AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene06906

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06906.t1 MTR_3g091700 87.967 241 16 4 1 237 30 261 1.92e-153 427
MS.gene06906.t1 MTR_3g435550 47.321 112 53 1 130 235 59 170 6.34e-30 110
MS.gene06906.t1 MTR_5g024070 38.400 125 59 2 124 230 190 314 1.51e-21 91.7
MS.gene06906.t1 MTR_3g091720 63.462 52 12 1 186 237 19 63 3.11e-13 63.2
MS.gene06906.t1 MTR_0140s0010 47.143 70 28 2 160 220 150 219 6.64e-12 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06906.t1 AT5G53040 57.143 105 45 0 130 234 148 252 1.05e-34 125
MS.gene06906.t1 AT5G66990 53.153 111 41 2 135 234 164 274 6.58e-32 118
MS.gene06906.t1 AT1G18790 49.565 115 48 1 127 231 125 239 2.88e-30 113
MS.gene06906.t1 AT1G74480 45.082 122 57 1 116 227 121 242 3.44e-29 111
MS.gene06906.t1 AT4G35590 32.593 135 71 2 114 228 169 303 2.21e-17 80.1
MS.gene06906.t1 AT4G35590 32.593 135 71 2 114 228 219 353 3.86e-17 79.7
MS.gene06906.t1 AT5G16100 37.113 97 53 1 118 206 342 438 6.46e-13 67.8

Find 41 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTAGCAGCCATTGTTAA+AGG 0.208533 3.2:+77132463 None:intergenic
AATGTTGTCTTGCCTGAGTT+GGG 0.325768 3.2:-77132715 MS.gene06906:CDS
CAATGTTGTCTTGCCTGAGT+TGG 0.335905 3.2:-77132716 MS.gene06906:CDS
ATGATTTCTTTGAGTTTGAT+TGG 0.342407 3.2:-77132867 MS.gene06906:CDS
GAAGATGTTGGAGAAACTTC+CGG 0.360968 3.2:-77131576 MS.gene06906:CDS
CAGCAATAGTCTCACCTTTG+TGG 0.390633 3.2:+77132683 None:intergenic
AAGATGTTGGAGAAACTTCC+GGG 0.393818 3.2:-77131575 MS.gene06906:CDS
TCATCATTCAAATCCATTCC+CGG 0.427588 3.2:+77131557 None:intergenic
TTGTGAAGAAAGAGAAGGAA+TGG 0.429732 3.2:-77132612 MS.gene06906:CDS
AGAATTGTCATTAGTTCCAT+TGG 0.430301 3.2:-77132581 MS.gene06906:CDS
CAGAAAACTGAGGAGCTTGA+TGG 0.447810 3.2:-77132374 MS.gene06906:CDS
GTACGAGTACTAGCATCATT+AGG 0.450426 3.2:-77132537 MS.gene06906:CDS
CTCGTACTGCTACTTGTACT+TGG 0.454025 3.2:+77132553 None:intergenic
GGTACTCATCGACAACCTTA+AGG 0.457457 3.2:-77132353 MS.gene06906:intron
GTTGGAGAAACTTCCGGGAA+TGG 0.462988 3.2:-77131570 MS.gene06906:CDS
CCTCAAAATTATTCTGATCA+AGG 0.463476 3.2:+77132755 None:intergenic
TGATTTCTTTGAGTTTGATT+GGG 0.465378 3.2:-77132866 MS.gene06906:CDS
TGTGAAGAAAGAGAAGGAAT+GGG 0.479018 3.2:-77132611 MS.gene06906:CDS
TGTTGTGTGATGCAGGAAAA+GGG 0.482015 3.2:-77131635 MS.gene06906:intron
ATGATGAAATCAAGAAGCTT+AGG 0.499327 3.2:-77131541 MS.gene06906:CDS
CTTGTACTTGGCAATGCCAA+TGG 0.515278 3.2:+77132565 None:intergenic
GGAGAAGCAAAAGAAGATGT+TGG 0.518512 3.2:-77131588 MS.gene06906:CDS
GCTTCTGTGAAAACTGAAAG+TGG 0.520217 3.2:-77132637 MS.gene06906:CDS
AACTCAAAGAAATCATCAAA+CGG 0.523633 3.2:+77132874 None:intergenic
GACTAAGGAAGTTGCCATGT+TGG 0.527747 3.2:-77131609 MS.gene06906:CDS
ATGTTGTCTTGCCTGAGTTG+GGG 0.533975 3.2:-77132714 MS.gene06906:CDS
GCAGGAAAAGGGTTTGACTA+AGG 0.541768 3.2:-77131624 MS.gene06906:intron
TGGTTGTAATGCCCCAACTC+AGG 0.557980 3.2:+77132703 None:intergenic
AATTATTCTGATCAAGGTGT+GGG 0.571228 3.2:+77132761 None:intergenic
CTCAGGCAAGACAACATTGA+GGG 0.577274 3.2:+77132720 None:intergenic
GTACTAGCATCATTAGGAAG+AGG 0.587268 3.2:-77132531 MS.gene06906:CDS
TATTCTGATCAAGGTGTGGG+AGG 0.607927 3.2:+77132764 None:intergenic
AAATTATTCTGATCAAGGTG+TGG 0.609905 3.2:+77132760 None:intergenic
GCAGGGAGCTCAATATCACT+AGG 0.629741 3.2:-77132405 MS.gene06906:CDS
GCTGCTAAGAAAATGAATGT+TGG 0.631864 3.2:-77132451 MS.gene06906:CDS
TCAGGCAAGACAACATTGAG+GGG 0.654617 3.2:+77132721 None:intergenic
ACTATTGCTGATGCTGAGAG+TGG 0.657284 3.2:-77132670 MS.gene06906:CDS
ACTCAGGCAAGACAACATTG+AGG 0.692460 3.2:+77132719 None:intergenic
GGGAGCTCAATATCACTAGG+TGG 0.701034 3.2:-77132402 MS.gene06906:CDS
TTGGGGCATTACAACCACAA+AGG 0.718163 3.2:-77132697 MS.gene06906:CDS
GGTGGCCTCACAGAAAACTG+AGG 0.738213 3.2:-77132384 MS.gene06906:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTAAAAAACATAAAAAAAT+TGG + chr3.2:77132350-77132369 None:intergenic 10.0%
!! AAAGAAAAAGAATATTCTTA+AGG + chr3.2:77132274-77132293 None:intergenic 15.0%
!! ATTAGTTATTTATTGTCAAA+TGG - chr3.2:77132692-77132711 MS.gene06906:CDS 15.0%
!! TCATGTAAAAATGATTACTT+TGG + chr3.2:77131546-77131565 None:intergenic 20.0%
! AAACCATTATTTACTCTGTT+TGG - chr3.2:77132094-77132113 MS.gene06906:intron 25.0%
! AACTCAAAGAAATCATCAAA+CGG + chr3.2:77131499-77131518 None:intergenic 25.0%
! AATCCAAACAGAGTAAATAA+TGG + chr3.2:77132100-77132119 None:intergenic 25.0%
! ACAACATAGAATATACCTTA+AGG + chr3.2:77132035-77132054 None:intergenic 25.0%
! ACACATCTTATATTCTCTTT+AGG - chr3.2:77132373-77132392 MS.gene06906:CDS 25.0%
! CATTTCAAATACATCTACAA+TGG - chr3.2:77132398-77132417 MS.gene06906:CDS 25.0%
! TAAAGAGAATATAAGATGTG+TGG + chr3.2:77132374-77132393 None:intergenic 25.0%
! TTTCATGTACTTGAAAATGT+GGG + chr3.2:77132077-77132096 None:intergenic 25.0%
!! ATGATTTCTTTGAGTTTGAT+TGG - chr3.2:77131503-77131522 MS.gene06906:CDS 25.0%
!! TATTCTATGTTGTTTGAGTT+TGG - chr3.2:77132042-77132061 MS.gene06906:intron 25.0%
!! TGATTTCTTTGAGTTTGATT+GGG - chr3.2:77131504-77131523 MS.gene06906:CDS 25.0%
!! TTTTGATGTTCCTTTAACAA+TGG - chr3.2:77131897-77131916 MS.gene06906:intron 25.0%
AAATTATTCTGATCAAGGTG+TGG + chr3.2:77131613-77131632 None:intergenic 30.0%
AATTATTCTGATCAAGGTGT+GGG + chr3.2:77131612-77131631 None:intergenic 30.0%
AGAATTGTCATTAGTTCCAT+TGG - chr3.2:77131789-77131808 MS.gene06906:intron 30.0%
ATGATGAAATCAAGAAGCTT+AGG - chr3.2:77132829-77132848 MS.gene06906:CDS 30.0%
CCTCAAAATTATTCTGATCA+AGG + chr3.2:77131618-77131637 None:intergenic 30.0%
GTTTCATGTACTTGAAAATG+TGG + chr3.2:77132078-77132097 None:intergenic 30.0%
TGGGAATGATAATTGAAACA+TGG - chr3.2:77132168-77132187 MS.gene06906:intron 30.0%
TTAGTTTCTTCGATAGTAGA+TGG - chr3.2:77132492-77132511 MS.gene06906:CDS 30.0%
TTCATGTACTTGAAAATGTG+GGG + chr3.2:77132076-77132095 None:intergenic 30.0%
! CCTTGATCAGAATAATTTTG+AGG - chr3.2:77131615-77131634 MS.gene06906:CDS 30.0%
! TGTACCTTAGACTAAGTTTT+TGG - chr3.2:77132133-77132152 MS.gene06906:intron 30.0%
!! CCTTTTGAAAAAAAGATGCA+GGG - chr3.2:77131948-77131967 MS.gene06906:intron 30.0%
!!! CCTGCATCTTTTTTTCAAAA+GGG + chr3.2:77131950-77131969 None:intergenic 30.0%
CTATGAAACATGACAACTCT+AGG - chr3.2:77132219-77132238 MS.gene06906:intron 35.0%
GCTGCTAAGAAAATGAATGT+TGG - chr3.2:77131919-77131938 MS.gene06906:intron 35.0%
GTTTCAATTATCATTCCCAG+CGG + chr3.2:77132167-77132186 None:intergenic 35.0%
TCATCATTCAAATCCATTCC+CGG + chr3.2:77132816-77132835 None:intergenic 35.0%
TGGACCAAAAACTTAGTCTA+AGG + chr3.2:77132140-77132159 None:intergenic 35.0%
TGTGAAGAAAGAGAAGGAAT+GGG - chr3.2:77131759-77131778 MS.gene06906:intron 35.0%
TTCTTAGCAGCCATTGTTAA+AGG + chr3.2:77131910-77131929 None:intergenic 35.0%
TTGTGAAGAAAGAGAAGGAA+TGG - chr3.2:77131758-77131777 MS.gene06906:intron 35.0%
TTTCAATTATCATTCCCAGC+GGG + chr3.2:77132166-77132185 None:intergenic 35.0%
! AAAATGTATCGACGCAACAA+TGG - chr3.2:77132433-77132452 MS.gene06906:CDS 35.0%
! CTTTGTTTCGACACTTAGAT+CGG - chr3.2:77132290-77132309 MS.gene06906:intron 35.0%
!! ATTGTTTTGTTGTGTGATGC+AGG - chr3.2:77132728-77132747 MS.gene06906:CDS 35.0%
!! CCCTTTTGAAAAAAAGATGC+AGG - chr3.2:77131947-77131966 MS.gene06906:intron 35.0%
!!! CCCTGCATCTTTTTTTCAAA+AGG + chr3.2:77131951-77131970 None:intergenic 35.0%
!!! TGGTTTTGTGAAGAAAGAGA+AGG - chr3.2:77131753-77131772 MS.gene06906:intron 35.0%
AAGATGTTGGAGAAACTTCC+GGG - chr3.2:77132795-77132814 MS.gene06906:CDS 40.0%
AATGTTGTCTTGCCTGAGTT+GGG - chr3.2:77131655-77131674 MS.gene06906:intron 40.0%
GAAGATGTTGGAGAAACTTC+CGG - chr3.2:77132794-77132813 MS.gene06906:CDS 40.0%
GCTTCTGTGAAAACTGAAAG+TGG - chr3.2:77131733-77131752 MS.gene06906:intron 40.0%
GGAGAAGCAAAAGAAGATGT+TGG - chr3.2:77132782-77132801 MS.gene06906:CDS 40.0%
GTACGAGTACTAGCATCATT+AGG - chr3.2:77131833-77131852 MS.gene06906:intron 40.0%
GTACTAGCATCATTAGGAAG+AGG - chr3.2:77131839-77131858 MS.gene06906:intron 40.0%
TGTTGTGTGATGCAGGAAAA+GGG - chr3.2:77132735-77132754 MS.gene06906:CDS 40.0%
TTGTTGTGTGATGCAGGAAA+AGG - chr3.2:77132734-77132753 MS.gene06906:CDS 40.0%
! CTTCTTTTGCTTCTCCAACA+TGG + chr3.2:77132778-77132797 None:intergenic 40.0%
ACTATTGCTGATGCTGAGAG+TGG - chr3.2:77131700-77131719 MS.gene06906:intron 45.0%
ACTCAGGCAAGACAACATTG+AGG + chr3.2:77131654-77131673 None:intergenic 45.0%
ATGTTGTCTTGCCTGAGTTG+GGG - chr3.2:77131656-77131675 MS.gene06906:intron 45.0%
CAATGTTGTCTTGCCTGAGT+TGG - chr3.2:77131654-77131673 MS.gene06906:intron 45.0%
CAGAAAACTGAGGAGCTTGA+TGG - chr3.2:77131996-77132015 MS.gene06906:intron 45.0%
CAGCAATAGTCTCACCTTTG+TGG + chr3.2:77131690-77131709 None:intergenic 45.0%
CTCAGGCAAGACAACATTGA+GGG + chr3.2:77131653-77131672 None:intergenic 45.0%
CTTGTACTTGGCAATGCCAA+TGG + chr3.2:77131808-77131827 None:intergenic 45.0%
GACTAAGGAAGTTGCCATGT+TGG - chr3.2:77132761-77132780 MS.gene06906:CDS 45.0%
GCAGGAAAAGGGTTTGACTA+AGG - chr3.2:77132746-77132765 MS.gene06906:CDS 45.0%
GGTACTCATCGACAACCTTA+AGG - chr3.2:77132017-77132036 MS.gene06906:intron 45.0%
TATTCTGATCAAGGTGTGGG+AGG + chr3.2:77131609-77131628 None:intergenic 45.0%
TCAGGCAAGACAACATTGAG+GGG + chr3.2:77131652-77131671 None:intergenic 45.0%
! AAGCTCCTCAGTTTTCTGTG+AGG + chr3.2:77131994-77132013 None:intergenic 45.0%
! CTCGTACTGCTACTTGTACT+TGG + chr3.2:77131820-77131839 None:intergenic 45.0%
! TTGGGGCATTACAACCACAA+AGG - chr3.2:77131673-77131692 MS.gene06906:intron 45.0%
GCAGGGAGCTCAATATCACT+AGG - chr3.2:77131965-77131984 MS.gene06906:intron 50.0%
GGGAGCTCAATATCACTAGG+TGG - chr3.2:77131968-77131987 MS.gene06906:intron 50.0%
GTTGGAGAAACTTCCGGGAA+TGG - chr3.2:77132800-77132819 MS.gene06906:CDS 50.0%
TGGTTGTAATGCCCCAACTC+AGG + chr3.2:77131670-77131689 None:intergenic 50.0%
TTATCATTCCCAGCGGGTCA+TGG + chr3.2:77132160-77132179 None:intergenic 50.0%
!! TTTTTGGTCCATGACCCGCT+GGG - chr3.2:77132149-77132168 MS.gene06906:intron 50.0%
GGTGGCCTCACAGAAAACTG+AGG - chr3.2:77131986-77132005 MS.gene06906:intron 55.0%
!!! GTTTTTGGTCCATGACCCGC+TGG - chr3.2:77132148-77132167 MS.gene06906:intron 55.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 77131484 77132908 77131484 ID=MS.gene06906
chr3.2 mRNA 77131484 77132908 77131484 ID=MS.gene06906.t1;Parent=MS.gene06906
chr3.2 exon 77132354 77132908 77132354 ID=MS.gene06906.t1.exon1;Parent=MS.gene06906.t1
chr3.2 CDS 77132354 77132908 77132354 ID=cds.MS.gene06906.t1;Parent=MS.gene06906.t1
chr3.2 exon 77131484 77131642 77131484 ID=MS.gene06906.t1.exon2;Parent=MS.gene06906.t1
chr3.2 CDS 77131484 77131642 77131484 ID=cds.MS.gene06906.t1;Parent=MS.gene06906.t1
Gene Sequence

>MS.gene06906

ATGGATGTTGCGCCGTTTGATGATTTCTTTGAGTTTGATTGGGCAACTCAATTTTCATACCAAAGTAATCATTTTTACATGAATGACTTCAATGATCTTGAAGATTTCAACTTTGATTTCAACCTCCCACACCTTGATCAGAATAATTTTGAGGTTGATCAAAAACCCCTCAATGTTGTCTTGCCTGAGTTGGGGCATTACAACCACAAAGGTGAGACTATTGCTGATGCTGAGAGTGGTTATGTTGAAGCTTCTGTGAAAACTGAAAGTGGTTTTGTGAAGAAAGAGAAGGAATGGGAGAATCAAGAATTGTCATTAGTTCCATTGGCATTGCCAAGTACAAGTAGCAGTACGAGTACTAGCATCATTAGGAAGAGGTCATCTTCATTGCAGTATGATGACATAAAGAAACATTTTGATGTTCCTTTAACAATGGCTGCTAAGAAAATGAATGTTGGTGTGACCCTTTTGAAAAAAAGATGCAGGGAGCTCAATATCACTAGGTGGCCTCACAGAAAACTGAGGAGCTTGATGGTACTCATCGACAACCTTAAGGTATATTCTATGTTGTTTGAGTTTGGTCACTCTGCCCCACATTTTCAAGTACATGAAACCATTATTTACTCTGTTTGGATTACTCATTTTTATTTGTACCTTAGACTAAGTTTTTGGTCCATGACCCGCTGGGAATGATAATTGAAACATGGTATATAGTTGTCAATTATGTGTCATTAGCTATGAAACATGACAACTCTAGGATCAGACGTGTCAGATATCTCATACAAATCCTTAAGAATATTCTTTTTCTTTGTTTCGACACTTAGATCGGTGTCTGACGTGTCACACAAACTAAGACAAGTGTTCCAATTTTTTTATGTTTTTTACTTCCACACATCTTATATTCTCTTTAGGCACATTTCAAATACATCTACAATGGTTAAAATTAAAAAAAATGTATCGACGCAACAATGGATTCATTACATTACATTAAATTTGACTACAATATTTTTAGTTTCTTCGATAGTAGATGGATAAATATATATCAAATTTTATTGCGTGTTGTTTTAATTTTTTTAATGAGACGAGTGACTCGATTTAAATACACATCTATTTATTTTGATTCTCAATTATGATTTTTTTTTATAATTAATAGATTAATATACGTGTATGCTGTCTCTGTCTTATGATTTTTACATGCTTCATAGTTCATTAGTTATTTATTGTCAAATGGTCAAAGATTTCATATTGTTTTGTTGTGTGATGCAGGAAAAGGGTTTGACTAAGGAAGTTGCCATGTTGGAGAAGCAAAAGAAGATGTTGGAGAAACTTCCGGGAATGGATTTGAATGATGAAATCAAGAAGCTTAGGCAAGCATGCTTTAAAGCTAATTACAAGAACAGAAAACTAATTGCTCTCTGTCCTTGA
Protein sequence

>MS.gene06906.t1

MDVAPFDDFFEFDWATQFSYQSNHFYMNDFNDLEDFNFDFNLPHLDQNNFEVDQKPLNVVLPELGHYNHKGETIADAESGYVEASVKTESGFVKKEKEWENQELSLVPLALPSTSSSTSTSIIRKRSSSLQYDDIKKHFDVPLTMAAKKMNVGVTLLKKRCRELNITRWPHRKLRSLMVLIDNLKEKGLTKEVAMLEKQKKMLEKLPGMDLNDEIKKLRQACFKANYKNRKLIALCP