AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene34423

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene34423.t1 MTR_1g102380 94.611 167 9 0 1 167 1 167 2.57e-113 320
MS.gene34423.t1 MTR_0007s0330 38.816 152 90 2 17 167 4 153 2.66e-35 121
MS.gene34423.t1 MTR_0007s0330 39.474 152 89 2 17 167 16 165 5.22e-35 121
MS.gene34423.t1 MTR_1g102370 41.060 151 83 2 17 167 73 217 8.27e-32 114
MS.gene34423.t1 MTR_0007s0380 37.500 152 85 3 18 167 70 213 2.46e-29 108
MS.gene34423.t1 MTR_2g013920 27.703 148 103 2 23 170 12 155 1.30e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene34423.t1 AT5G51780 35.802 162 93 3 13 167 19 176 1.16e-25 97.8
MS.gene34423.t1 AT5G51780 35.256 156 90 3 19 167 2 153 1.77e-23 91.3
MS.gene34423.t1 AT5G51790 32.500 160 90 5 18 167 26 177 2.29e-22 89.0
MS.gene34423.t1 AT5G51790 32.500 160 90 5 18 167 26 177 2.42e-22 89.4
MS.gene34423.t1 AT5G51790 32.500 160 90 5 18 167 91 242 7.77e-22 89.0
MS.gene34423.t1 AT5G51790 32.500 160 90 5 18 167 91 242 8.38e-22 89.4
MS.gene34423.t1 AT1G12540 38.365 159 85 7 19 167 75 230 9.19e-22 89.0
MS.gene34423.t1 AT4G25410 32.258 155 87 3 24 167 48 195 1.05e-21 87.8
MS.gene34423.t1 AT4G25400 32.258 155 96 4 15 167 19 166 7.53e-21 84.7
MS.gene34423.t1 AT4G25400 32.215 149 94 3 19 167 25 166 8.64e-21 84.7
MS.gene34423.t1 AT1G62975 34.503 171 94 4 15 167 70 240 1.34e-20 85.5
MS.gene34423.t1 AT1G62975 34.503 171 94 4 15 167 70 240 1.79e-20 85.5

Find 27 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCACGTTTATCAGATTTAA+TGG 0.200332 1.2:-76161702 MS.gene34423:CDS
ACACACTTCACTACACTTGT+AGG 0.335290 1.2:+76161788 None:intergenic
TGTGTTACCAACCAAGTAAA+TGG 0.368730 1.2:-76161644 MS.gene34423:CDS
GTCAAGATTGATCTAATTCC+AGG 0.380052 1.2:-76161767 MS.gene34423:CDS
GAGAGATAAGATCAAAGAAA+TGG 0.392291 1.2:-76161855 MS.gene34423:CDS
AGTTCAAGTAGGGTTGAAAC+TGG 0.407760 1.2:-76161830 MS.gene34423:CDS
AAGACCTTGATGAGCTCAAA+AGG 0.412689 1.2:+76162069 None:intergenic
TTTATGCTGATTCAGATCTT+CGG 0.455944 1.2:+76162200 None:intergenic
AAGAAATGGTTAGTTCAAGT+AGG 0.512409 1.2:-76161841 MS.gene34423:CDS
AGAAATGGTTAGTTCAAGTA+GGG 0.521680 1.2:-76161840 MS.gene34423:CDS
ATAACAATTTCCACCCCACC+TGG 0.524411 1.2:+76161749 None:intergenic
GTGGAAATTGTTATATGTAG+TGG 0.547521 1.2:-76161740 MS.gene34423:CDS
ATGGAAATAATACTTCAAGA+AGG 0.552508 1.2:-76161683 MS.gene34423:CDS
TGATCTAATTCCAGGTGGGG+TGG 0.577334 1.2:-76161759 MS.gene34423:CDS
AGACCTTGATGAGCTCAAAA+GGG 0.578199 1.2:+76162070 None:intergenic
ATTTCATACTATTAAATCTG+AGG 0.580870 1.2:-76161615 MS.gene34423:intron
GCATAAAATATTAACTACAT+CGG 0.611900 1.2:-76162184 MS.gene34423:CDS
GATTGATCTAATTCCAGGTG+GGG 0.621637 1.2:-76161762 MS.gene34423:CDS
AGATTGATCTAATTCCAGGT+GGG 0.625836 1.2:-76161763 MS.gene34423:CDS
GCTCAAAAGGGAGTGAAGAA+CGG 0.633531 1.2:+76162082 None:intergenic
GTAGGGAAGTTGAAAAGCAA+AGG 0.634358 1.2:-76162137 MS.gene34423:CDS
AAAAGGGAGTGAAGAACGGA+GGG 0.640895 1.2:+76162086 None:intergenic
CGTTCAGTATCAGATCACAT+AGG 0.655166 1.2:-76161935 MS.gene34423:CDS
AGTATCAGATCACATAGGTG+AGG 0.667408 1.2:-76161930 MS.gene34423:CDS
CAAAAGGGAGTGAAGAACGG+AGG 0.674543 1.2:+76162085 None:intergenic
GGGAAGTTGAAAAGCAAAGG+AGG 0.678696 1.2:-76162134 MS.gene34423:CDS
AAGATTGATCTAATTCCAGG+TGG 0.682027 1.2:-76161764 MS.gene34423:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATATATATATATGTTATG+AGG - chr1.2:76161474-76161493 MS.gene34423:intron 10.0%
!!! GAATTTTGTAATTTTTTTTT+AGG - chr1.2:76162193-76162212 MS.gene34423:CDS 10.0%
!! AACTTAATAATTAATTAGCT+AGG + chr1.2:76161192-76161211 None:intergenic 15.0%
!!! ATTATTGTTGTTGAATATAT+AGG - chr1.2:76161325-76161344 MS.gene34423:intron 15.0%
!! ATTTCATACTATTAAATCTG+AGG - chr1.2:76161164-76161183 MS.gene34423:intron 20.0%
!! GCATAAAATATTAACTACAT+CGG - chr1.2:76160595-76160614 MS.gene34423:intron 20.0%
!! TTAAAGATATAGAGAACAAA+TGG - chr1.2:76161836-76161855 MS.gene34423:CDS 20.0%
!!! TAATTTTCTGCTTCAAAATT+TGG + chr1.2:76160888-76160907 None:intergenic 20.0%
!!! TCATAACATCTTTGATTTTA+GGG - chr1.2:76160817-76160836 MS.gene34423:intron 20.0%
!!! TCATGTTGATAAATAATAAG+AGG + chr1.2:76160757-76160776 None:intergenic 20.0%
!!! TTCATAACATCTTTGATTTT+AGG - chr1.2:76160816-76160835 MS.gene34423:intron 20.0%
!!! TTTGTAATTTTTTTTTAGGG+AGG - chr1.2:76162197-76162216 MS.gene34423:CDS 20.0%
! AATTCAAATCTACTCAGATA+CGG + chr1.2:76161966-76161985 None:intergenic 25.0%
! ATGGAAATAATACTTCAAGA+AGG - chr1.2:76161096-76161115 MS.gene34423:intron 25.0%
! CAAGATAAAATCAAGATTTG+TGG - chr1.2:76162054-76162073 MS.gene34423:intron 25.0%
! TAATGGTATATAACATAGAC+TGG + chr1.2:76161784-76161803 None:intergenic 25.0%
! TGCAAATTAAGACAGTTTAA+TGG + chr1.2:76161801-76161820 None:intergenic 25.0%
! TTCACGTTTATCAGATTTAA+TGG - chr1.2:76161077-76161096 MS.gene34423:intron 25.0%
!! ATCACGCAATTTTATTGTAA+AGG - chr1.2:76161396-76161415 MS.gene34423:intron 25.0%
!! ATTGTTGTTGAATATATAGG+TGG - chr1.2:76161328-76161347 MS.gene34423:intron 25.0%
!!! GAAATATTTTGCCATTTACT+TGG + chr1.2:76161149-76161168 None:intergenic 25.0%
AATTACATTCAGATCAACCA+AGG + chr1.2:76161635-76161654 None:intergenic 30.0%
ATGAGAAAAAGATGATTCGT+AGG - chr1.2:76160624-76160643 MS.gene34423:intron 30.0%
CTCTATATCTTTAAGCAACA+AGG + chr1.2:76161830-76161849 None:intergenic 30.0%
GAGAGATAAGATCAAAGAAA+TGG - chr1.2:76160924-76160943 MS.gene34423:intron 30.0%
GTAGTTGCATGTAAATCTAA+TGG + chr1.2:76161720-76161739 None:intergenic 30.0%
GTGGAAATTGTTATATGTAG+TGG - chr1.2:76161039-76161058 MS.gene34423:intron 30.0%
TAGAGAACAAATGGATAGAA+TGG - chr1.2:76161845-76161864 MS.gene34423:CDS 30.0%
TGAGAAAAAGATGATTCGTA+GGG - chr1.2:76160625-76160644 MS.gene34423:intron 30.0%
! AAGAAATGGTTAGTTCAAGT+AGG - chr1.2:76160938-76160957 MS.gene34423:intron 30.0%
! AGAAATGGTTAGTTCAAGTA+GGG - chr1.2:76160939-76160958 MS.gene34423:intron 30.0%
!! TATTTTGCCATTTACTTGGT+TGG + chr1.2:76161145-76161164 None:intergenic 30.0%
!! TGTTATATGTAGTGGTTTTG+AGG - chr1.2:76161047-76161066 MS.gene34423:intron 30.0%
!! TTTATGCTGATTCAGATCTT+CGG + chr1.2:76160582-76160601 None:intergenic 30.0%
AACATTGGAAGTCAGTTTAG+TGG + chr1.2:76162021-76162040 None:intergenic 35.0%
AAGATTGATCTAATTCCAGG+TGG - chr1.2:76161015-76161034 MS.gene34423:intron 35.0%
ACTCAGATACGGTTGTAAAA+TGG + chr1.2:76161955-76161974 None:intergenic 35.0%
AGATTGATCTAATTCCAGGT+GGG - chr1.2:76161016-76161035 MS.gene34423:intron 35.0%
GTCAAGATTGATCTAATTCC+AGG - chr1.2:76161012-76161031 MS.gene34423:intron 35.0%
TACCTTCGTTCATCAGATTA+AGG + chr1.2:76161693-76161712 None:intergenic 35.0%
TGTCTCAAGTTTGACAACAT+TGG + chr1.2:76162036-76162055 None:intergenic 35.0%
TGTGTTACCAACCAAGTAAA+TGG - chr1.2:76161135-76161154 MS.gene34423:intron 35.0%
! GTATATAACATAGACTGGTC+AGG + chr1.2:76161779-76161798 None:intergenic 35.0%
! TGAGGATTCTCAATTTTCCT+TGG - chr1.2:76161615-76161634 MS.gene34423:intron 35.0%
!! TCTAGGGTATTTCTGAGTTT+TGG - chr1.2:76161264-76161283 MS.gene34423:intron 35.0%
AAGACCTTGATGAGCTCAAA+AGG + chr1.2:76160713-76160732 None:intergenic 40.0%
ACACACTTCACTACACTTGT+AGG + chr1.2:76160994-76161013 None:intergenic 40.0%
AGACCTTGATGAGCTCAAAA+GGG + chr1.2:76160712-76160731 None:intergenic 40.0%
AGTATCAGATCACATAGGTG+AGG - chr1.2:76160849-76160868 MS.gene34423:intron 40.0%
AGTTCAAGTAGGGTTGAAAC+TGG - chr1.2:76160949-76160968 MS.gene34423:intron 40.0%
CGTTCAGTATCAGATCACAT+AGG - chr1.2:76160844-76160863 MS.gene34423:intron 40.0%
CTACTAACTCATCCACAACT+TGG - chr1.2:76161753-76161772 MS.gene34423:CDS 40.0%
GATTGATCTAATTCCAGGTG+GGG - chr1.2:76161017-76161036 MS.gene34423:intron 40.0%
GTAAATGTGTGACTGTGATG+AGG - chr1.2:76161597-76161616 MS.gene34423:intron 40.0%
GTAGGGAAGTTGAAAAGCAA+AGG - chr1.2:76160642-76160661 MS.gene34423:intron 40.0%
TACGATCTAGCTAGAGTCTA+GGG - chr1.2:76161248-76161267 MS.gene34423:intron 40.0%
TGCCTTAATCTGATGAACGA+AGG - chr1.2:76161688-76161707 MS.gene34423:CDS 40.0%
TGCTCAGCTGCAAAATAAAC+TGG - chr1.2:76161373-76161392 MS.gene34423:intron 40.0%
TTACGATCTAGCTAGAGTCT+AGG - chr1.2:76161247-76161266 MS.gene34423:intron 40.0%
TTTGCAGCTGAGCAAGATTA+AGG + chr1.2:76161367-76161386 None:intergenic 40.0%
!! AATTAACTTGTACCTGTGCG+TGG - chr1.2:76161552-76161571 MS.gene34423:intron 40.0%
!!! ATTTTTTTGTCTCCACGCAC+AGG + chr1.2:76161567-76161586 None:intergenic 40.0%
AAAAGGGAGTGAAGAACGGA+GGG + chr1.2:76160696-76160715 None:intergenic 45.0%
ATAACAATTTCCACCCCACC+TGG + chr1.2:76161033-76161052 None:intergenic 45.0%
GCTCAAAAGGGAGTGAAGAA+CGG + chr1.2:76160700-76160719 None:intergenic 45.0%
GGGAAGTTGAAAAGCAAAGG+AGG - chr1.2:76160645-76160664 MS.gene34423:intron 45.0%
! ACTCCCTTTTGAGCTCATCA+AGG - chr1.2:76160706-76160725 MS.gene34423:intron 45.0%
! GTGGCATTCACGTTAGTTTG+TGG - chr1.2:76162073-76162092 MS.gene34423:intron 45.0%
!!! AATTTTGTAATTTTTTTTTA+GGG - chr1.2:76162194-76162213 MS.gene34423:CDS 5.0%
CAAAAGGGAGTGAAGAACGG+AGG + chr1.2:76160697-76160716 None:intergenic 50.0%
TGATCTAATTCCAGGTGGGG+TGG - chr1.2:76161020-76161039 MS.gene34423:intron 50.0%
! AGACTGGTCAGGCCAAGTTG+TGG + chr1.2:76161768-76161787 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 76160575 76162226 76160575 ID=MS.gene34423
chr1.2 mRNA 76160575 76162226 76160575 ID=MS.gene34423.t1;Parent=MS.gene34423
chr1.2 exon 76162074 76162226 76162074 ID=MS.gene34423.t1.exon1;Parent=MS.gene34423.t1
chr1.2 CDS 76162074 76162226 76162074 ID=cds.MS.gene34423.t1;Parent=MS.gene34423.t1
chr1.2 exon 76161616 76161963 76161616 ID=MS.gene34423.t1.exon2;Parent=MS.gene34423.t1
chr1.2 CDS 76161616 76161963 76161616 ID=cds.MS.gene34423.t1;Parent=MS.gene34423.t1
chr1.2 exon 76160575 76160586 76160575 ID=MS.gene34423.t1.exon3;Parent=MS.gene34423.t1
chr1.2 CDS 76160575 76160586 76160575 ID=cds.MS.gene34423.t1;Parent=MS.gene34423.t1
Gene Sequence

>MS.gene34423

ATGGCCGAAGATCTGAATCAGCATAAAATATTAACTACATCGGACAATGATGAGAAAAAGATGATTCGTAGGGAAGTTGAAAAGCAAAGGAGGATGCAAATGTCTAGTCTATGTTCATCCCTCCGTTCTTCACTCCCTTTTGAGCTCATCAAGGTCTTTAATTAATTGTATTTTTTTTTCCTCTTATTATTTATCAACATGATGTTAATTGTAGTACATATTATTATATTATATTGTATTTTTCATAACATCTTTGATTTTAGGGTAAGCGTTCAGTATCAGATCACATAGGTGAGGCTGCAAATTATGTCCAAATTTTGAAGCAGAAAATTAATGAACTTGAAATAAAGAGAGATAAGATCAAAGAAATGGTTAGTTCAAGTAGGGTTGAAACTGGAAATGAATTATCAGCAGATCCTACAAGTGTAGTGAAGTGTGTCAAGATTGATCTAATTCCAGGTGGGGTGGAAATTGTTATATGTAGTGGTTTTGAGGATTGTAGTTCACGTTTATCAGATTTAATGGAAATAATACTTCAAGAAGGATGTGATGTTGTTCATTGTGTTACCAACCAAGTAAATGGCAAAATATTTCATACTATTAAATCTGAGGTACCTAGCTAATTAATTATTAAGTTACTTAGTTTTATTTTGTGTATACTAATTAGTTATATTACGATCTAGCTAGAGTCTAGGGTATTTCTGAGTTTTGGAATTTGCACAAGTTTAATTAATAAGCATATATATATGAATTATTGTTGTTGAATATATAGGTGGAGAACTTGACACGCCTTAATCTTGCTCAGCTGCAAAATAAACTGGATCACGCAATTTTATTGTAAAGGTAATCATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATGTTATGAGGAGTCGATCTCTAGTACAATCATATATATGATCAGTATTCTCAGTTTTCTTTTGTTAATTAACTTGTACCTGTGCGTGGAGACAAAAAAATTCTTATTGAAGTAAATGTGTGACTGTGATGAGGATTCTCAATTTTCCTTGGTTGATCTGAATGTAATTGTTACTAGTATTGATGTTTAGTTTTTTATTGCATGCCTTAATCTGATGAACGAAGGTAAAGACCATTAGATTTACATGCAACTACTTATTTCTCTTGACTACTAACTCATCCACAACTTGGCCTGACCAGTCTATGTTATATACCATTAAACTGTCTTAATTTGCATGTATTCCTTGTTGCTTAAAGATATAGAGAACAAATGGATAGAATGGTCACTATAGTTTTTAAAACAATGTTAATTTTTTTATAAAAAAAATTGAGAAAAGTTGAAATTATTATTAAAGTGATACAAATGACCATTTTACAACCGTATCTGAGTAGATTTGAATTATGTTCATTGAAATAGCGAAATCAAACTCTCGCCACTAAACTGACTTCCAATGTTGTCAAACTTGAGACAAGATAAAATCAAGATTTGTGGCATTCACGTTAGTTTGTGGACTTGTCTGATAAAAAAATTCATCTACATACTTTCTCATCATTCTCTTTATGTATATATGTTGCATGTAAAAATTGTGTTATTTTTAGTGCTAACTTGAATTTTGTAATTTTTTTTTAGGGAGGAGAATGA
Protein sequence

>MS.gene34423.t1

MAEDLNQHKILTTSDNDEKKMIRREVEKQRRMQMSSLCSSLRSSLPFELIKGKRSVSDHIGEAANYVQILKQKINELEIKRDKIKEMVSSSRVETGNELSADPTSVVKCVKIDLIPGGVEIVICSGFEDCSSRLSDLMEIILQEGCDVVHCVTNQVNGKIFHTIKSEGGE