AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene60716

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene60716.t1 MTR_1g098170 100.000 152 0 0 1 152 1 152 6.47e-112 314
MS.gene60716.t1 MTR_1g098220 100.000 152 0 0 1 152 1 152 6.47e-112 314
MS.gene60716.t1 MTR_6g043210 98.684 152 2 0 1 152 1 152 6.70e-111 311
MS.gene60716.t1 MTR_1g492710 97.945 146 3 0 1 146 794 939 1.21e-97 303
MS.gene60716.t1 MTR_1g098220 99.160 119 1 0 1 119 1 119 2.71e-84 243
MS.gene60716.t1 MTR_5g027650 95.098 102 5 0 39 140 11 112 7.93e-69 203
MS.gene60716.t1 MTR_5g027580 93.137 102 7 0 39 140 48 149 7.08e-68 202
MS.gene60716.t1 MTR_5g027670 94.382 89 5 0 52 140 1 89 2.79e-58 176
MS.gene60716.t1 MTR_5g027615 94.382 89 5 0 52 140 1 89 7.00e-58 175
MS.gene60716.t1 MTR_5g027605 94.382 89 5 0 52 140 1 89 7.00e-58 175
MS.gene60716.t1 MTR_5g027640 94.382 89 5 0 52 140 1 89 7.00e-58 175
MS.gene60716.t1 MTR_5g027600 94.382 89 5 0 52 140 1 89 7.00e-58 175
MS.gene60716.t1 MTR_1005s0010 94.186 86 5 0 55 140 2 87 2.51e-56 171
MS.gene60716.t1 MTR_4g015960 70.270 74 15 2 68 137 10 80 2.32e-27 106
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene60716.t1 AT4G09800 92.763 152 11 0 1 152 1 152 1.89e-105 298
MS.gene60716.t1 AT1G34030 92.763 152 11 0 1 152 1 152 1.89e-105 298
MS.gene60716.t1 AT1G22780 92.763 152 11 0 1 152 1 152 1.89e-105 298

Find 35 sgRNAs with CRISPR-Local

Find 94 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGAAGTTGAGAGATGATT+TGG 0.279609 1.2:-71131055 MS.gene60716:CDS
TCCTCTGCGGCCAGTGGTCT+TGG 0.330714 1.2:+71130032 None:intergenic
CAACTTCATGTCGAGCTGAT+TGG 0.366903 1.2:+71131068 None:intergenic
TCTCCTTCCAATACCCTTGA+TGG 0.378241 1.2:+71131388 None:intergenic
ATCGCGGATTGAGGCACTAC+TGG 0.386606 1.2:-71130080 MS.gene60716:CDS
TACTGGGGCCTTCGTGTTCG+TGG 0.449083 1.2:-71130063 MS.gene60716:CDS
ATGACCTCCATCAAGGGTAT+TGG 0.453879 1.2:-71131395 MS.gene60716:CDS
TGCGAATCCTCGTCAATTCA+AGG 0.456574 1.2:-71131154 MS.gene60716:CDS
TGATGGAGGTCATGGCGAAC+TGG 0.458767 1.2:+71131405 None:intergenic
CAAGGATGGCAAATTCTCTC+AGG 0.484690 1.2:-71131097 MS.gene60716:CDS
GTCAATTCAAGGTTCCAGAT+TGG 0.495981 1.2:-71131143 MS.gene60716:CDS
TTATTTATTACAGTCTTTGG+TGG 0.501150 1.2:-71131492 MS.gene60716:intron
TGGAGAGACTCAAGAAGATC+CGG 0.515884 1.2:-71131035 MS.gene60716:intron
TCGCGGATTGAGGCACTACT+GGG 0.518159 1.2:-71130079 MS.gene60716:CDS
GAACAGAAAGAAGGATTACA+AGG 0.525479 1.2:-71131115 MS.gene60716:CDS
CTTCTGCTTTCCATCGACGT+TGG 0.527308 1.2:+71131430 None:intergenic
GTTCGCCATGACCTCCATCA+AGG 0.531639 1.2:-71131402 MS.gene60716:CDS
TGAATTGAGCGCTGCAGAGT+TGG 0.555206 1.2:-71131196 MS.gene60716:CDS
GCAGCAATCATCGCGGATTG+AGG 0.565565 1.2:-71130089 MS.gene60716:intron
AGAAAGAAGGATTACAAGGA+TGG 0.565673 1.2:-71131111 MS.gene60716:CDS
TGTCTTTCCTCTGCGGCCAG+TGG 0.569872 1.2:+71130026 None:intergenic
GTGCTCAACACCAACGTCGA+TGG 0.579384 1.2:-71131440 MS.gene60716:CDS
AATACCCTTGATGGAGGTCA+TGG 0.580255 1.2:+71131397 None:intergenic
CTGATGTTGACATGAACAAG+AGG 0.595729 1.2:-71131340 MS.gene60716:intron
ACCAAGACCACTGGCCGCAG+AGG 0.604789 1.2:-71130033 MS.gene60716:CDS
GGTCAGCATACCAAGACCAC+TGG 0.607362 1.2:-71130042 MS.gene60716:CDS
TTCGCCATGACCTCCATCAA+GGG 0.609308 1.2:-71131401 MS.gene60716:CDS
GGCCGCAGAGGAAAGACAGT+TGG 0.619052 1.2:-71130021 MS.gene60716:CDS
CGCGGATTGAGGCACTACTG+GGG 0.645604 1.2:-71130078 MS.gene60716:CDS
CCTCCATCAAGGGTATTGGA+AGG 0.646589 1.2:-71131391 MS.gene60716:CDS
TCTGGAACCTTGAATTGACG+AGG 0.669518 1.2:+71131147 None:intergenic
CCTTCCAATACCCTTGATGG+AGG 0.688567 1.2:+71131391 None:intergenic
CTATTATGCAGCAATCATCG+CGG 0.703201 1.2:-71130096 MS.gene60716:intron
CACCAACTGTCTTTCCTCTG+CGG 0.721731 1.2:+71130019 None:intergenic
TATGCTGACCACGAACACGA+AGG 0.739225 1.2:+71130055 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTGTATTCAATAATATAA+TGG - chr1.2:71131402-71131421 MS.gene60716:CDS 10.0%
!! TTTGATATTATTGTTGAAAT+GGG - chr1.2:71130319-71130338 MS.gene60716:intron 15.0%
!!! ATTTTTGTTGTTAAGATTAA+TGG - chr1.2:71130292-71130311 MS.gene60716:intron 15.0%
!!! TTTTGATATTATTGTTGAAA+TGG - chr1.2:71130318-71130337 MS.gene60716:intron 15.0%
!!! TTTTTGTTGTTAAGATTAAT+GGG - chr1.2:71130293-71130312 MS.gene60716:intron 15.0%
!! AGTTTACTTGAATAATCATA+TGG - chr1.2:71131006-71131025 MS.gene60716:intron 20.0%
!! TATAAGATGAAAACAGTTTA+TGG - chr1.2:71131312-71131331 MS.gene60716:intron 20.0%
!!! AATAATATAATGGATGTATG+TGG - chr1.2:71131412-71131431 MS.gene60716:CDS 20.0%
!!! ATAATTATTGCTTTGATGAT+TGG - chr1.2:71130734-71130753 MS.gene60716:intron 20.0%
! AACACTACTTATTAAAGTTG+AGG - chr1.2:71130687-71130706 MS.gene60716:intron 25.0%
! ATAGTACAAAAATGTGAAGA+AGG + chr1.2:71131125-71131144 None:intergenic 25.0%
! ATTAAAACTGGTTAGGAAAA+TGG + chr1.2:71130871-71130890 None:intergenic 25.0%
! TCGTTATTTATTACAGTCTT+TGG - chr1.2:71130075-71130094 MS.gene60716:CDS 25.0%
! TTATTTATTACAGTCTTTGG+TGG - chr1.2:71130078-71130097 MS.gene60716:CDS 25.0%
! TTTGTTGCTGGATTTATTTA+GGG - chr1.2:71130347-71130366 MS.gene60716:intron 25.0%
!! TTTTGTTGCTGGATTTATTT+AGG - chr1.2:71130346-71130365 MS.gene60716:intron 25.0%
!!! ATGACTATTTGTTTTTCTGT+TGG - chr1.2:71131081-71131100 MS.gene60716:CDS 25.0%
!!! ATTTTCCTAACCAGTTTTAA+TGG - chr1.2:71130870-71130889 MS.gene60716:intron 25.0%
!!! TTAGTTTTCACAATAGTGTT+TGG - chr1.2:71130957-71130976 MS.gene60716:intron 25.0%
ACGAAAAATTACAGAATCAG+TGG + chr1.2:71130059-71130078 None:intergenic 30.0%
ATCAAGTTCAAACACTATCA+TGG + chr1.2:71130778-71130797 None:intergenic 30.0%
ATGATTGCTGCATAATAGAA+AGG + chr1.2:71131472-71131491 None:intergenic 30.0%
CAATTCCATTAAAACTGGTT+AGG + chr1.2:71130878-71130897 None:intergenic 30.0%
CTAGAAAGATGATTCTTACT+CGG - chr1.2:71130630-71130649 MS.gene60716:intron 30.0%
TAGTGCAATTCCATTAAAAC+TGG + chr1.2:71130883-71130902 None:intergenic 30.0%
TTTCTGTTCAAAAACCAATC+TGG + chr1.2:71130444-71130463 None:intergenic 30.0%
!! ATCATCTTTCTAGTTAACAC+AGG + chr1.2:71130623-71130642 None:intergenic 30.0%
!! TTGGTTTTTGAACAGAAAGA+AGG - chr1.2:71130446-71130465 MS.gene60716:intron 30.0%
AAAATGTGAAGAAGGCAACT+TGG + chr1.2:71131117-71131136 None:intergenic 35.0%
AAAGATGATTCTTACTCGGT+TGG - chr1.2:71130634-71130653 MS.gene60716:intron 35.0%
AAATGTGAAGAAGGCAACTT+GGG + chr1.2:71131116-71131135 None:intergenic 35.0%
ACAATAAAGTAGCAACTGAC+CGG + chr1.2:71130557-71130576 None:intergenic 35.0%
ACAGAACAAGGATTCACTAT+TGG - chr1.2:71130810-71130829 MS.gene60716:intron 35.0%
AGAAAGAAGGATTACAAGGA+TGG - chr1.2:71130459-71130478 MS.gene60716:intron 35.0%
AGAGATGTCCATAAACTGTT+TGG + chr1.2:71131369-71131388 None:intergenic 35.0%
AGATGTCCATAAACTGTTTG+GGG + chr1.2:71131367-71131386 None:intergenic 35.0%
AGTGTTCGAATAACAGAACA+AGG - chr1.2:71130798-71130817 MS.gene60716:intron 35.0%
ATCACACACAATCAAAGCAA+TGG + chr1.2:71130934-71130953 None:intergenic 35.0%
ATGGATGTATGTGGAGAAAT+TGG - chr1.2:71131421-71131440 MS.gene60716:CDS 35.0%
CATGAAGTTGAGAGATGATT+TGG - chr1.2:71130515-71130534 MS.gene60716:intron 35.0%
GAACAGAAAGAAGGATTACA+AGG - chr1.2:71130455-71130474 MS.gene60716:intron 35.0%
GAGATGTCCATAAACTGTTT+GGG + chr1.2:71131368-71131387 None:intergenic 35.0%
TAGGAAAATGGTGAATACAG+TGG + chr1.2:71130859-71130878 None:intergenic 35.0%
TGGATGTATGTGGAGAAATT+GGG - chr1.2:71131422-71131441 MS.gene60716:CDS 35.0%
! TTCACAATAGTGTTTGGAAC+TGG - chr1.2:71130963-71130982 MS.gene60716:intron 35.0%
!!! AAATGGGTTGTTTTTGTTGC+TGG - chr1.2:71130335-71130354 MS.gene60716:intron 35.0%
!!! TTAGCCCAGTTTTAGCTTAT+GGG + chr1.2:71131034-71131053 None:intergenic 35.0%
!!! TTTAGCCCAGTTTTAGCTTA+TGG + chr1.2:71131035-71131054 None:intergenic 35.0%
AAACTAATAGCACTTCCTCG+TGG + chr1.2:71130991-71131010 None:intergenic 40.0%
ACTGGGCTAAAGTTATTTGC+TGG - chr1.2:71131044-71131063 MS.gene60716:CDS 40.0%
ATGTCCATAAACTGTTTGGG+GGG + chr1.2:71131365-71131384 None:intergenic 40.0%
ATTGCACTAGACACGATAAG+AGG - chr1.2:71130894-71130913 MS.gene60716:intron 40.0%
CTATTATGCAGCAATCATCG+CGG - chr1.2:71131474-71131493 MS.gene60716:CDS 40.0%
CTGATGTTGACATGAACAAG+AGG - chr1.2:71130230-71130249 MS.gene60716:intron 40.0%
GACAGAGATGAAATCGAGAT+CGG + chr1.2:71130016-71130035 None:intergenic 40.0%
GATGTCCATAAACTGTTTGG+GGG + chr1.2:71131366-71131385 None:intergenic 40.0%
GGTTCCCATAAGCTAAAACT+GGG - chr1.2:71131027-71131046 MS.gene60716:intron 40.0%
GTCAATTCAAGGTTCCAGAT+TGG - chr1.2:71130427-71130446 MS.gene60716:intron 40.0%
TATGTGGAGAAATTGGGCAT+TGG - chr1.2:71131428-71131447 MS.gene60716:CDS 40.0%
TGGTTCCCATAAGCTAAAAC+TGG - chr1.2:71131026-71131045 MS.gene60716:intron 40.0%
TTGCACTAGACACGATAAGA+GGG - chr1.2:71130895-71130914 MS.gene60716:intron 40.0%
! TTGCTGGATTTATTTAGGGC+TGG - chr1.2:71130351-71130370 MS.gene60716:intron 40.0%
AATACCCTTGATGGAGGTCA+TGG + chr1.2:71130176-71130195 None:intergenic 45.0%
CAACTTCATGTCGAGCTGAT+TGG + chr1.2:71130505-71130524 None:intergenic 45.0%
CAAGGATGGCAAATTCTCTC+AGG - chr1.2:71130473-71130492 MS.gene60716:intron 45.0%
TCTCCTTCCAATACCCTTGA+TGG + chr1.2:71130185-71130204 None:intergenic 45.0%
TGCGAATCCTCGTCAATTCA+AGG - chr1.2:71130416-71130435 MS.gene60716:intron 45.0%
TGGAGAGACTCAAGAAGATC+CGG - chr1.2:71130535-71130554 MS.gene60716:intron 45.0%
! AGTGGTAGTGCATGATGCTT+CGG + chr1.2:71130841-71130860 None:intergenic 45.0%
! ATGACCTCCATCAAGGGTAT+TGG - chr1.2:71130175-71130194 MS.gene60716:intron 45.0%
! TCTGGAACCTTGAATTGACG+AGG + chr1.2:71130426-71130445 None:intergenic 45.0%
CACCAACTGTCTTTCCTCTG+CGG + chr1.2:71131554-71131573 None:intergenic 50.0%
CCTTCCAATACCCTTGATGG+AGG + chr1.2:71130182-71130201 None:intergenic 50.0%
CGTTCCCCCCAAACAGTTTA+TGG - chr1.2:71131358-71131377 MS.gene60716:CDS 50.0%
CTTCTGCTTTCCATCGACGT+TGG + chr1.2:71130143-71130162 None:intergenic 50.0%
TATGCTGACCACGAACACGA+AGG + chr1.2:71131518-71131537 None:intergenic 50.0%
TTCGCCATGACCTCCATCAA+GGG - chr1.2:71130169-71130188 MS.gene60716:intron 50.0%
! TGAATTGAGCGCTGCAGAGT+TGG - chr1.2:71130374-71130393 MS.gene60716:intron 50.0%
! TGTTTGGAACTGGATCCACG+AGG - chr1.2:71130973-71130992 MS.gene60716:intron 50.0%
!! CCTCCATCAAGGGTATTGGA+AGG - chr1.2:71130179-71130198 MS.gene60716:intron 50.0%
!! TGGAGAAATTGGGCATTGGC+TGG - chr1.2:71131432-71131451 MS.gene60716:CDS 50.0%
GGTCAGCATACCAAGACCAC+TGG - chr1.2:71131528-71131547 MS.gene60716:intron 55.0%
GTGCTCAACACCAACGTCGA+TGG - chr1.2:71130130-71130149 MS.gene60716:intron 55.0%
GTTCGCCATGACCTCCATCA+AGG - chr1.2:71130168-71130187 MS.gene60716:intron 55.0%
TGATGGAGGTCATGGCGAAC+TGG + chr1.2:71130168-71130187 None:intergenic 55.0%
! ATCGCGGATTGAGGCACTAC+TGG - chr1.2:71131490-71131509 MS.gene60716:intron 55.0%
! GCAGCAATCATCGCGGATTG+AGG - chr1.2:71131481-71131500 MS.gene60716:CDS 55.0%
! TCGCGGATTGAGGCACTACT+GGG - chr1.2:71131491-71131510 MS.gene60716:intron 55.0%
GGCCGCAGAGGAAAGACAGT+TGG - chr1.2:71131549-71131568 MS.gene60716:intron 60.0%
TACTGGGGCCTTCGTGTTCG+TGG - chr1.2:71131507-71131526 MS.gene60716:intron 60.0%
TGTCTTTCCTCTGCGGCCAG+TGG + chr1.2:71131547-71131566 None:intergenic 60.0%
! CGCGGATTGAGGCACTACTG+GGG - chr1.2:71131492-71131511 MS.gene60716:intron 60.0%
ACCAAGACCACTGGCCGCAG+AGG - chr1.2:71131537-71131556 MS.gene60716:intron 65.0%
TCCTCTGCGGCCAGTGGTCT+TGG + chr1.2:71131541-71131560 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 71130002 71131590 71130002 ID=MS.gene60716
chr1.2 mRNA 71130002 71131590 71130002 ID=MS.gene60716.t1;Parent=MS.gene60716
chr1.2 exon 71131588 71131590 71131588 ID=MS.gene60716.t1.exon1;Parent=MS.gene60716.t1
chr1.2 CDS 71131588 71131590 71131588 ID=cds.MS.gene60716.t1;Parent=MS.gene60716.t1
chr1.2 exon 71131341 71131501 71131341 ID=MS.gene60716.t1.exon2;Parent=MS.gene60716.t1
chr1.2 CDS 71131341 71131501 71131341 ID=cds.MS.gene60716.t1;Parent=MS.gene60716.t1
chr1.2 exon 71131036 71131224 71131036 ID=MS.gene60716.t1.exon3;Parent=MS.gene60716.t1
chr1.2 CDS 71131036 71131224 71131036 ID=cds.MS.gene60716.t1;Parent=MS.gene60716.t1
chr1.2 exon 71130002 71130107 71130002 ID=MS.gene60716.t1.exon4;Parent=MS.gene60716.t1
chr1.2 CDS 71130002 71130107 71130002 ID=cds.MS.gene60716.t1;Parent=MS.gene60716.t1
Gene Sequence

>MS.gene60716

ATGGTACGTTTCCGATCTCGATTTCATCTCTGTCTTCACTATGTAGCTTTTTCACCACTGATTCTGTAATTTTTCGTTATTTATTACAGTCTTTGGTGGCGAACGAAGAATTTCAGCACATTCTGCGTGTGCTCAACACCAACGTCGATGGAAAGCAGAAGATCCAGTTCGCCATGACCTCCATCAAGGGTATTGGAAGGAGATTTGCTAACATATGCTGTAAGAAAGCTGATGTTGACATGAACAAGAGGTTCGTACTTGTGATTTTGATCTCACTTTTAAAATCACTCATTTTTGTTGTTAAGATTAATGGGTTTTTTGATATTATTGTTGAAATGGGTTGTTTTTGTTGCTGGATTTATTTAGGGCTGGTGAATTGAGCGCTGCAGAGTTGGATAATATAATGACAGTTGTTGCGAATCCTCGTCAATTCAAGGTTCCAGATTGGTTTTTGAACAGAAAGAAGGATTACAAGGATGGCAAATTCTCTCAGGTTGTCTCCAATCAGCTCGACATGAAGTTGAGAGATGATTTGGAGAGACTCAAGAAGATCCGGTCAGTTGCTACTTTATTGTTTATTTCATTATTTTTTGTGTGTGATGATGATATTATTGTTTGCCTGTGTTAACTAGAAAGATGATTCTTACTCGGTTGGTCTTTTAGTGTACGTGTAAATTAACATTCTAACACTACTTATTAAAGTTGAGGTGTAGTAGTAAGATGATAGAATTAATAATTATTGCTTTGATGATTGGTTCTTGATATTTTAGATTCCATGATAGTGTTTGAACTTGATAGTGTTCGAATAACAGAACAAGGATTCACTATTGGAGAATCCGAAGCATCATGCACTACCACTGTATTCACCATTTTCCTAACCAGTTTTAATGGAATTGCACTAGACACGATAAGAGGGATAAAACTAATGTCCATTGCTTTGATTGTGTGTGATGCTTTAGTTTTCACAATAGTGTTTGGAACTGGATCCACGAGGAAGTGCTATTAGTTTACTTGAATAATCATATGGTTCCCATAAGCTAAAACTGGGCTAAAGTTATTTGCTGGTTCTTATTTATCAAATGACTATTTGTTTTTCTGTTGGCTATATAGTCCCAAGTTGCCTTCTTCACATTTTTGTACTATATATAATATTCATGTAAATCATACAAGTGCTTATGTGTTAGCTATTTTGATGACAATCATACAAGTGCTTATATATAAGCTGTTTTTATAGCAAGATAAAATAAAGTTAAATTGTTTTCATTTAATCTCTTAATTTTTTTTTCATTAGCTATTTATAGTTGTATGAATATAAGATGAAAACAGTTTATGGACATGTCATAAACTGATTCTATACGTTCCCCCCAAACAGTTTATGGACATCTCTTAATTTTTTTTTTTTTTGTATTCAATAATATAATGGATGTATGTGGAGAAATTGGGCATTGGCTGGTTGAAGACTAACATCCTTTCTATTATGCAGCAATCATCGCGGATTGAGGCACTACTGGGGCCTTCGTGTTCGTGGTCAGCATACCAAGACCACTGGCCGCAGAGGAAAGACAGTTGGTGTCTCAAAGAAGCGTTAA
Protein sequence

>MS.gene60716.t1

MSLVANEEFQHILRVLNTNVDGKQKIQFAMTSIKGIGRRFANICCKKADVDMNKRAGELSAAELDNIMTVVANPRQFKVPDWFLNRKKDYKDGKFSQVVSNQLDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR