AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene046251

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene046251.t1 MTR_3g013635 98.601 143 2 0 1 143 1 143 1.08e-104 295
MS.gene046251.t1 MTR_3g013635 98.601 143 2 0 1 143 1 143 1.08e-104 295
MS.gene046251.t1 MTR_8g040740 88.811 143 16 0 1 143 1 143 3.92e-97 276
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene046251.t1 AT5G61170 82.394 142 25 0 1 142 1 142 9.05e-90 257
MS.gene046251.t1 AT3G02080 80.420 143 28 0 1 143 1 143 9.05e-90 257
MS.gene046251.t1 AT5G15520 82.734 139 24 0 1 139 1 139 6.82e-88 253

Find 50 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTGAAGACTGCAAGGTTTA+AGG 0.181111 3.4:+9479258 MS.gene046251:CDS
GGTGGATTCCAGAGGATTTA+TGG 0.272697 3.4:+9479496 MS.gene046251:CDS
TTCCAGTGGCAGGAGGGATT+TGG 0.312675 3.4:+9479937 MS.gene046251:CDS
TTCACAATATCTGTCCATTC+TGG 0.341460 3.4:-9479241 None:intergenic
AGGGATTTGGACCAAGTTGC+TGG 0.349640 3.4:+9479950 MS.gene046251:CDS
CCTTGGTGTCCATCTCAATA+AGG 0.385015 3.4:-9479612 None:intergenic
TCCCCTCAAGTAGATCTTCC+TGG 0.406265 3.4:-9479461 None:intergenic
GACTGCAAGGTTTAAGGAGT+TGG 0.416477 3.4:+9479264 MS.gene046251:CDS
AGGGGAGGACTCGGTGTTGG+TGG 0.437986 3.4:+9479478 MS.gene046251:CDS
GTCCAAATCCCTCCTGCCAC+TGG 0.442468 3.4:-9479939 None:intergenic
GGCTTCCACCATAAATCCTC+TGG 0.445267 3.4:-9479504 None:intergenic
ATCTACTTGAGGGGAGGACT+CGG 0.467280 3.4:+9479469 MS.gene046251:CDS
GTGGGCGACTGCCATTCCTC+TGG 0.472369 3.4:-9479525 None:intergenic
TCTGCTCATCTCAAAAGATC+TGG 0.481965 3.4:+9478321 MS.gene046251:CDS
GTGCCGCAGCTTCCATGGCC+AGG 0.485644 3.4:+9479443 MS.gene046251:intron
GCTCTGACGTAGTACCAGTC+AGG 0.489319 3.4:-9479298 None:intergenic
TAGTACCAGTCAGGGTCATA+AGG 0.498306 3.4:-9479289 None:intergenic
CAAGTAGATCTTCCTGGCCA+TGG 0.517027 3.4:-9479455 None:intergenic
GGCCAGGAAGATCTACTTGA+GGG 0.520468 3.4:+9479459 MS.gene046251:CDS
GGAAGATCACTTCCAGTGGC+AGG 0.522712 3.4:+9479927 MS.gene046251:CDS
AACAGTCCTTGCGGTAGCCA+TGG 0.523894 3.4:-9478262 None:intergenic
TTGAGGGGAGGACTCGGTGT+TGG 0.529114 3.4:+9479475 MS.gene046251:CDS
TAACAATACGTCCAGCAACT+TGG 0.533492 3.4:-9479961 None:intergenic
TGGCTCCTTATGACCCTGAC+TGG 0.535373 3.4:+9479284 MS.gene046251:CDS
GACTGGTACTACGTCAGAGC+TGG 0.543992 3.4:+9479301 MS.gene046251:CDS
AACAGATGGAGCTTCCAGAA+TGG 0.551656 3.4:+9479227 MS.gene046251:intron
TGCTCTTGCAGAAATGTGGT+GGG 0.558681 3.4:-9479543 None:intergenic
GAACATGAACCTTATTGAGA+TGG 0.561257 3.4:+9479603 MS.gene046251:CDS
CTGCTCTTGCAGAAATGTGG+TGG 0.566836 3.4:-9479544 None:intergenic
TTGAAGAATGTGACGAGCAA+TGG 0.567297 3.4:-9479572 None:intergenic
CCACATTTCTGCAAGAGCAG+TGG 0.597531 3.4:+9479547 MS.gene046251:CDS
CCACTGCTCTTGCAGAAATG+TGG 0.600910 3.4:-9479547 None:intergenic
TATGGTGGAAGCCAGAGGAA+TGG 0.608896 3.4:+9479514 MS.gene046251:CDS
AGATCACTTCCAGTGGCAGG+AGG 0.615298 3.4:+9479930 MS.gene046251:CDS
CAGATATTGTGAAGACTGCA+AGG 0.617924 3.4:+9479251 MS.gene046251:CDS
CTCTGACGTAGTACCAGTCA+GGG 0.627550 3.4:-9479297 None:intergenic
TCATCTCAAAAGATCTGGCA+AGG 0.635281 3.4:+9478326 MS.gene046251:CDS
GCACAACCATGGCTACCGCA+AGG 0.635383 3.4:+9478256 None:intergenic
GGATTTATGGTGGAAGCCAG+AGG 0.643091 3.4:+9479509 MS.gene046251:CDS
TGGCCAGGAAGATCTACTTG+AGG 0.644765 3.4:+9479458 MS.gene046251:CDS
GATCACTTCCAGTGGCAGGA+GGG 0.646734 3.4:+9479931 MS.gene046251:CDS
CTTATTGAGATGGACACCAA+GGG 0.649426 3.4:+9479613 MS.gene046251:CDS
GGCAGGAAGATCACTTCCAG+TGG 0.650796 3.4:+9479923 MS.gene046251:CDS
TCGGTGTTGGTGGATTCCAG+AGG 0.651385 3.4:+9479488 MS.gene046251:CDS
AGGAAGATCTACTTGAGGGG+AGG 0.656289 3.4:+9479463 MS.gene046251:CDS
CCTTATTGAGATGGACACCA+AGG 0.671459 3.4:+9479612 MS.gene046251:CDS
GGATTCCAGAGGATTTATGG+TGG 0.673361 3.4:+9479499 MS.gene046251:CDS
AACATCTTGAACAGTCCTTG+CGG 0.675305 3.4:-9478271 None:intergenic
GCCAGGAAGATCTACTTGAG+GGG 0.680202 3.4:+9479460 MS.gene046251:CDS
TTATTGAGATGGACACCAAG+GGG 0.704884 3.4:+9479614 MS.gene046251:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATATATGTAATTAGAATA+AGG - chr3.4:9478995-9479014 None:intergenic 10.0%
!!! TTTTTTGTTAATTTAAACAA+AGG - chr3.4:9479363-9479382 None:intergenic 10.0%
!! TCTAATTACATATATTACTT+GGG + chr3.4:9478998-9479017 MS.gene046251:intron 15.0%
!! TTCTAATTACATATATTACT+TGG + chr3.4:9478997-9479016 MS.gene046251:intron 15.0%
!! TTGTATAGTTTAAATTTAGT+TGG + chr3.4:9479159-9479178 MS.gene046251:intron 15.0%
!!! AAAACCAAAATGAAATTTTT+CGG - chr3.4:9478364-9478383 None:intergenic 15.0%
!!! ATCAAAAACATTTTTTTGTT+AGG - chr3.4:9478669-9478688 None:intergenic 15.0%
!!! TTGTTTTTGTTAATCAAATT+AGG + chr3.4:9478870-9478889 MS.gene046251:intron 15.0%
!!! TTTGATTTTTTTTTTTGAAG+AGG + chr3.4:9478413-9478432 MS.gene046251:intron 15.0%
!! AAAAACCAATGTTAAAAACA+TGG - chr3.4:9479891-9479910 None:intergenic 20.0%
!! AACAAAAAAATAACTTTCGA+GGG + chr3.4:9479374-9479393 MS.gene046251:intron 20.0%
!! TAACAAAAAAATAACTTTCG+AGG + chr3.4:9479373-9479392 MS.gene046251:intron 20.0%
!! TTATAATGATACGAATGAAA+TGG + chr3.4:9479128-9479147 MS.gene046251:intron 20.0%
!!! ACAAATTTTGAAAGTTCAAA+AGG - chr3.4:9478964-9478983 None:intergenic 20.0%
!!! CAAATTTTGAAAGTTCAAAA+GGG - chr3.4:9478963-9478982 None:intergenic 20.0%
!!! TATTTTGATTGTGTATGATT+CGG + chr3.4:9478385-9478404 MS.gene046251:intron 20.0%
!!! TGAATGTTATGTTTTTTGTT+GGG + chr3.4:9478573-9478592 MS.gene046251:intron 20.0%
!!! TGTTTTTGATTTGATTTGAT+TGG + chr3.4:9478679-9478698 MS.gene046251:intron 20.0%
!!! TTAACCGAAAAATTTCATTT+TGG + chr3.4:9478357-9478376 MS.gene046251:intron 20.0%
!!! TTGAATGTTATGTTTTTTGT+TGG + chr3.4:9478572-9478591 MS.gene046251:intron 20.0%
! ATGTTAAAAACATGGTATGA+AGG - chr3.4:9479883-9479902 None:intergenic 25.0%
! CATCTGTTCATAACAAAATA+AGG - chr3.4:9479215-9479234 None:intergenic 25.0%
! TGTTAAAAACATGGTATGAA+GGG - chr3.4:9479882-9479901 None:intergenic 25.0%
!! GTGCTATTATTTATAGTGAT+TGG + chr3.4:9479819-9479838 MS.gene046251:intron 25.0%
!! TAGCTATTTGATTTACATTG+CGG - chr3.4:9479733-9479752 None:intergenic 25.0%
!!! ATTTGTTTTGATTTGCTTCA+TGG + chr3.4:9478437-9478456 MS.gene046251:intron 25.0%
!!! CTTATTTTGTTATGAACAGA+TGG + chr3.4:9479213-9479232 MS.gene046251:intron 25.0%
!!! GAACTTTCAAAATTTGTTGT+TGG + chr3.4:9478967-9478986 MS.gene046251:intron 25.0%
!!! TCATACCATGTTTTTAACAT+TGG + chr3.4:9479883-9479902 MS.gene046251:intron 25.0%
!!! TTTGTTTTGATTTGCTTCAT+GGG + chr3.4:9478438-9478457 MS.gene046251:intron 25.0%
AACTACTGCTAAACAAATGT+TGG - chr3.4:9479782-9479801 None:intergenic 30.0%
GTTAATTTAAACAAAGGACC+AGG - chr3.4:9479357-9479376 None:intergenic 30.0%
TTACATATATTACTTGGGCA+TGG + chr3.4:9479003-9479022 MS.gene046251:intron 30.0%
! ACATTGCAATTTTCAACAAC+AGG - chr3.4:9479416-9479435 None:intergenic 30.0%
!! TTGGTTTTTCTTTATCACAG+TGG + chr3.4:9479902-9479921 MS.gene046251:intron 30.0%
!!! GTTATGTTTTTTGTTGGGTT+TGG + chr3.4:9478578-9478597 MS.gene046251:intron 30.0%
ACGGTTTACAATAGGGAATA+GGG + chr3.4:9479666-9479685 MS.gene046251:intron 35.0%
GAACATGAACCTTATTGAGA+TGG + chr3.4:9479603-9479622 MS.gene046251:CDS 35.0%
GCTAAACAAATGTTGGTATC+AGG - chr3.4:9479775-9479794 None:intergenic 35.0%
TACGGTTTACAATAGGGAAT+AGG + chr3.4:9479665-9479684 MS.gene046251:intron 35.0%
TTCACAATATCTGTCCATTC+TGG - chr3.4:9479244-9479263 None:intergenic 35.0%
! TTATCTTTGTTAGCCTGCTA+CGG + chr3.4:9479647-9479666 MS.gene046251:intron 35.0%
! TTTTTCTTTATCACAGTGGC+AGG + chr3.4:9479906-9479925 MS.gene046251:intron 35.0%
!! GTTTGATTTTGTGCATTTCC+TGG + chr3.4:9479336-9479355 MS.gene046251:intron 35.0%
AACATCTTGAACAGTCCTTG+CGG - chr3.4:9478274-9478293 None:intergenic 40.0%
CAGATATTGTGAAGACTGCA+AGG + chr3.4:9479251-9479270 MS.gene046251:CDS 40.0%
CTTATTGAGATGGACACCAA+GGG + chr3.4:9479613-9479632 MS.gene046251:CDS 40.0%
GATAATGAGTTCTTACCCCT+TGG - chr3.4:9479632-9479651 None:intergenic 40.0%
GTATTCAAGCTCTACTTCAC+TGG + chr3.4:9479094-9479113 MS.gene046251:intron 40.0%
TAACAATACGTCCAGCAACT+TGG - chr3.4:9479964-9479983 None:intergenic 40.0%
TCATCTCAAAAGATCTGGCA+AGG + chr3.4:9478326-9478345 MS.gene046251:CDS 40.0%
TCTGCTCATCTCAAAAGATC+TGG + chr3.4:9478321-9478340 MS.gene046251:CDS 40.0%
TGTGAAGACTGCAAGGTTTA+AGG + chr3.4:9479258-9479277 MS.gene046251:CDS 40.0%
TTATTGAGATGGACACCAAG+GGG + chr3.4:9479614-9479633 MS.gene046251:CDS 40.0%
TTGAAGAATGTGACGAGCAA+TGG - chr3.4:9479575-9479594 None:intergenic 40.0%
AACAGATGGAGCTTCCAGAA+TGG + chr3.4:9479227-9479246 MS.gene046251:intron 45.0%
AGCCTGCTACGGTTTACAAT+AGG + chr3.4:9479658-9479677 MS.gene046251:intron 45.0%
CATGGTTTCAACTCACGTGT+TGG + chr3.4:9479021-9479040 MS.gene046251:intron 45.0%
CCTTATTGAGATGGACACCA+AGG + chr3.4:9479612-9479631 MS.gene046251:CDS 45.0%
GACTGCAAGGTTTAAGGAGT+TGG + chr3.4:9479264-9479283 MS.gene046251:CDS 45.0%
GCCTGCTACGGTTTACAATA+GGG + chr3.4:9479659-9479678 MS.gene046251:intron 45.0%
GGATTCCAGAGGATTTATGG+TGG + chr3.4:9479499-9479518 MS.gene046251:CDS 45.0%
TAGTACCAGTCAGGGTCATA+AGG - chr3.4:9479292-9479311 None:intergenic 45.0%
TCCCTATTGTAAACCGTAGC+AGG - chr3.4:9479663-9479682 None:intergenic 45.0%
TGCTCTTGCAGAAATGTGGT+GGG - chr3.4:9479546-9479565 None:intergenic 45.0%
! GGTGGATTCCAGAGGATTTA+TGG + chr3.4:9479496-9479515 MS.gene046251:CDS 45.0%
!! CCTTGGTGTCCATCTCAATA+AGG - chr3.4:9479615-9479634 None:intergenic 45.0%
AGGAAGATCTACTTGAGGGG+AGG + chr3.4:9479463-9479482 MS.gene046251:CDS 50.0%
AGGGATTTGGACCAAGTTGC+TGG + chr3.4:9479950-9479969 MS.gene046251:CDS 50.0%
ATCTACTTGAGGGGAGGACT+CGG + chr3.4:9479469-9479488 MS.gene046251:CDS 50.0%
CAAGTAGATCTTCCTGGCCA+TGG - chr3.4:9479458-9479477 None:intergenic 50.0%
CCACATTTCTGCAAGAGCAG+TGG + chr3.4:9479547-9479566 MS.gene046251:CDS 50.0%
CCACTGCTCTTGCAGAAATG+TGG - chr3.4:9479550-9479569 None:intergenic 50.0%
CTCTGACGTAGTACCAGTCA+GGG - chr3.4:9479300-9479319 None:intergenic 50.0%
CTGCTCTTGCAGAAATGTGG+TGG - chr3.4:9479547-9479566 None:intergenic 50.0%
GCCAGGAAGATCTACTTGAG+GGG + chr3.4:9479460-9479479 MS.gene046251:CDS 50.0%
GGCCAGGAAGATCTACTTGA+GGG + chr3.4:9479459-9479478 MS.gene046251:CDS 50.0%
GGCTTCCACCATAAATCCTC+TGG - chr3.4:9479507-9479526 None:intergenic 50.0%
TCCCCTCAAGTAGATCTTCC+TGG - chr3.4:9479464-9479483 None:intergenic 50.0%
TGGCCAGGAAGATCTACTTG+AGG + chr3.4:9479458-9479477 MS.gene046251:CDS 50.0%
! GGATTTATGGTGGAAGCCAG+AGG + chr3.4:9479509-9479528 MS.gene046251:CDS 50.0%
! TATGGTGGAAGCCAGAGGAA+TGG + chr3.4:9479514-9479533 MS.gene046251:CDS 50.0%
! TTTTTGTGCCGCAGCTTCCA+TGG + chr3.4:9479438-9479457 MS.gene046251:intron 50.0%
AGATCACTTCCAGTGGCAGG+AGG + chr3.4:9479930-9479949 MS.gene046251:CDS 55.0%
GACTGGTACTACGTCAGAGC+TGG + chr3.4:9479301-9479320 MS.gene046251:CDS 55.0%
GATCACTTCCAGTGGCAGGA+GGG + chr3.4:9479931-9479950 MS.gene046251:CDS 55.0%
GCTCTGACGTAGTACCAGTC+AGG - chr3.4:9479301-9479320 None:intergenic 55.0%
GGAAGATCACTTCCAGTGGC+AGG + chr3.4:9479927-9479946 MS.gene046251:CDS 55.0%
GGCAGGAAGATCACTTCCAG+TGG + chr3.4:9479923-9479942 MS.gene046251:CDS 55.0%
TGGCTCCTTATGACCCTGAC+TGG + chr3.4:9479284-9479303 MS.gene046251:CDS 55.0%
TTCCAGTGGCAGGAGGGATT+TGG + chr3.4:9479937-9479956 MS.gene046251:CDS 55.0%
!! TCGGTGTTGGTGGATTCCAG+AGG + chr3.4:9479488-9479507 MS.gene046251:CDS 55.0%
CTTCCTGGCCATGGAAGCTG+CGG - chr3.4:9479449-9479468 None:intergenic 60.0%
GTCCAAATCCCTCCTGCCAC+TGG - chr3.4:9479942-9479961 None:intergenic 60.0%
!! TTGAGGGGAGGACTCGGTGT+TGG + chr3.4:9479475-9479494 MS.gene046251:CDS 60.0%
GTGGGCGACTGCCATTCCTC+TGG - chr3.4:9479528-9479547 None:intergenic 65.0%
!! AGGGGAGGACTCGGTGTTGG+TGG + chr3.4:9479478-9479497 MS.gene046251:CDS 65.0%
GTGCCGCAGCTTCCATGGCC+AGG + chr3.4:9479443-9479462 MS.gene046251:intron 70.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 9478264 9479994 9478264 ID=MS.gene046251
chr3.4 mRNA 9478264 9479994 9478264 ID=MS.gene046251.t1;Parent=MS.gene046251
chr3.4 exon 9478264 9478347 9478264 ID=MS.gene046251.t1.exon1;Parent=MS.gene046251.t1
chr3.4 CDS 9478264 9478347 9478264 ID=cds.MS.gene046251.t1;Parent=MS.gene046251.t1
chr3.4 exon 9479232 9479322 9479232 ID=MS.gene046251.t1.exon2;Parent=MS.gene046251.t1
chr3.4 CDS 9479232 9479322 9479232 ID=cds.MS.gene046251.t1;Parent=MS.gene046251.t1
chr3.4 exon 9479452 9479635 9479452 ID=MS.gene046251.t1.exon3;Parent=MS.gene046251.t1
chr3.4 CDS 9479452 9479635 9479452 ID=cds.MS.gene046251.t1;Parent=MS.gene046251.t1
chr3.4 exon 9479922 9479994 9479922 ID=MS.gene046251.t1.exon4;Parent=MS.gene046251.t1
chr3.4 CDS 9479922 9479994 9479922 ID=cds.MS.gene046251.t1;Parent=MS.gene046251.t1
Gene Sequence

>MS.gene046251

ATGGCTACCGCAAGGACTGTTCAAGATGTTTCTTCACACGAGTTTGTCAAAGCTTACTCTGCTCATCTCAAAAGATCTGGCAAGGTTAATCAATTAACCGAAAAATTTCATTTTGGTTTTCTATTTTGATTGTGTATGATTCGGTTTGTTTTGATTTTTTTTTTTGAAGAGGAATTTGTTTTGATTTGCTTCATGGGTTCATGAAATTTTGTTGAATTAATCTGTTTTAGTAGCTTTTTTGTTTTTGTTATTTTTATTTATTTATAAATTGTCATGCTTTATTGTTTAGATTTGTGTTTTTTTGTGTTTTGAATGTTATGTTTTTTGTTGGGTTTGGTTAAAGTTTATAACTTGATCTACTTCGTTGCTGTGTCTTGTTGAATGTAGTTTTGTTTGTCTAATCCTAACAAAAAAATGTTTTTGATTTGATTTGATTGGATTAATAAATAGAAAAATGTTCGTTGTGATGTTAATATGCTCTAATTTTTATTAGTGATTGATTCAGAGTAAGCATTTGTCAGAAAACTAGTGACATGATAGATTTGTGATTTTTCTCTTACACTTGTTTTTGATTAGTTTTAGTGAAAACATTCAAGTTGATTATGATTGTTTTTGTTAATCAAATTAGGAATGATTTTCTGTATTATATGATGTTGATGACAGTTTTTATTTTTTTTATGCTATGAATTGTAATGTCCCTTTTGAACTTTCAAAATTTGTTGTTGGATCCTTATTCTAATTACATATATTACTTGGGCATGGTTTCAACTCACGTGTTGGCTTAGTTTTAGAAATAACTTTCATTATGCTTTTGATTTTTTATGTATTATGTATTCAAGCTCTACTTCACTGGTGTGATCTAGTTTATAATGATACGAATGAAATGGCTGTGTAATTGTATAGTTTAAATTTAGTTGGATTATTATTCTAATTATAGATTTTTGTTTTCCTTATTTTGTTATGAACAGATGGAGCTTCCAGAATGGACAGATATTGTGAAGACTGCAAGGTTTAAGGAGTTGGCTCCTTATGACCCTGACTGGTACTACGTCAGAGCTGGTGAGTTTCTTGTGTTTGATTTTGTGCATTTCCTGGTCCTTTGTTTAAATTAACAAAAAAATAACTTTCGAGGGAACATTTTTTGATCAACCTGTTGTTGAAAATTGCAATGTGTTTTTTGTGCCGCAGCTTCCATGGCCAGGAAGATCTACTTGAGGGGAGGACTCGGTGTTGGTGGATTCCAGAGGATTTATGGTGGAAGCCAGAGGAATGGCAGTCGCCCACCACATTTCTGCAAGAGCAGTGGTTCCATTGCTCGTCACATTCTTCAACAGTTGCAGAACATGAACCTTATTGAGATGGACACCAAGGGGTAAGAACTCATTATCTTTGTTAGCCTGCTACGGTTTACAATAGGGAATAGGGATGTTACGATTAAGATAATAGTAACAATAGATTAGTCAAAGCCGCAATGTAAATCAAATAGCTATTTTAATGTTCACTTGTATCCTGATACCAACATTTGTTTAGCAGTAGTTGATGCTTTTCTGCATCTGTGCTATTATTTATAGTGATTGGCATTTTCTCAGAAATAGTTTATGCTATTCTGCATCAGCCCTTCATACCATGTTTTTAACATTGGTTTTTCTTTATCACAGTGGCAGGAAGATCACTTCCAGTGGCAGGAGGGATTTGGACCAAGTTGCTGGACGTATTGTTATTGCACCTTGA
Protein sequence

>MS.gene046251.t1

MATARTVQDVSSHEFVKAYSAHLKRSGKMELPEWTDIVKTARFKELAPYDPDWYYVRAASMARKIYLRGGLGVGGFQRIYGGSQRNGSRPPHFCKSSGSIARHILQQLQNMNLIEMDTKGGRKITSSGRRDLDQVAGRIVIAP