AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene20812


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20812.t1 MTR_1g086940 97.826 92 2 0 1 92 213 304 2.98e-62 191
MS.gene20812.t1 MTR_7g109610 92.391 92 7 0 1 92 210 301 6.15e-58 180
MS.gene20812.t1 MTR_7g082980 55.714 70 31 0 1 70 181 250 5.01e-19 79.3
MS.gene20812.t1 MTR_5g026840 51.429 70 34 0 1 70 190 259 1.77e-18 77.8
MS.gene20812.t1 MTR_4g075100 44.944 89 49 0 1 89 147 235 2.79e-18 76.3
MS.gene20812.t1 MTR_4g069800 44.286 70 39 0 1 70 169 238 3.22e-13 62.8
MS.gene20812.t1 MTR_4g069800 44.286 70 39 0 1 70 201 270 3.86e-13 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20812.t1 AT1G02560 96.386 83 3 0 1 83 216 298 1.05e-53 169
MS.gene20812.t1 AT5G45390 52.857 70 33 0 1 70 181 250 5.98e-20 81.6
MS.gene20812.t1 AT1G66670 52.857 70 33 0 1 70 187 256 1.85e-17 75.1
MS.gene20812.t1 AT5G23140 39.560 91 53 2 1 90 150 239 8.03e-14 64.7
MS.gene20812.t1 AT1G11750 45.714 70 38 0 1 70 198 267 8.75e-14 64.7
MS.gene20812.t1 AT1G11750 45.714 70 38 0 1 70 216 285 1.36e-13 64.3
MS.gene20812.t1 AT4G17040 37.234 94 47 2 1 93 215 297 1.12e-11 59.3

Find 23 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCGATGAGTCCATATTCTT+TGG 0.288327 1.2:+65379683 None:intergenic
GCAAAAGAAGCCAAAGAATA+TGG 0.292792 1.2:-65379693 MS.gene20812:CDS
GATAGGACAGATACCCATTC+AGG 0.309008 1.2:+65379775 None:intergenic
GCAAACTGACATAGATATTC+AGG 0.327655 1.2:-65380235 MS.gene20812:intron
TAAACTTTGCCCAGTTTGAT+AGG 0.348450 1.2:+65379758 None:intergenic
GGGTATCTGTCCTATCAAAC+TGG 0.363774 1.2:-65379768 MS.gene20812:CDS
TCTCAAAGCTCTTCAGCCTT+TGG 0.393350 1.2:-65379643 MS.gene20812:CDS
CCCTCTTCTGCAGCTGCCAA+AGG 0.448770 1.2:+65379627 None:intergenic
CATCACAAGGCAAACCTGAA+TGG 0.459835 1.2:-65379789 MS.gene20812:CDS
ATCACAAGGCAAACCTGAAT+GGG 0.495914 1.2:-65379788 MS.gene20812:CDS
GCCTTTGGCAGCTGCAGAAG+AGG 0.529560 1.2:-65379628 MS.gene20812:CDS
ATGATTCATCAACCGCTTGG+TGG 0.536787 1.2:-65380270 MS.gene20812:CDS
CTGCAGAAGAGGGTAAAGAC+CGG 0.577540 1.2:-65379617 MS.gene20812:CDS
AAATGAAATGCTGCATCACA+AGG 0.584369 1.2:-65379802 MS.gene20812:CDS
CCTTTGGCAGCTGCAGAAGA+GGG 0.585082 1.2:-65379627 MS.gene20812:CDS
AAGTTTAGAGAAAATTAACC+AGG 0.591158 1.2:-65379742 MS.gene20812:CDS
GAAATTAGGAAATAATAGCC+CGG 0.595521 1.2:+65379598 None:intergenic
ATAATGATTCATCAACCGCT+TGG 0.597203 1.2:-65380273 MS.gene20812:CDS
TGCAGAAGAGGGTAAAGACC+GGG 0.605444 1.2:-65379616 MS.gene20812:CDS
GGTATCTGTCCTATCAAACT+GGG 0.622810 1.2:-65379767 MS.gene20812:CDS
AAAGAATATGGACTCATCGA+TGG 0.623110 1.2:-65379681 MS.gene20812:CDS
AAAGGCTGAAGAGCTTTGAG+AGG 0.630190 1.2:+65379645 None:intergenic
CCTCCTTGAAAACCACCAAG+CGG 0.689995 1.2:+65380258 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAATATTATCATGGTTTA+GGG + chr1.2:65379796-65379815 None:intergenic 15.0%
!!! TCTTTTTCATAGAAAATTAA+AGG - chr1.2:65379735-65379754 MS.gene20812:CDS 15.0%
!! AAAATAGGAATATAAGAGTA+TGG + chr1.2:65379836-65379855 None:intergenic 20.0%
!! AATAAAAATAGAACAGGTAT+AGG + chr1.2:65379865-65379884 None:intergenic 20.0%
!! ATAGATATTCAGGTATATAT+AGG - chr1.2:65379647-65379666 MS.gene20812:CDS 20.0%
!! GTTTAATATTATCATGGTTT+AGG + chr1.2:65379797-65379816 None:intergenic 20.0%
!!! ATTTTATCAAAAGAAACAAG+AGG + chr1.2:65379709-65379728 None:intergenic 20.0%
! AAGTTTAGAGAAAATTAACC+AGG - chr1.2:65380130-65380149 MS.gene20812:intron 25.0%
! GAATGGAATAAAAATAGAAC+AGG + chr1.2:65379871-65379890 None:intergenic 25.0%
! TTTGAACACCTATACAATAA+GGG - chr1.2:65379944-65379963 MS.gene20812:intron 25.0%
!! TTTTGAACACCTATACAATA+AGG - chr1.2:65379943-65379962 MS.gene20812:intron 25.0%
AAATAGAACAGGTATAGGAA+AGG + chr1.2:65379860-65379879 None:intergenic 30.0%
AGAAAATTAAAGGCTATCAC+AGG - chr1.2:65379745-65379764 MS.gene20812:CDS 30.0%
AGAGTATGGAACAATATTGT+GGG + chr1.2:65379822-65379841 None:intergenic 30.0%
AGGTATAGGAAAGGAAAAAT+AGG + chr1.2:65379851-65379870 None:intergenic 30.0%
GATGATATCCCTTATTGTAT+AGG + chr1.2:65379955-65379974 None:intergenic 30.0%
TGGGGAGTTTAATATTATCA+TGG + chr1.2:65379803-65379822 None:intergenic 30.0%
TTATGATTCATAATCCTCTC+AGG - chr1.2:65380046-65380065 MS.gene20812:intron 30.0%
TTGCACTCATGAAAAAATCA+CGG + chr1.2:65380163-65380182 None:intergenic 30.0%
! AAGAGTATGGAACAATATTG+TGG + chr1.2:65379823-65379842 None:intergenic 30.0%
!!! TTTTGGCTTTAGTTGGTTTT+TGG - chr1.2:65379901-65379920 MS.gene20812:intron 30.0%
AAAGAATATGGACTCATCGA+TGG - chr1.2:65380191-65380210 MS.gene20812:intron 35.0%
AAATGAAATGCTGCATCACA+AGG - chr1.2:65380070-65380089 MS.gene20812:intron 35.0%
ATCGATGAGTCCATATTCTT+TGG + chr1.2:65380192-65380211 None:intergenic 35.0%
ATGGTTTAGGGATAACTCAT+TGG + chr1.2:65379784-65379803 None:intergenic 35.0%
GAGTATGGAACAATATTGTG+GGG + chr1.2:65379821-65379840 None:intergenic 35.0%
GCAAAAGAAGCCAAAGAATA+TGG - chr1.2:65380179-65380198 MS.gene20812:intron 35.0%
GCAAACTGACATAGATATTC+AGG - chr1.2:65379637-65379656 MS.gene20812:CDS 35.0%
TAAACTTTGCCCAGTTTGAT+AGG + chr1.2:65380117-65380136 None:intergenic 35.0%
! CTAAAGCCAAAAGTATGACA+TGG + chr1.2:65379893-65379912 None:intergenic 35.0%
! TCCATTCCATGTCATACTTT+TGG - chr1.2:65379884-65379903 MS.gene20812:intron 35.0%
!!! GCTTTAGTTGGTTTTTGGAT+TGG - chr1.2:65379906-65379925 MS.gene20812:intron 35.0%
!!! GTCATACTTTTGGCTTTAGT+TGG - chr1.2:65379894-65379913 MS.gene20812:intron 35.0%
AAAAATCACGGTCTGTATCC+TGG + chr1.2:65380151-65380170 None:intergenic 40.0%
AGGTTTGTGCCATCAAATGA+GGG + chr1.2:65379689-65379708 None:intergenic 40.0%
ATCACAAGGCAAACCTGAAT+GGG - chr1.2:65380084-65380103 MS.gene20812:intron 40.0%
CTAACCAATCATGTCTTCCT+TGG + chr1.2:65379984-65380003 None:intergenic 40.0%
GGTATCTGTCCTATCAAACT+GGG - chr1.2:65380105-65380124 MS.gene20812:intron 40.0%
! CAAGGAAGACATGATTGGTT+AGG - chr1.2:65379982-65380001 MS.gene20812:intron 40.0%
! GCCAAAAGTATGACATGGAA+TGG + chr1.2:65379888-65379907 None:intergenic 40.0%
ATCATGTCTTCCTTGGCACA+TGG + chr1.2:65379977-65379996 None:intergenic 45.0%
ATGATTCATCAACCGCTTGG+TGG - chr1.2:65379602-65379621 MS.gene20812:CDS 45.0%
CAGCATTTCATTTGCCTGAG+AGG + chr1.2:65380063-65380082 None:intergenic 45.0%
CATCACAAGGCAAACCTGAA+TGG - chr1.2:65380083-65380102 MS.gene20812:intron 45.0%
GAGGTTTGTGCCATCAAATG+AGG + chr1.2:65379690-65379709 None:intergenic 45.0%
GATAGGACAGATACCCATTC+AGG + chr1.2:65380100-65380119 None:intergenic 45.0%
GGGTATCTGTCCTATCAAAC+TGG - chr1.2:65380104-65380123 MS.gene20812:intron 45.0%
GGTTTGTGCCATCAAATGAG+GGG + chr1.2:65379688-65379707 None:intergenic 45.0%
GTTTGTGCCATCAAATGAGG+GGG + chr1.2:65379687-65379706 None:intergenic 45.0%
TCTCAAAGCTCTTCAGCCTT+TGG - chr1.2:65380229-65380248 MS.gene20812:intron 45.0%
TGTGCCAAGGAAGACATGAT+TGG - chr1.2:65379977-65379996 MS.gene20812:intron 45.0%
TTTGTGCCATCAAATGAGGG+GGG + chr1.2:65379686-65379705 None:intergenic 45.0%
!! AAAGGCTGAAGAGCTTTGAG+AGG + chr1.2:65380230-65380249 None:intergenic 45.0%
AATGAGGGGGGGAAGAAAAC+AGG + chr1.2:65379674-65379693 None:intergenic 50.0%
ATGAGGGGGGGAAGAAAACA+GGG + chr1.2:65379673-65379692 None:intergenic 50.0%
CCTCCTTGAAAACCACCAAG+CGG + chr1.2:65379617-65379636 None:intergenic 50.0%
CTGCAGAAGAGGGTAAAGAC+CGG - chr1.2:65380255-65380274 MS.gene20812:CDS 50.0%
GGGATATCATCCATGTGCCA+AGG - chr1.2:65379964-65379983 MS.gene20812:intron 50.0%
TGCAGAAGAGGGTAAAGACC+GGG - chr1.2:65380256-65380275 MS.gene20812:CDS 50.0%
TTCTTCCCCCCCTCATTTGA+TGG - chr1.2:65379677-65379696 MS.gene20812:CDS 50.0%
TTGTGCCATCAAATGAGGGG+GGG + chr1.2:65379685-65379704 None:intergenic 50.0%
!! CAACCGCTTGGTGGTTTTCA+AGG - chr1.2:65379611-65379630 MS.gene20812:CDS 50.0%
!! CGCTTGGTGGTTTTCAAGGA+GGG - chr1.2:65379615-65379634 MS.gene20812:CDS 50.0%
CCTTTGGCAGCTGCAGAAGA+GGG - chr1.2:65380245-65380264 MS.gene20812:CDS 55.0%
!! CCGCTTGGTGGTTTTCAAGG+AGG - chr1.2:65379614-65379633 MS.gene20812:CDS 55.0%
CCCTCTTCTGCAGCTGCCAA+AGG + chr1.2:65380248-65380267 None:intergenic 60.0%
GCCTTTGGCAGCTGCAGAAG+AGG - chr1.2:65380244-65380263 MS.gene20812:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 65379602 65380292 65379602 ID=MS.gene20812
chr1.2 mRNA 65379602 65380292 65379602 ID=MS.gene20812.t1;Parent=MS.gene20812
chr1.2 exon 65380236 65380292 65380236 ID=MS.gene20812.t1.exon1;Parent=MS.gene20812.t1
chr1.2 CDS 65380236 65380292 65380236 ID=cds.MS.gene20812.t1;Parent=MS.gene20812.t1
chr1.2 exon 65379602 65379826 65379602 ID=MS.gene20812.t1.exon2;Parent=MS.gene20812.t1
chr1.2 CDS 65379602 65379826 65379602 ID=cds.MS.gene20812.t1;Parent=MS.gene20812.t1
Gene Sequence

>MS.gene20812

ATGATTCATCAACCGCTTGGTGGTTTTCAAGGAGGGCAAACTGACATAGATATTCAGGTATATATAGGCCCTGTTTTCTTCCCCCCCTCATTTGATGGCACAAACCTCTTGTTTCTTTTGATAAAATCATATATCTTTTTCATAGAAAATTAAAGGCTATCACAGGTAGCACTTGAAGTCCAATGAGTTATCCCTAAACCATGATAATATTAAACTCCCCACAATATTGTTCCATACTCTTATATTCCTATTTTTCCTTTCCTATACCTGTTCTATTTTTATTCCATTCCATGTCATACTTTTGGCTTTAGTTGGTTTTTGGATTGGATTTGATTAGTTGATTTTGAACACCTATACAATAAGGGATATCATCCATGTGCCAAGGAAGACATGATTGGTTAGGTTGTACAATTAATATTTTGCATAAGCATCATAAATTCACAATTATGATTCATAATCCTCTCAGGCAAATGAAATGCTGCATCACAAGGCAAACCTGAATGGGTATCTGTCCTATCAAACTGGGCAAAGTTTAGAGAAAATTAACCAGGATACAGACCGTGATTTTTTCATGAGTGCAAAAGAAGCCAAAGAATATGGACTCATCGATGGTGTCATCATGAATCCTCTCAAAGCTCTTCAGCCTTTGGCAGCTGCAGAAGAGGGTAAAGACCGGGCTATTATTTCCTAA

Protein sequence

>MS.gene20812.t1

MIHQPLGGFQGGQTDIDIQANEMLHHKANLNGYLSYQTGQSLEKINQDTDRDFFMSAKEAKEYGLIDGVIMNPLKALQPLAAAEEGKDRAIIS