AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene032647

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene032647.t1 MTR_7g117590 71.605 162 31 2 2 149 12 172 2.37e-78 230
MS.gene032647.t1 MTR_1g054470 52.778 144 42 4 2 145 23 140 1.74e-43 140
MS.gene032647.t1 MTR_2g012700 37.273 110 68 1 40 148 10 119 1.43e-28 102
MS.gene032647.t1 MTR_2g062330 39.655 116 65 3 34 148 27 138 6.23e-27 98.6
MS.gene032647.t1 MTR_5g071400 67.925 53 15 2 3 55 9 59 1.87e-17 72.8
MS.gene032647.t1 MTR_0010s0310 35.556 90 55 1 53 139 151 240 1.41e-15 71.6
MS.gene032647.t1 MTR_6g477950 37.255 102 60 3 48 148 46 144 2.02e-14 68.9
MS.gene032647.t1 MTR_5g078270 33.708 89 56 1 54 139 210 298 2.09e-13 66.2
MS.gene032647.t1 MTR_7g117585 36.905 84 50 2 68 149 64 146 5.89e-12 60.1
MS.gene032647.t1 MTR_6g087720 34.940 83 53 1 55 136 216 298 1.02e-11 61.6
MS.gene032647.t1 MTR_3g008190 29.167 96 67 1 54 148 6 101 1.09e-11 58.2
MS.gene032647.t1 MTR_5g071400 73.684 38 8 2 18 55 1 36 3.54e-11 55.8
MS.gene032647.t1 MTR_0010s0290 31.373 102 63 3 54 149 223 323 3.65e-11 60.1
MS.gene032647.t1 MTR_0010s0320 32.609 92 55 3 54 139 192 282 7.94e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCATCAACTATTCGAATTT+TGG 0.090848 6.3:+707435 None:intergenic
TACAGGTAATGGGTGAAAAT+TGG 0.209416 6.3:+707723 None:intergenic
CCATCGACTTCTTCTTCATT+TGG 0.245009 6.3:+707691 None:intergenic
GTGGATGGTTTGAGTTTGTT+AGG 0.256057 6.3:-707345 MS.gene032647:CDS
TACTTTGAATTGCAATCTTC+CGG 0.260223 6.3:+707473 None:intergenic
GGCTGTTGGACGGAGTGTTC+TGG 0.356206 6.3:-707593 MS.gene032647:intron
CGAATAGTTGATGATGAAAC+TGG 0.373610 6.3:-707427 MS.gene032647:CDS
GAATGTGAAGTTCGTGATAA+AGG 0.381874 6.3:-707394 MS.gene032647:CDS
ACTTTGAATTGCAATCTTCC+GGG 0.386700 6.3:+707474 None:intergenic
AAGTTCGTGATAAAGGAAAT+TGG 0.388847 6.3:-707387 MS.gene032647:CDS
ACAGGTAATGGGTGAAAATT+GGG 0.407202 6.3:+707724 None:intergenic
ATTAGTTCTGCTACGGCTGT+TGG 0.467637 6.3:-707607 MS.gene032647:CDS
TGGATGGTTTGAGTTTGTTA+GGG 0.477462 6.3:-707344 MS.gene032647:CDS
AAATGTCTTCTTCTAGTAGC+AGG 0.479507 6.3:-707854 MS.gene032647:intron
CTGCAGCCATGTAATTGATC+CGG 0.509939 6.3:-707764 MS.gene032647:intron
TTTGAAATTGTGCAGATACT+GGG 0.510532 6.3:+707668 None:intergenic
ATGGAGAAATACGTTGGTAG+TGG 0.538951 6.3:-707364 MS.gene032647:CDS
CCATGTAATTGATCCGGAGT+TGG 0.545499 6.3:-707758 MS.gene032647:CDS
GGCATCAATTCGTCCAACTC+CGG 0.549037 6.3:+707745 None:intergenic
CCAACTCCGGATCAATTACA+TGG 0.550497 6.3:+707758 None:intergenic
AGAAATACGTTGGTAGTGGA+TGG 0.551017 6.3:-707360 MS.gene032647:CDS
TCGTGATAAAGGAAATTGGA+TGG 0.565929 6.3:-707383 MS.gene032647:CDS
TGAATGTGTAGCATATTCCC+CGG 0.571619 6.3:-707492 MS.gene032647:intron
GCATAGTATTAGTTCTGCTA+CGG 0.580120 6.3:-707614 MS.gene032647:CDS
AGGGCAAAAGAACTCAAAGA+AGG 0.584629 6.3:-707325 MS.gene032647:CDS
GATACAAATAATTTGTGTGG+AGG 0.593345 6.3:+707274 None:intergenic
GTTCTGCTACGGCTGTTGGA+CGG 0.598239 6.3:-707603 MS.gene032647:CDS
CTTTGAATTGCAATCTTCCG+GGG 0.600541 6.3:+707475 None:intergenic
AATTGGATGGAGAAATACGT+TGG 0.604235 6.3:-707370 MS.gene032647:CDS
ACTGATACAAATAATTTGTG+TGG 0.607437 6.3:+707271 None:intergenic
CCAAATGAAGAAGAAGTCGA+TGG 0.658231 6.3:-707691 MS.gene032647:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAATTTCAAAAATTTCAAAA+CGG - chr6.3:707458-707477 MS.gene032647:CDS 15.0%
!!! AGTTTTAATTTTATTTTTGC+TGG - chr6.3:707545-707564 MS.gene032647:intron 15.0%
!!! TTTTTGTTTTTTTAATCTTC+TGG - chr6.3:707303-707322 MS.gene032647:CDS 15.0%
!! ACTGATACAAATAATTTGTG+TGG + chr6.3:707845-707864 None:intergenic 25.0%
!! ATCATCAACTATTCGAATTT+TGG + chr6.3:707681-707700 None:intergenic 25.0%
AAGTTCGTGATAAAGGAAAT+TGG - chr6.3:707726-707745 MS.gene032647:CDS 30.0%
TACTTTGAATTGCAATCTTC+CGG + chr6.3:707643-707662 None:intergenic 30.0%
! AAAACGGTGATCATACTTTT+TGG - chr6.3:707474-707493 MS.gene032647:CDS 30.0%
! GATACAAATAATTTGTGTGG+AGG + chr6.3:707842-707861 None:intergenic 30.0%
! TTTGAAATTGTGCAGATACT+GGG + chr6.3:707448-707467 None:intergenic 30.0%
!!! TTTTGAAATTGTGCAGATAC+TGG + chr6.3:707449-707468 None:intergenic 30.0%
AATTGGATGGAGAAATACGT+TGG - chr6.3:707743-707762 MS.gene032647:CDS 35.0%
ACTTTGAATTGCAATCTTCC+GGG + chr6.3:707642-707661 None:intergenic 35.0%
GAATGTGAAGTTCGTGATAA+AGG - chr6.3:707719-707738 MS.gene032647:CDS 35.0%
TCGTGATAAAGGAAATTGGA+TGG - chr6.3:707730-707749 MS.gene032647:CDS 35.0%
! GATTTTCGTCTACAGGTAAT+GGG + chr6.3:707403-707422 None:intergenic 35.0%
! TCATTTGGATTTTCGTCTAC+AGG + chr6.3:707410-707429 None:intergenic 35.0%
!! ACAGGTAATGGGTGAAAATT+GGG + chr6.3:707392-707411 None:intergenic 35.0%
!! CGAATAGTTGATGATGAAAC+TGG - chr6.3:707686-707705 MS.gene032647:CDS 35.0%
!! GCATAGTATTAGTTCTGCTA+CGG - chr6.3:707499-707518 MS.gene032647:intron 35.0%
!! TACAGGTAATGGGTGAAAAT+TGG + chr6.3:707393-707412 None:intergenic 35.0%
!! TGGATGGTTTGAGTTTGTTA+GGG - chr6.3:707769-707788 MS.gene032647:intron 35.0%
AGGGCAAAAGAACTCAAAGA+AGG - chr6.3:707788-707807 MS.gene032647:intron 40.0%
CCAAATGAAGAAGAAGTCGA+TGG - chr6.3:707422-707441 MS.gene032647:CDS 40.0%
CTTTGAATTGCAATCTTCCG+GGG + chr6.3:707641-707660 None:intergenic 40.0%
TGAATGTGTAGCATATTCCC+CGG - chr6.3:707621-707640 MS.gene032647:CDS 40.0%
TTGCTGGATTATTTGCGCAT+GGG - chr6.3:707561-707580 MS.gene032647:intron 40.0%
TTTGCTGGATTATTTGCGCA+TGG - chr6.3:707560-707579 MS.gene032647:intron 40.0%
! ATGGAGAAATACGTTGGTAG+TGG - chr6.3:707749-707768 MS.gene032647:CDS 40.0%
! GGATTTTCGTCTACAGGTAA+TGG + chr6.3:707404-707423 None:intergenic 40.0%
! GTGGATGGTTTGAGTTTGTT+AGG - chr6.3:707768-707787 MS.gene032647:intron 40.0%
!! AGAAATACGTTGGTAGTGGA+TGG - chr6.3:707753-707772 MS.gene032647:CDS 40.0%
!! CCATCGACTTCTTCTTCATT+TGG + chr6.3:707425-707444 None:intergenic 40.0%
CCAACTCCGGATCAATTACA+TGG + chr6.3:707358-707377 None:intergenic 45.0%
CCATGTAATTGATCCGGAGT+TGG - chr6.3:707355-707374 MS.gene032647:CDS 45.0%
CTGCAGCCATGTAATTGATC+CGG - chr6.3:707349-707368 MS.gene032647:CDS 45.0%
!! ATTAGTTCTGCTACGGCTGT+TGG - chr6.3:707506-707525 MS.gene032647:intron 45.0%
CTGGATTATTTGCGCATGGG+TGG - chr6.3:707564-707583 MS.gene032647:intron 50.0%
GATTATTTGCGCATGGGTGG+TGG - chr6.3:707567-707586 MS.gene032647:intron 50.0%
GGCATCAATTCGTCCAACTC+CGG + chr6.3:707371-707390 None:intergenic 50.0%
GTTCTGCTACGGCTGTTGGA+CGG - chr6.3:707510-707529 MS.gene032647:intron 55.0%
! GGCTGTTGGACGGAGTGTTC+TGG - chr6.3:707520-707539 MS.gene032647:intron 60.0%
! GCGCATGGGTGGTGGCTTTG+TGG - chr6.3:707575-707594 MS.gene032647:intron 65.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 707261 707874 707261 ID=MS.gene032647
chr6.3 mRNA 707261 707874 707261 ID=MS.gene032647.t1;Parent=MS.gene032647
chr6.3 exon 707855 707874 707855 ID=MS.gene032647.t1.exon1;Parent=MS.gene032647.t1
chr6.3 CDS 707855 707874 707855 ID=cds.MS.gene032647.t1;Parent=MS.gene032647.t1
chr6.3 exon 707594 707780 707594 ID=MS.gene032647.t1.exon2;Parent=MS.gene032647.t1
chr6.3 CDS 707594 707780 707594 ID=cds.MS.gene032647.t1;Parent=MS.gene032647.t1
chr6.3 exon 707261 707503 707261 ID=MS.gene032647.t1.exon3;Parent=MS.gene032647.t1
chr6.3 CDS 707261 707503 707261 ID=cds.MS.gene032647.t1;Parent=MS.gene032647.t1
Gene Sequence

>MS.gene032647

ATGTCTTCTTCTAGTAGCAGGTAACTTCAATGTTTGAGTTGTTTTTTGTTTTTTTAATCTTCTGGTTATTTATTAGATTTTGTTGAAACTGCAGCCATGTAATTGATCCGGAGTTGGACGAATTGATGCCCAATTTTCACCCATTACCTGTAGACGAAAATCCAAATGAAGAAGAAGTCGATGGCCCAGTATCTGCACAATTTCAAAAATTTCAAAACGGTGATCATACTTTTTGGATGCATAGTATTAGTTCTGCTACGGCTGTTGGACGGAGTGTTCTGGTTAGTTTTAATTTTATTTTTGCTGGATTATTTGCGCATGGGTGGTGGCTTTGTGGTTGAAAAGTAATATTATTTGTTTTGAATGTGTAGCATATTCCCCGGAAGATTGCAATTCAAAGTATGTATGTGAATCAATCCAAAATTCGAATAGTTGATGATGAAACTGGAGAAGAATATGAATGTGAAGTTCGTGATAAAGGAAATTGGATGGAGAAATACGTTGGTAGTGGATGGTTTGAGTTTGTTAGGGCAAAAGAACTCAAAGAAGGAGATTCGTTGTTCTTCACTATTGATAATCCTCCACACAAATTATTTGTATCAGTGATTAGATAG
Protein sequence

>MS.gene032647.t1

MSSSSSSHVIDPELDELMPNFHPLPVDENPNEEEVDGPVSAQFQKFQNGDHTFWMHSISSATAVGRSVLHIPRKIAIQSMYVNQSKIRIVDDETGEEYECEVRDKGNWMEKYVGSGWFEFVRAKELKEGDSLFFTIDNPPHKLFVSVIR