AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene83866

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83866.t1 MTR_4g088015 66.667 54 17 1 121 174 220 272 6.32e-17 77.4
MS.gene83866.t1 MTR_3g463400 59.259 54 21 1 121 174 132 184 3.77e-15 72.4
MS.gene83866.t1 MTR_5g070020 59.259 54 21 1 121 174 121 173 1.08e-14 70.9
MS.gene83866.t1 MTR_7g451170 59.259 54 21 1 121 174 190 242 2.16e-14 70.1
MS.gene83866.t1 MTR_5g049190 54.237 59 26 1 116 174 13 70 2.98e-14 68.6
MS.gene83866.t1 MTR_3g077650 57.407 54 22 1 121 174 180 232 2.80e-13 67.0
MS.gene83866.t1 MTR_7g035350 53.704 54 24 1 121 174 224 276 3.30e-13 67.0
MS.gene83866.t1 MTR_7g037260 55.556 54 23 1 121 174 144 196 5.53e-13 65.9
MS.gene83866.t1 MTR_4g105660 41.667 84 38 3 101 174 149 231 1.08e-12 65.5
MS.gene83866.t1 MTR_1g057980 52.830 53 24 1 122 174 80 131 2.95e-12 63.5
MS.gene83866.t1 MTR_7g037130 51.852 54 25 1 121 174 144 196 5.80e-11 60.1
MS.gene83866.t1 MTR_0008s0390 42.188 64 36 1 112 174 4 67 7.37e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83866.t1 AT3G27785 60.345 58 22 1 117 174 184 240 2.19e-15 73.2
MS.gene83866.t1 AT5G11050 57.407 54 22 1 121 174 104 156 3.36e-14 69.7
MS.gene83866.t1 AT5G58850 55.556 54 23 1 121 174 104 156 3.89e-14 69.7
MS.gene83866.t1 AT4G18770 49.180 61 30 1 114 174 209 268 1.83e-13 67.8
MS.gene83866.t1 AT5G40360 31.852 135 64 4 67 174 76 209 1.18e-12 65.1

Find 37 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATATAGGGAACTTGTGAAAT+TGG 0.218457 6.1:+9731478 MS.gene83866:intron
CGCTCCAAACATGGATATTC+TGG 0.220757 6.1:-9730852 None:intergenic
TTCAAGATATTGGGATTATT+AGG 0.258151 6.1:-9730981 None:intergenic
TAGACGCATGTTCAAGATAT+TGG 0.258678 6.1:-9730991 None:intergenic
TCATCTCCGTCCAAACATTA+AGG 0.270772 6.1:+9731592 MS.gene83866:CDS
GGAACATAAACCTTAATGTT+TGG 0.342814 6.1:-9731602 None:intergenic
CCAGACGTCAACAAAGCTTA+TGG 0.359040 6.1:+9731134 MS.gene83866:CDS
AGACGCATGTTCAAGATATT+GGG 0.359386 6.1:-9730990 None:intergenic
GTTTCCAGAATATCCATGTT+TGG 0.387556 6.1:+9730848 MS.gene83866:CDS
CCATAAGCTTTGTTGACGTC+TGG 0.394101 6.1:-9731134 None:intergenic
AAATGGATGACATGCATGTT+AGG 0.397171 6.1:-9731017 None:intergenic
TTCGTCAATCTTGCAATTTG+AGG 0.432664 6.1:-9731527 None:intergenic
CAAAACAGTGTCGTGATAGA+TGG 0.437524 6.1:+9731564 MS.gene83866:CDS
GAACGAGAATTGACCTTTGT+GGG 0.444047 6.1:-9730887 None:intergenic
ATGATGACATGCCACATAAA+TGG 0.444183 6.1:-9731034 None:intergenic
TATTAGGTACACTCAAGATA+TGG 0.470686 6.1:-9730965 None:intergenic
TTGTTGACGTCTGGTGCAAA+TGG 0.494806 6.1:-9731125 None:intergenic
CATAAACCTTAATGTTTGGA+CGG 0.508200 6.1:-9731598 None:intergenic
AAGGGATTGTTCTGAGGAGG+TGG 0.523100 6.1:-9730909 None:intergenic
GGAACGAGAATTGACCTTTG+TGG 0.525598 6.1:-9730888 None:intergenic
ATTCTGGAAACAGATTCAAA+AGG 0.540825 6.1:-9730836 None:intergenic
TCGAAAGATTGAGAAATGAC+AGG 0.547098 6.1:-9731065 None:intergenic
GTGAAATTGGTGAACCAACA+TGG 0.548528 6.1:+9731491 MS.gene83866:CDS
TGAATCACACGCTCCAAACA+TGG 0.559827 6.1:-9730861 None:intergenic
AACAAGGGATTGTTCTGAGG+AGG 0.564533 6.1:-9730912 None:intergenic
ATGCATGTCATCCATTTATG+TGG 0.566202 6.1:+9731023 MS.gene83866:CDS
TTGAGATGGTAGTTTAACAA+GGG 0.576755 6.1:-9730927 None:intergenic
TTTAACAAGGGATTGTTCTG+AGG 0.590649 6.1:-9730915 None:intergenic
CATGTAAATTAGTGTTGAGA+TGG 0.594522 6.1:-9730941 None:intergenic
GTTGAGATGGTAGTTTAACA+AGG 0.598487 6.1:-9730928 None:intergenic
ACAAAGCTTATGGAATCAGA+AGG 0.604961 6.1:+9731144 MS.gene83866:CDS
ATTGCAAGATTGACGAAGCG+AGG 0.637873 6.1:+9731533 MS.gene83866:CDS
TGAAATTGGTGAACCAACAT+GGG 0.667572 6.1:+9731492 MS.gene83866:CDS
CTTATGGAATCAGAAGGCAA+TGG 0.671225 6.1:+9731150 MS.gene83866:CDS
AACGAGAATTGACCTTTGTG+GGG 0.672668 6.1:-9730886 None:intergenic
AAGGCAATGGACAACCAATG+AGG 0.693483 6.1:+9731163 MS.gene83866:CDS
GTGTGATTCATACCCCACAA+AGG 0.701235 6.1:+9730874 MS.gene83866:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGGTTTTTTAATGTTAAAA+GGG + chr6.1:9731345-9731364 MS.gene83866:intron 15.0%
!!! TAAGGTTTTTTAATGTTAAA+AGG + chr6.1:9731344-9731363 MS.gene83866:intron 15.0%
!!! TTAATTTGTGATTTCATATA+GGG + chr6.1:9731463-9731482 MS.gene83866:intron 15.0%
!! CTTGAAAAAATCCAAATAAA+GGG - chr6.1:9731240-9731259 None:intergenic 20.0%
!! TCTTGAAAAAATCCAAATAA+AGG - chr6.1:9731241-9731260 None:intergenic 20.0%
!!! AGGTTTTTTAATGTTAAAAG+GGG + chr6.1:9731346-9731365 MS.gene83866:intron 20.0%
!!! CTTAATTTGTGATTTCATAT+AGG + chr6.1:9731462-9731481 MS.gene83866:intron 20.0%
!!! TATATCTTTTTCCCTTTATT+TGG + chr6.1:9731226-9731245 MS.gene83866:intron 20.0%
! AACCTTATATTGACGAAAAA+TGG - chr6.1:9731331-9731350 None:intergenic 25.0%
! TTCAAGATATTGGGATTATT+AGG - chr6.1:9730984-9731003 None:intergenic 25.0%
!! GAGTGTTTAATCTTAATTTG+TGG + chr6.1:9731371-9731390 MS.gene83866:intron 25.0%
!! TTTTACATACATATCCTCAT+TGG - chr6.1:9731180-9731199 None:intergenic 25.0%
!!! GGTTTTTTAATGTTAAAAGG+GGG + chr6.1:9731347-9731366 MS.gene83866:intron 25.0%
!!! TACCATTTTTCGTCAATATA+AGG + chr6.1:9731326-9731345 MS.gene83866:intron 25.0%
ATATAGGGAACTTGTGAAAT+TGG + chr6.1:9731478-9731497 MS.gene83866:intron 30.0%
TATTAGGTACACTCAAGATA+TGG - chr6.1:9730968-9730987 None:intergenic 30.0%
TTGAGATGGTAGTTTAACAA+GGG - chr6.1:9730930-9730949 None:intergenic 30.0%
! ATTCTGGAAACAGATTCAAA+AGG - chr6.1:9730839-9730858 None:intergenic 30.0%
! CATGTAAATTAGTGTTGAGA+TGG - chr6.1:9730944-9730963 None:intergenic 30.0%
! TAACTGTGCTGTTCAATTAT+TGG + chr6.1:9731291-9731310 MS.gene83866:intron 30.0%
!!! TGTTGAGAAAAGCATTTTGA+TGG - chr6.1:9731103-9731122 None:intergenic 30.0%
AAATGGATGACATGCATGTT+AGG - chr6.1:9731020-9731039 None:intergenic 35.0%
ACAAAGCTTATGGAATCAGA+AGG + chr6.1:9731144-9731163 MS.gene83866:CDS 35.0%
AGACGCATGTTCAAGATATT+GGG - chr6.1:9730993-9731012 None:intergenic 35.0%
ATGATGACATGCCACATAAA+TGG - chr6.1:9731037-9731056 None:intergenic 35.0%
ATGCATGTCATCCATTTATG+TGG + chr6.1:9731023-9731042 MS.gene83866:CDS 35.0%
GTTGAGATGGTAGTTTAACA+AGG - chr6.1:9730931-9730950 None:intergenic 35.0%
GTTTCCAGAATATCCATGTT+TGG + chr6.1:9730848-9730867 MS.gene83866:CDS 35.0%
TAGACGCATGTTCAAGATAT+TGG - chr6.1:9730994-9731013 None:intergenic 35.0%
TCGAAAGATTGAGAAATGAC+AGG - chr6.1:9731068-9731087 None:intergenic 35.0%
TGAAATTGGTGAACCAACAT+GGG + chr6.1:9731492-9731511 MS.gene83866:CDS 35.0%
TTCGTCAATCTTGCAATTTG+AGG - chr6.1:9731530-9731549 None:intergenic 35.0%
TTTAACAAGGGATTGTTCTG+AGG - chr6.1:9730918-9730937 None:intergenic 35.0%
!! AGCATTTTGATGGAAACATC+TGG - chr6.1:9731093-9731112 None:intergenic 35.0%
AACGAGAATTGACCTTTGTG+GGG - chr6.1:9730889-9730908 None:intergenic 40.0%
CAAAACAGTGTCGTGATAGA+TGG + chr6.1:9731564-9731583 MS.gene83866:CDS 40.0%
CTTATGGAATCAGAAGGCAA+TGG + chr6.1:9731150-9731169 MS.gene83866:CDS 40.0%
GAACGAGAATTGACCTTTGT+GGG - chr6.1:9730890-9730909 None:intergenic 40.0%
GTGAAATTGGTGAACCAACA+TGG + chr6.1:9731491-9731510 MS.gene83866:CDS 40.0%
! ACCAACATGGGCTGAAAAAA+TGG + chr6.1:9731504-9731523 MS.gene83866:CDS 40.0%
AAGGCAATGGACAACCAATG+AGG + chr6.1:9731163-9731182 MS.gene83866:CDS 45.0%
ATTGCAAGATTGACGAAGCG+AGG + chr6.1:9731533-9731552 MS.gene83866:CDS 45.0%
CCAGACGTCAACAAAGCTTA+TGG + chr6.1:9731134-9731153 MS.gene83866:CDS 45.0%
CGCTCCAAACATGGATATTC+TGG - chr6.1:9730855-9730874 None:intergenic 45.0%
GGAACGAGAATTGACCTTTG+TGG - chr6.1:9730891-9730910 None:intergenic 45.0%
GTGTGATTCATACCCCACAA+AGG + chr6.1:9730874-9730893 MS.gene83866:CDS 45.0%
TGAATCACACGCTCCAAACA+TGG - chr6.1:9730864-9730883 None:intergenic 45.0%
TTGTTGACGTCTGGTGCAAA+TGG - chr6.1:9731128-9731147 None:intergenic 45.0%
!! AACAAGGGATTGTTCTGAGG+AGG - chr6.1:9730915-9730934 None:intergenic 45.0%
!! CCATAAGCTTTGTTGACGTC+TGG - chr6.1:9731137-9731156 None:intergenic 45.0%
!!! GCCATTTTTTCAGCCCATGT+TGG - chr6.1:9731508-9731527 None:intergenic 45.0%
!! AAGGGATTGTTCTGAGGAGG+TGG - chr6.1:9730912-9730931 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 9730798 9731613 9730798 ID=MS.gene83866
chr6.1 mRNA 9730798 9731613 9730798 ID=MS.gene83866.t1;Parent=MS.gene83866
chr6.1 exon 9730798 9731189 9730798 ID=MS.gene83866.t1.exon1;Parent=MS.gene83866.t1
chr6.1 CDS 9730798 9731189 9730798 ID=cds.MS.gene83866.t1;Parent=MS.gene83866.t1
chr6.1 exon 9731484 9731613 9731484 ID=MS.gene83866.t1.exon2;Parent=MS.gene83866.t1
chr6.1 CDS 9731484 9731613 9731484 ID=cds.MS.gene83866.t1;Parent=MS.gene83866.t1
Gene Sequence

>MS.gene83866

ATGGAACTCAATATTAACAATCGAGCAAAGCATTCAAACCTTTTGAATCTGTTTCCAGAATATCCATGTTTGGAGCGTGTGATTCATACCCCACAAAGGTCAATTCTCGTTCCACCTCCTCAGAACAATCCCTTGTTAAACTACCATCTCAACACTAATTTACATGACCATATCTTGAGTGTACCTAATAATCCCAATATCTTGAACATGCGTCTATCTCCTAACATGCATGTCATCCATTTATGTGGCATGTCATCATCAACATCGCCTGTCATTTCTCAATCTTTCGAAACCAGATGTTTCCATCAAAATGCTTTTCTCAACACTCCATTTGCACCAGACGTCAACAAAGCTTATGGAATCAGAAGGCAATGGACAACCAATGAGGATATGTATGTAAAATATTTATTCATTTCTTAATCTCTCTCTATATCTTTTTCCCTTTATTTGGATTTTTTCAAGAAAAAAAAAATATAATAGAATTAAATTACATTAACTGTGCTGTTCAATTATTGGTAGTTTTATAGATACCATTTTTCGTCAATATAAGGTTTTTTAATGTTAAAAGGGGGTGAGTGTTTAATCTTAATTTGTGGTAGTTTTATAGATACCATTTTTCGTCAATATAAGGTTTTTTAATGTTAAAAGGGGGTGAGTGTTTAATCTTAATTTGTGATTTCATATAGGGAACTTGTGAAATTGGTGAACCAACATGGGCTGAAAAAATGGCCTCAAATTGCAAGATTGACGAAGCGAGGAAGAAATGCAAAACAGTGTCGTGATAGATGGCTCAATCATCTCCGTCCAAACATTAAG
Protein sequence

>MS.gene83866.t1

MELNINNRAKHSNLLNLFPEYPCLERVIHTPQRSILVPPPQNNPLLNYHLNTNLHDHILSVPNNPNILNMRLSPNMHVIHLCGMSSSTSPVISQSFETRCFHQNAFLNTPFAPDVNKAYGIRRQWTTNEDMELVKLVNQHGLKKWPQIARLTKRGRNAKQCRDRWLNHLRPNIK