AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene47273

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene47273.t1 MTR_4g088015 66.667 54 17 1 121 174 220 272 3.06e-17 78.6
MS.gene47273.t1 MTR_3g463400 57.407 54 22 1 121 174 132 184 6.11e-15 72.0
MS.gene47273.t1 MTR_5g070020 57.407 54 22 1 121 174 121 173 1.50e-14 70.5
MS.gene47273.t1 MTR_5g049190 52.542 59 27 1 116 174 13 70 1.75e-14 69.3
MS.gene47273.t1 MTR_7g451170 57.407 54 22 1 121 174 190 242 2.94e-14 70.1
MS.gene47273.t1 MTR_7g037260 55.556 54 23 1 121 174 144 196 2.68e-13 67.0
MS.gene47273.t1 MTR_7g035350 52.727 55 25 1 120 174 223 276 3.23e-13 67.0
MS.gene47273.t1 MTR_3g077650 55.556 54 23 1 121 174 180 232 4.69e-13 66.6
MS.gene47273.t1 MTR_1g057980 56.364 55 22 2 121 174 78 131 7.90e-13 65.5
MS.gene47273.t1 MTR_4g105660 44.156 77 35 2 108 177 159 234 3.76e-12 63.9
MS.gene47273.t1 MTR_7g037130 51.852 54 25 1 121 174 144 196 2.73e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene47273.t1 AT3G27785 58.621 58 23 1 117 174 184 240 1.31e-15 73.9
MS.gene47273.t1 AT5G11050 55.556 54 23 1 121 174 104 156 4.27e-14 69.7
MS.gene47273.t1 AT5G58850 53.704 54 24 1 121 174 104 156 4.48e-14 69.7
MS.gene47273.t1 AT4G18770 47.541 61 31 1 114 174 209 268 1.34e-13 68.2
MS.gene47273.t1 AT5G40360 50.769 65 30 2 111 174 146 209 9.02e-12 62.8

Find 37 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATATAGGGAACTTGTTAAAT+TGG 0.199609 6.3:-18983920 MS.gene47273:intron
CGCTCCAAACATGGATATTC+TGG 0.220757 6.3:+18984466 None:intergenic
TTCAAGATATTGGGATTATT+AGG 0.258151 6.3:+18984337 None:intergenic
TCATCTCCGTCCAAACATTA+AGG 0.270772 6.3:-18983806 MS.gene47273:CDS
TAGACGCCTATTCAAGATAT+TGG 0.282677 6.3:+18984327 None:intergenic
ATGATGACATGCCACGTAAA+TGG 0.337422 6.3:+18984284 None:intergenic
GGAACATAAACCTTAATGTT+TGG 0.342814 6.3:+18983796 None:intergenic
TTCATCAATCTTGCAATTTG+AGG 0.352946 6.3:+18983871 None:intergenic
AGACGCCTATTCAAGATATT+GGG 0.366416 6.3:+18984328 None:intergenic
ATAATCCCAATATCTTGAAT+AGG 0.420305 6.3:-18984333 MS.gene47273:CDS
GCATAAGCTTTGTTGACGTC+TGG 0.422118 6.3:+18984184 None:intergenic
CAAAACAGTGTCGTGATAGA+TGG 0.437524 6.3:-18983834 MS.gene47273:CDS
GAACGAGAATTGACCTTTGT+GGG 0.444047 6.3:+18984431 None:intergenic
AAATGGATGACATGCATGTT+TGG 0.446835 6.3:+18984301 None:intergenic
TTGTTGACGTCTGGTACAAA+TGG 0.468340 6.3:+18984193 None:intergenic
TATTAGGTACACTCAAGATA+TGG 0.470686 6.3:+18984353 None:intergenic
ACCATCTCGATGGAAACATC+TGG 0.493183 6.3:+18984228 None:intergenic
CTTATGCAATCAGAAAGAAA+TGG 0.496059 6.3:-18984168 MS.gene47273:CDS
CATAAACCTTAATGTTTGGA+CGG 0.508200 6.3:+18983800 None:intergenic
GTTAAATTGGTGAATCAACA+TGG 0.522743 6.3:-18983907 MS.gene47273:CDS
AAGGGATTGTTCTGAGGAGG+TGG 0.523100 6.3:+18984409 None:intergenic
GGAACGAGAATTGACCTTTG+TGG 0.525598 6.3:+18984430 None:intergenic
ACCAGATGTTTCCATCGAGA+TGG 0.544531 6.3:-18984229 MS.gene47273:CDS
TCGAAAGATTCAGAAATGAC+AGG 0.550974 6.3:+18984253 None:intergenic
TGAATCACACGCTCCAAACA+TGG 0.559827 6.3:+18984457 None:intergenic
AACAAGGGATTGTTCTGAGG+AGG 0.564533 6.3:+18984406 None:intergenic
TTGAGATGGTAGTTTAACAA+GGG 0.576755 6.3:+18984391 None:intergenic
TTTAACAAGGGATTGTTCTG+AGG 0.590649 6.3:+18984403 None:intergenic
CATGTAAATTAGTGTTGAGA+TGG 0.594522 6.3:+18984377 None:intergenic
TGTTAAGAAAACCATCTCGA+TGG 0.597227 6.3:+18984218 None:intergenic
GTTGAGATGGTAGTTTAACA+AGG 0.598487 6.3:+18984390 None:intergenic
AAAGAAATGGACAACCAATG+AGG 0.657128 6.3:-18984155 MS.gene47273:CDS
TTAAATTGGTGAATCAACAT+GGG 0.666593 6.3:-18983906 MS.gene47273:CDS
ATTGCAAGATTGATGAAGCG+AGG 0.667312 6.3:-18983865 MS.gene47273:CDS
AACGAGAATTGACCTTTGTG+GGG 0.672668 6.3:+18984432 None:intergenic
ATGCATGTCATCCATTTACG+TGG 0.700922 6.3:-18984295 MS.gene47273:CDS
GTGTGATTCATACCCCACAA+AGG 0.701235 6.3:-18984444 MS.gene47273:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAATTGTGATTTCATATA+GGG - chr6.3:18984377-18984396 MS.gene47273:CDS 15.0%
!!! AGGTTTTTTTAATGTTAAAA+TGG - chr6.3:18984339-18984358 MS.gene47273:CDS 15.0%
!!! GGTTTTTTTAATGTTAAAAT+GGG - chr6.3:18984340-18984359 MS.gene47273:CDS 15.0%
!!! GTTTTTTTAATGTTAAAATG+GGG - chr6.3:18984341-18984360 MS.gene47273:CDS 15.0%
!! AACCTTATATTGATGAAAAA+TGG + chr6.3:18984324-18984343 None:intergenic 20.0%
!! CTTAAATTGTGATTTCATAT+AGG - chr6.3:18984376-18984395 MS.gene47273:CDS 20.0%
!! TATAGAAAAAATCCAAAGAA+AGG + chr6.3:18984235-18984254 None:intergenic 20.0%
!!! TACCATTTTTCATCAATATA+AGG - chr6.3:18984319-18984338 MS.gene47273:CDS 20.0%
!!! TTTATCTTTTTTCCTTTCTT+TGG - chr6.3:18984220-18984239 MS.gene47273:CDS 20.0%
! ATAATCCCAATATCTTGAAT+AGG - chr6.3:18983979-18983998 MS.gene47273:intron 25.0%
! TTAAATTGGTGAATCAACAT+GGG - chr6.3:18984406-18984425 MS.gene47273:CDS 25.0%
! TTCAAGATATTGGGATTATT+AGG + chr6.3:18983978-18983997 None:intergenic 25.0%
!! ATTCTGGAAAAAGATTCAAA+AGG + chr6.3:18983833-18983852 None:intergenic 25.0%
!! TTTTACATACATATCCTCAT+TGG + chr6.3:18984174-18984193 None:intergenic 25.0%
!!! ATATAGGGAACTTGTTAAAT+TGG - chr6.3:18984392-18984411 MS.gene47273:CDS 25.0%
CATAAACCTTAATGTTTGGA+CGG + chr6.3:18984515-18984534 None:intergenic 30.0%
CTTATGCAATCAGAAAGAAA+TGG - chr6.3:18984144-18984163 MS.gene47273:intron 30.0%
GGAACATAAACCTTAATGTT+TGG + chr6.3:18984519-18984538 None:intergenic 30.0%
GTTAAATTGGTGAATCAACA+TGG - chr6.3:18984405-18984424 MS.gene47273:CDS 30.0%
TATTAGGTACACTCAAGATA+TGG + chr6.3:18983962-18983981 None:intergenic 30.0%
TTCATCAATCTTGCAATTTG+AGG + chr6.3:18984444-18984463 None:intergenic 30.0%
TTGAGATGGTAGTTTAACAA+GGG + chr6.3:18983924-18983943 None:intergenic 30.0%
! CATGTAAATTAGTGTTGAGA+TGG + chr6.3:18983938-18983957 None:intergenic 30.0%
! TTTTCCAGAATATCCATGTT+TGG - chr6.3:18983842-18983861 MS.gene47273:CDS 30.0%
AAAGAAATGGACAACCAATG+AGG - chr6.3:18984157-18984176 MS.gene47273:CDS 35.0%
AAATGGATGACATGCATGTT+TGG + chr6.3:18984014-18984033 None:intergenic 35.0%
AGACGCCTATTCAAGATATT+GGG + chr6.3:18983987-18984006 None:intergenic 35.0%
CTACCAATAATTGAACAGTG+CGG + chr6.3:18984290-18984309 None:intergenic 35.0%
GTTGAGATGGTAGTTTAACA+AGG + chr6.3:18983925-18983944 None:intergenic 35.0%
TAACCGCACTGTTCAATTAT+TGG - chr6.3:18984284-18984303 MS.gene47273:CDS 35.0%
TAGACGCCTATTCAAGATAT+TGG + chr6.3:18983988-18984007 None:intergenic 35.0%
TCGAAAGATTCAGAAATGAC+AGG + chr6.3:18984062-18984081 None:intergenic 35.0%
TGTTAAGAAAACCATCTCGA+TGG + chr6.3:18984097-18984116 None:intergenic 35.0%
TTTAACAAGGGATTGTTCTG+AGG + chr6.3:18983912-18983931 None:intergenic 35.0%
! ATCAACATGGGCTGAAAAAA+TGG - chr6.3:18984418-18984437 MS.gene47273:CDS 35.0%
AACGAGAATTGACCTTTGTG+GGG + chr6.3:18983883-18983902 None:intergenic 40.0%
ATGATGACATGCCACGTAAA+TGG + chr6.3:18984031-18984050 None:intergenic 40.0%
ATGCATGTCATCCATTTACG+TGG - chr6.3:18984017-18984036 MS.gene47273:intron 40.0%
ATTGCAAGATTGATGAAGCG+AGG - chr6.3:18984447-18984466 MS.gene47273:CDS 40.0%
CAAAACAGTGTCGTGATAGA+TGG - chr6.3:18984478-18984497 MS.gene47273:CDS 40.0%
GAACGAGAATTGACCTTTGT+GGG + chr6.3:18983884-18983903 None:intergenic 40.0%
TCATCTCCGTCCAAACATTA+AGG - chr6.3:18984506-18984525 MS.gene47273:CDS 40.0%
TTGTTGACGTCTGGTACAAA+TGG + chr6.3:18984122-18984141 None:intergenic 40.0%
ACCAGATGTTTCCATCGAGA+TGG - chr6.3:18984083-18984102 MS.gene47273:intron 45.0%
ACCATCTCGATGGAAACATC+TGG + chr6.3:18984087-18984106 None:intergenic 45.0%
CGCTCCAAACATGGATATTC+TGG + chr6.3:18983849-18983868 None:intergenic 45.0%
GGAACGAGAATTGACCTTTG+TGG + chr6.3:18983885-18983904 None:intergenic 45.0%
GTGTGATTCATACCCCACAA+AGG - chr6.3:18983868-18983887 MS.gene47273:CDS 45.0%
TGAATCACACGCTCCAAACA+TGG + chr6.3:18983858-18983877 None:intergenic 45.0%
!! AACAAGGGATTGTTCTGAGG+AGG + chr6.3:18983909-18983928 None:intergenic 45.0%
!! GCATAAGCTTTGTTGACGTC+TGG + chr6.3:18984131-18984150 None:intergenic 45.0%
!! AAGGGATTGTTCTGAGGAGG+TGG + chr6.3:18983906-18983925 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 18983792 18984542 18983792 ID=MS.gene47273
chr6.3 mRNA 18983792 18984542 18983792 ID=MS.gene47273.t1;Parent=MS.gene47273
chr6.3 exon 18984151 18984542 18984151 ID=MS.gene47273.t1.exon1;Parent=MS.gene47273.t1
chr6.3 CDS 18984151 18984542 18984151 ID=cds.MS.gene47273.t1;Parent=MS.gene47273.t1
chr6.3 exon 18983792 18983936 18983792 ID=MS.gene47273.t1.exon2;Parent=MS.gene47273.t1
chr6.3 CDS 18983792 18983936 18983792 ID=cds.MS.gene47273.t1;Parent=MS.gene47273.t1
Gene Sequence

>MS.gene47273

ATGGAACTCAATCTTAACAATCGAGCAAAGCATTCAAACCTTTTGAATCTTTTTCCAGAATATCCATGTTTGGAGCGTGTGATTCATACCCCACAAAGGTCAATTCTCGTTCCACCTCCTCAGAACAATCCCTTGTTAAACTACCATCTCAACACTAATTTACATGACCATATCTTGAGTGTACCTAATAATCCCAATATCTTGAATAGGCGTCTATCTCCAAACATGCATGTCATCCATTTACGTGGCATGTCATCATCATTATCGCCTGTCATTTCTGAATCTTTCGAAACCAGATGTTTCCATCGAGATGGTTTTCTTAACACTCCATTTGTACCAGACGTCAACAAAGCTTATGCAATCAGAAAGAAATGGACAACCAATGAGGATATGTATGTAAAATATTTATTCATTTCTTAATCTCTCTCTTTATCTTTTTTCCTTTCTTTGGATTTTTTCTATAAAAAAAAATATAATAGAATTAAATTACATTAACCGCACTGTTCAATTATTGGTAGTTTTATAGATACCATTTTTCATCAATATAAGGTTTTTTTAATGTTAAAATGGGGTGAGTGTTTAATCTTAAATTGTGATTTCATATAGGGAACTTGTTAAATTGGTGAATCAACATGGGCTGAAAAAATGGCCTCAAATTGCAAGATTGATGAAGCGAGGAAGAAATGCAAAACAGTGTCGTGATAGATGGCTCAATCATCTCCGTCCAAACATTAAGGTTTATGTTCCCTAA
Protein sequence

>MS.gene47273.t1

MELNLNNRAKHSNLLNLFPEYPCLERVIHTPQRSILVPPPQNNPLLNYHLNTNLHDHILSVPNNPNILNRRLSPNMHVIHLRGMSSSLSPVISESFETRCFHRDGFLNTPFVPDVNKAYAIRKKWTTNEDMELVKLVNQHGLKKWPQIARLMKRGRNAKQCRDRWLNHLRPNIKVYVP