:CDS 40.0%
GGTTCTTCAACTACAACTTC+AGG - chr4.2:50134636-50134655 MS.gene98608:CDS 40.0%
GTTGAAGAACCCTTACTACT+TGG + chr4.2:50134627-50134646 None:intergenic 40.0%
TCAACTACAACTTCAGGTGA+AGG - chr4.2:50134642-50134661 MS.gene98608:CDS 40.0%
!! GTTCATTAGTGGGCTTTGTT+TGG + chr4.2:50134757-50134776 None:intergenic 40.0%
CTATCGTCGATGCTACAAAC+GGG + chr4.2:50134675-50134694 None:intergenic 45.0%
TATCGTCGATGCTACAAACG+GGG + chr4.2:50134674-50134693 None:intergenic 45.0%
!!! TTGGCCTTTTGAGTTGGCTT+TGG + chr4.2:50134576-50134595 None:intergenic 45.0%
AAGCCCACTAATGAACACGG+TGG - chr4.2:50134761-50134780 MS.gene98608:CDS 50.0%
CGAGCCAAAGCCAACTCAAA+AGG - chr4.2:50134569-50134588 MS.gene98608:CDS 50.0%
TCATGAAGCTTTCCCGGACA+AGG - chr4.2:50134959-50134978 MS.gene98608:CDS 50.0%
TTTCTCCACCACGACGTTCT+CGG - chr4.2:50134701-50134720 MS.gene98608:CDS 50.0%
AACATCCGAGAACGTCGTGG+TGG + chr4.2:50134709-50134728 None:intergenic 55.0%
ACCGCCACCGTGTTCATTAG+TGG + chr4.2:50134768-50134787 None:intergenic 55.0%
CAGTGCTACCAACCTTGTCC+GGG + chr4.2:50134974-50134993 None:intergenic 55.0%
CCCACTAATGAACACGGTGG+CGG - chr4.2:50134764-50134783 MS.gene98608:CDS 55.0%
CCGCCACCGTGTTCATTAGT+GGG + chr4.2:50134767-50134786 None:intergenic 55.0%
GAAGCTTTCCCGGACAAGGT+TGG - chr4.2:50134963-50134982 MS.gene98608:CDS 55.0%
GCAGTGCTACCAACCTTGTC+CGG + chr4.2:50134975-50134994 None:intergenic 55.0%
GCTAACATCCGAGAACGTCG+TGG + chr4.2:50134712-50134731 None:intergenic 55.0%
GGCGGTAGAGAAGGACTCTG+AGG - chr4.2:50134782-50134801 MS.gene98608:CDS 60.0%
! GAACACGGTGGCGGTAGAGA+AGG - chr4.2:50134773-50134792 MS.gene98608:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 50134480 50135013 50134480 ID=MS.gene98608
chr4.2 mRNA 50134480 50135013 50134480 ID=MS.gene98608.t1;Parent=MS.gene98608
chr4.2 exon 50134480 50135013 50134480 ID=MS.gene98608.t1.exon1;Parent=MS.gene98608.t1
chr4.2 CDS 50134480 50135013 50134480 ID=cds.MS.gene98608.t1;Parent=MS.gene98608.t1
Gene Sequence

>MS.gene98608

ATGTCTTCCAACAAGAAAAACCTTATAAGAACATTTTTCACATCAAATGGAAGTTGTGGATGTGCAAAAACAAAAGCAATTGAAGTACACGAGCCAAAGCCAACTCAAAAGGCCAAATTTTCTATTAATCAAAAGATCACAAACCCAAGTAGTAAGGGTTCTTCAACTACAACTTCAGGTGAAGGATATGGCCCCGTTTGTAGCATCGACGATAGTGATGATTTCTCCACCACGACGTTCTCGGATGTTAGCACAACAAACAACTACTCTGCACCCAAACAAAGCCCACTAATGAACACGGTGGCGGTAGAGAAGGACTCTGAGGATCCGTATCATGATTTCAAACATTCTATGCTTCAAATGATCTTTGAGAATGAGATCGATTTAGAAGATGATCTTCAAGATCTTCTCCGGTGTTTTCTTCATCTCAATTCCAGTTGTTATCATGGTGTTATCGTTAAAGTCTTCAATGACATATGTCATGAAGCTTTCCCGGACAAGGTTGGTAGCACTGCTGTCAAACCTTCCGAGTAA
Protein sequence

>MS.gene98608.t1

MSSNKKNLIRTFFTSNGSCGCAKTKAIEVHEPKPTQKAKFSINQKITNPSSKGSSTTTSGEGYGPVCSIDDSDDFSTTTFSDVSTTNNYSAPKQSPLMNTVAVEKDSEDPYHDFKHSMLQMIFENEIDLEDDLQDLLRCFLHLNSSCYHGVIVKVFNDICHEAFPDKVGSTAVKPSE