AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene067461


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067461.t1 MTR_2g104810 88.119 101 12 0 40 140 19 119 2.75e-62 190
MS.gene067461.t1 MTR_4g116860 49.451 91 35 1 107 197 1542 1621 4.64e-18 82.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067461.t1 AT1G80650 45.652 92 40 1 103 194 111 192 2.99e-18 79.3
MS.gene067461.t1 AT4G00420 44.330 97 43 3 103 199 59 144 2.29e-16 73.6
MS.gene067461.t1 AT4G00420 44.330 97 43 3 103 199 80 165 3.64e-16 73.6
MS.gene067461.t1 AT4G00420 44.330 97 43 3 103 199 81 166 3.71e-16 73.6
MS.gene067461.t1 AT4G00420 44.330 97 43 3 103 199 81 166 3.71e-16 73.6
MS.gene067461.t1 AT4G00420 44.330 97 43 3 103 199 81 166 3.71e-16 73.6
MS.gene067461.t1 AT5G20320 39.823 113 57 1 85 197 1586 1687 6.84e-15 73.2
MS.gene067461.t1 AT5G20320 39.823 113 57 1 85 197 1375 1476 7.29e-15 72.8
MS.gene067461.t1 AT5G20320 39.823 113 57 1 85 197 1600 1701 7.32e-15 72.8
MS.gene067461.t1 AT1G80650 39.130 92 36 1 103 194 111 182 9.35e-12 61.6

Find 24 sgRNAs with CRISPR-Local

Find 107 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCTAAAATGACACTCTCTT+TGG 0.292490 2.4:-785634 None:intergenic
CTTGAATAATCAAATGAAAA+TGG 0.300650 2.4:+785536 MS.gene067461:CDS
ATTCAAGGTTATTGTTGAAA+TGG 0.336999 2.4:+786844 MS.gene067461:CDS
TTCATTTGATTATTCAAGTT+GGG 0.380029 2.4:-785531 None:intergenic
TTCTTCTCACTCCACCTTCA+AGG 0.388623 2.4:+785361 MS.gene067461:CDS
TGTTTGTTAGGTATGAAGAA+AGG 0.445413 2.4:+785782 MS.gene067461:intron
TTGTGGTACTTAAAGCATAT+AGG 0.446945 2.4:+786986 MS.gene067461:CDS
GTTTGTTAGGTATGAAGAAA+GGG 0.447288 2.4:+785783 MS.gene067461:intron
TTTCATTTGATTATTCAAGT+TGG 0.449161 2.4:-785532 None:intergenic
TGGAAGATGAAACTGAAGAT+TGG 0.449737 2.4:-785614 None:intergenic
GTTATTGTTGAAATGGAGAC+AGG 0.475716 2.4:+786851 MS.gene067461:CDS
AGACATGTGCTGTAAATCAT+TGG 0.504933 2.4:+785828 MS.gene067461:CDS
GGCAGCAGACAATGCAGCCG+AGG 0.547846 2.4:+786958 MS.gene067461:CDS
TAAGTACCACAATGCACCCT+CGG 0.553491 2.4:-786975 None:intergenic
AAGACAACAACTTCAGATGA+AGG 0.557587 2.4:+785657 MS.gene067461:CDS
TTAGGTATGAAGAAAGGGTG+TGG 0.557962 2.4:+785788 MS.gene067461:intron
TGTGTTTGAGTGTTGTAAAG+AGG 0.558213 2.4:+785859 MS.gene067461:CDS
GCAGCAGACAATGCAGCCGA+GGG 0.565055 2.4:+786959 MS.gene067461:CDS
TCTTTACAACACTCAAACAC+AGG 0.578805 2.4:-785857 None:intergenic
ATTATACACAATACAAAACA+TGG 0.645969 2.4:+785325 MS.gene067461:CDS
TTTGAGTGTTGTAAAGAGGA+AGG 0.648639 2.4:+785863 MS.gene067461:CDS
TTACAACACTCAAACACAGG+AGG 0.658087 2.4:-785854 None:intergenic
ACTTACATTATGCAATGACA+TGG 0.673466 2.4:-785887 None:intergenic
ATGCAGCCGAGGGTGCATTG+TGG 0.682343 2.4:+786969 MS.gene067461:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAATTAAAATAAATAATT+GGG + chr2.4:785408-785427 MS.gene067461:intron 0.0%
!!! TTTTAATTAAAATAAATAAT+TGG + chr2.4:785407-785426 MS.gene067461:intron 0.0%
!!! TTTTATTTATGAAAAATGAA+GGG + chr2.4:785912-785931 MS.gene067461:intron 10.0%
!!! TTTTTATTTATGAAAAATGA+AGG + chr2.4:785911-785930 MS.gene067461:intron 10.0%
!! AAAAAAAATTATTACCTTGA+AGG - chr2.4:785378-785397 None:intergenic 15.0%
!!! ACAAAAAAAATGAACTTTTT+TGG - chr2.4:785712-785731 None:intergenic 15.0%
!! ATATAAACAACTTACAACTT+AGG + chr2.4:786201-786220 MS.gene067461:intron 20.0%
!! ATTATACACAATACAAAACA+TGG + chr2.4:785325-785344 MS.gene067461:CDS 20.0%
!! CTTGAATAATCAAATGAAAA+TGG + chr2.4:785536-785555 MS.gene067461:CDS 20.0%
!! TCATTATGAATTGTAGAAAA+GGG - chr2.4:786754-786773 None:intergenic 20.0%
!! TTCATTATGAATTGTAGAAA+AGG - chr2.4:786755-786774 None:intergenic 20.0%
!! TTTCATTTGATTATTCAAGT+TGG - chr2.4:785535-785554 None:intergenic 20.0%
!!! AATGAGAAAAATGAGTATTT+TGG + chr2.4:785753-785772 MS.gene067461:intron 20.0%
!!! GAAATGAAATTTTCTATAAG+TGG + chr2.4:785960-785979 MS.gene067461:intron 20.0%
!!! TTCATTTGATTATTCAAGTT+GGG - chr2.4:785534-785553 None:intergenic 20.0%
!!! TTTTGGTATTATTGTTTGTT+AGG + chr2.4:785770-785789 MS.gene067461:intron 20.0%
! AAAAACATTGTAGAGGTTTA+TGG + chr2.4:786911-786930 MS.gene067461:CDS 25.0%
! AAAAATTATTACCTTGAAGG+TGG - chr2.4:785375-785394 None:intergenic 25.0%
! AAAAGTTTATGCTGCAAAAA+TGG + chr2.4:785503-785522 MS.gene067461:CDS 25.0%
! AAAGGGAAGCAAAATATAAT+AGG - chr2.4:786737-786756 None:intergenic 25.0%
! AATATTGCAAAAGATTTAGC+TGG - chr2.4:786627-786646 None:intergenic 25.0%
! AATGAAGGGAAAAAAAACTA+TGG + chr2.4:785926-785945 MS.gene067461:intron 25.0%
! ACAATTCATAATGAAACTTG+AGG + chr2.4:786760-786779 MS.gene067461:intron 25.0%
! ATTCAAGGTTATTGTTGAAA+TGG + chr2.4:786844-786863 MS.gene067461:CDS 25.0%
! GGAAAACATGCAATAATTAA+TGG - chr2.4:785691-785710 None:intergenic 25.0%
! TCATGCAATAAGACAAATAT+TGG - chr2.4:786710-786729 None:intergenic 25.0%
! TCCTCATCAAAAAAAGAAAA+TGG + chr2.4:786937-786956 MS.gene067461:CDS 25.0%
! TCTCAAATTATTAACAGTGT+CGG + chr2.4:786390-786409 MS.gene067461:intron 25.0%
!! ATAAACCTCTACAATGTTTT+TGG - chr2.4:786912-786931 None:intergenic 25.0%
!! ATTTTCAACCAAGTGATTAT+AGG + chr2.4:786124-786143 MS.gene067461:intron 25.0%
!! TTTTCAACCAAGTGATTATA+GGG + chr2.4:786125-786144 MS.gene067461:intron 25.0%
AACCTGTGAAAAACATCAAT+TGG - chr2.4:786821-786840 None:intergenic 30.0%
AAGATTATTCCATTGCATGT+TGG + chr2.4:786598-786617 MS.gene067461:intron 30.0%
ACTTACATTATGCAATGACA+TGG - chr2.4:785890-785909 None:intergenic 30.0%
AGTAACCAAAAACATTGTAG+AGG + chr2.4:786904-786923 MS.gene067461:CDS 30.0%
TTAGAAGATGCATAGATTAG+TGG + chr2.4:786235-786254 MS.gene067461:intron 30.0%
TTGTGGTACTTAAAGCATAT+AGG + chr2.4:786986-787005 MS.gene067461:CDS 30.0%
! AAGTGGTATATTTTGTGTGT+TGG + chr2.4:785977-785996 MS.gene067461:intron 30.0%
! GACAAATATTGGTTGATATC+TGG - chr2.4:786699-786718 None:intergenic 30.0%
! GTTTGTTAGGTATGAAGAAA+GGG + chr2.4:785783-785802 MS.gene067461:intron 30.0%
! TGTTTGTTAGGTATGAAGAA+AGG + chr2.4:785782-785801 MS.gene067461:intron 30.0%
! TTGCAGCATAAACTTTTGTT+CGG - chr2.4:785500-785519 None:intergenic 30.0%
! TTTTCACAGGTTTACATTCA+AGG + chr2.4:786829-786848 MS.gene067461:intron 30.0%
!!! GCCATTTTCTTTTTTTGATG+AGG - chr2.4:786941-786960 None:intergenic 30.0%
AAGACAACAACTTCAGATGA+AGG + chr2.4:785657-785676 MS.gene067461:CDS 35.0%
AGACATGTGCTGTAAATCAT+TGG + chr2.4:785828-785847 MS.gene067461:CDS 35.0%
GTTATTGTTGAAATGGAGAC+AGG + chr2.4:786851-786870 MS.gene067461:CDS 35.0%
TCAGCTGTAGATTTCAAATC+AGG + chr2.4:786171-786190 MS.gene067461:intron 35.0%
TCTTTACAACACTCAAACAC+AGG - chr2.4:785860-785879 None:intergenic 35.0%
TGGAAGATGAAACTGAAGAT+TGG - chr2.4:785617-785636 None:intergenic 35.0%
TTATCGAACTTAAGTCACCA+AGG + chr2.4:786090-786109 MS.gene067461:intron 35.0%
! GAAAATTTGCTCTTCAACCT+TGG - chr2.4:786110-786129 None:intergenic 35.0%
! GACCAATTGATGTTTTTCAC+AGG + chr2.4:786816-786835 MS.gene067461:intron 35.0%
! TGTGTTTGAGTGTTGTAAAG+AGG + chr2.4:785859-785878 MS.gene067461:CDS 35.0%
! TTTGAGTGTTGTAAAGAGGA+AGG + chr2.4:785863-785882 MS.gene067461:CDS 35.0%
!!! CCAAAGAGAGTGTCATTTTA+GGG + chr2.4:785634-785653 MS.gene067461:CDS 35.0%
!!! GCATCAATGTTTTTCAAGAC+TGG - chr2.4:785591-785610 None:intergenic 35.0%
!!! TCCAAAGAGAGTGTCATTTT+AGG + chr2.4:785633-785652 MS.gene067461:CDS 35.0%
CCAAGTGATTATAGGGAAAC+TGG + chr2.4:786132-786151 MS.gene067461:intron 40.0%
CCAGTTTCCCTATAATCACT+TGG - chr2.4:786135-786154 None:intergenic 40.0%
CCCTAAAATGACACTCTCTT+TGG - chr2.4:785637-785656 None:intergenic 40.0%
GATGTTAGAGCCTAGTGTTT+CGG - chr2.4:786546-786565 None:intergenic 40.0%
TATATGTGTCAGTGTCGTGT+CGG - chr2.4:786348-786367 None:intergenic 40.0%
TATGTGCTTGAGTGCTTCAT+AGG - chr2.4:786276-786295 None:intergenic 40.0%
TTACAACACTCAAACACAGG+AGG - chr2.4:785857-785876 None:intergenic 40.0%
TTAGGTATGAAGAAAGGGTG+TGG + chr2.4:785788-785807 MS.gene067461:intron 40.0%
! GACGTTTTATGCAGGTATCT+GGG - chr2.4:786517-786536 None:intergenic 40.0%
ACTCAAGCACATACACTCCT+CGG + chr2.4:786283-786302 MS.gene067461:intron 45.0%
AGCTGGATACCAACATGCAA+TGG - chr2.4:786610-786629 None:intergenic 45.0%
ATGAAGCACGGATATGGACA+CGG - chr2.4:786445-786464 None:intergenic 45.0%
TAAGTACCACAATGCACCCT+CGG - chr2.4:786978-786997 None:intergenic 45.0%
TGAGTGCTTCATAGGTGTGT+GGG - chr2.4:786268-786287 None:intergenic 45.0%
TTCATAGCCACACACAGACA+CGG + chr2.4:786460-786479 MS.gene067461:intron 45.0%
TTCTTCTCACTCCACCTTCA+AGG + chr2.4:785361-785380 MS.gene067461:CDS 45.0%
TTGAGTGCTTCATAGGTGTG+TGG - chr2.4:786269-786288 None:intergenic 45.0%
! GGACGTTTTATGCAGGTATC+TGG - chr2.4:786518-786537 None:intergenic 45.0%
!!! ATTGTTTTTTTTTTTAAAAT+TGG + chr2.4:785441-785460 MS.gene067461:intron 5.0%
ACGGATATGGACACGGAAAC+CGG - chr2.4:786438-786457 None:intergenic 50.0%
CTGTGTGTGGCTATGAAGCA+CGG - chr2.4:786457-786476 None:intergenic 50.0%
GCACATACACTCCTCGGATT+AGG + chr2.4:786289-786308 MS.gene067461:intron 50.0%
GTGGCTATGAAGCACGGATA+TGG - chr2.4:786451-786470 None:intergenic 50.0%
TTCATAGGTGTGTGGGCACT+AGG - chr2.4:786261-786280 None:intergenic 50.0%
! GGAGTGTGGACGTTTTATGC+AGG - chr2.4:786525-786544 None:intergenic 50.0%
AGGTATCTGGGCTTGATCCC+AGG - chr2.4:786505-786524 None:intergenic 55.0%
CGTCCACACTCCGAAACACT+AGG + chr2.4:786533-786552 MS.gene067461:intron 55.0%
GAGCCTAGTGTTTCGGAGTG+TGG - chr2.4:786539-786558 None:intergenic 55.0%
GTCAGTATGCGTGTCGTGTC+CGG + chr2.4:786416-786435 MS.gene067461:intron 55.0%
! TGTCAGTGTCGTGTCGGTGT+TGG - chr2.4:786342-786361 None:intergenic 55.0%
ACACGACACCTGTCCGACAC+CGG - chr2.4:786319-786338 None:intergenic 60.0%
ACAGACACGGAGAGGGGGAA+GGG + chr2.4:786473-786492 MS.gene067461:intron 60.0%
AGCCACACACAGACACGGAG+AGG + chr2.4:786465-786484 MS.gene067461:intron 60.0%
AGGGGGAAGGGTGGAAACCT+GGG + chr2.4:786485-786504 MS.gene067461:intron 60.0%
CACACACAGACACGGAGAGG+GGG + chr2.4:786468-786487 MS.gene067461:intron 60.0%
CCACACACAGACACGGAGAG+GGG + chr2.4:786467-786486 MS.gene067461:intron 60.0%
GCAGCAGACAATGCAGCCGA+GGG + chr2.4:786959-786978 MS.gene067461:CDS 60.0%
GCCACACACAGACACGGAGA+GGG + chr2.4:786466-786485 MS.gene067461:intron 60.0%
! ACTCCTCGGATTAGGCGTCC+CGG + chr2.4:786297-786316 MS.gene067461:intron 60.0%
! ATGCAGCCGAGGGTGCATTG+TGG + chr2.4:786969-786988 MS.gene067461:CDS 60.0%
ACACCGGGACGCCTAATCCG+AGG - chr2.4:786303-786322 None:intergenic 65.0%
CACAGACACGGAGAGGGGGA+AGG + chr2.4:786472-786491 MS.gene067461:intron 65.0%
CACGACACCTGTCCGACACC+GGG - chr2.4:786318-786337 None:intergenic 65.0%
CCCCTCTCCGTGTCTGTGTG+TGG - chr2.4:786470-786489 None:intergenic 65.0%
GAGGGGGAAGGGTGGAAACC+TGG + chr2.4:786484-786503 MS.gene067461:intron 65.0%
GGCAGCAGACAATGCAGCCG+AGG + chr2.4:786958-786977 MS.gene067461:CDS 65.0%
! CGGATTAGGCGTCCCGGTGT+CGG + chr2.4:786303-786322 MS.gene067461:intron 65.0%
GACACGGAGAGGGGGAAGGG+TGG + chr2.4:786476-786495 MS.gene067461:intron 70.0%
! TAGGCGTCCCGGTGTCGGAC+AGG + chr2.4:786308-786327 MS.gene067461:intron 70.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 785270 787030 785270 ID=MS.gene067461
chr2.4 mRNA 785270 787030 785270 ID=MS.gene067461.t1;Parent=MS.gene067461
chr2.4 exon 785270 785382 785270 ID=MS.gene067461.t1.exon1;Parent=MS.gene067461.t1
chr2.4 CDS 785270 785382 785270 ID=cds.MS.gene067461.t1;Parent=MS.gene067461.t1
chr2.4 exon 785491 785678 785491 ID=MS.gene067461.t1.exon2;Parent=MS.gene067461.t1
chr2.4 CDS 785491 785678 785491 ID=cds.MS.gene067461.t1;Parent=MS.gene067461.t1
chr2.4 exon 785792 785903 785792 ID=MS.gene067461.t1.exon3;Parent=MS.gene067461.t1
chr2.4 CDS 785792 785903 785792 ID=cds.MS.gene067461.t1;Parent=MS.gene067461.t1
chr2.4 exon 786838 787030 786838 ID=MS.gene067461.t1.exon4;Parent=MS.gene067461.t1
chr2.4 CDS 786838 787030 786838 ID=cds.MS.gene067461.t1;Parent=MS.gene067461.t1
Gene Sequence

>MS.gene067461

ATGAAATTTCAACTATTTCATTCTGTTATTTGCACAGCTGAAGTCTGTTTACAGCATTATACACAATACAAAACATGGACAAGAGCAATAATTCTTCTCACTCCACCTTCAAGGTAATAATTTTTTTTCTTCATTTTTTTTAATTAAAATAAATAATTGGGTATATGAAAAATTGTTTTTTTTTTTAAAATTGGTTGAATTGAAATTCTTATCTTTTGCAGAGTAAACCGAACAAAAGTTTATGCTGCAAAAATGGTGAAACCCAACTTGAATAATCAAATGAAAATGGTTGAAACTGTTGAAAGCATTGTTCAAAATCCAGTCTTGAAAAACATTGATGCTGTCCAATCTTCAGTTTCATCTTCCAAAGAGAGTGTCATTTTAGGGAAGACAACAACTTCAGATGAAGGTAAACTAACCATTAATTATTGCATGTTTTCCAAAAAAGTTCATTTTTTTTGTATTTTTTTTCTTTCTTGTAAAAATGAGAAAAATGAGTATTTTGGTATTATTGTTTGTTAGGTATGAAGAAAGGGTGTGGTAGATCAAAGCTGTATGAGACATGTGCTGTAAATCATTGGAAGCCTCCTGTGTTTGAGTGTTGTAAAGAGGAAGGACCATGTCATTGCATAATGTAAGTCTTTTTATTTATGAAAAATGAAGGGAAAAAAAACTATGGTTATGATGATTGAAATGAAATTTTCTATAAGTGGTATATTTTGTGTGTTGGTAGCTGCAAGTTTATATAAATCAGAATCAATATAGCAAATAAGTGACATTTTCTATTTTGATTTATTCTTTTATTTTTTTCGCTGTGCGATTATCGAACTTAAGTCACCAAGGTTGAAGAGCAAATTTTCAACCAAGTGATTATAGGGAAACTGGCTTCTATGTTGATTTCTCAGCTGTAGATTTCAAATCAGGATTTTGTATATAAACAACTTACAACTTAGGTGCATAAGTTCTTAGAAGATGCATAGATTAGTGGCCTAGTGCCCACACACCTATGAAGCACTCAAGCACATACACTCCTCGGATTAGGCGTCCCGGTGTCGGACAGGTGTCGTGTCCAACACCGACACGACACTGACACATATAATTACACTAAATTATGTGATTTTCTCAAATTATTAACAGTGTCGGCATGTCAGTATGCGTGTCGTGTCCGGTTTCCGTGTCCATATCCGTGCTTCATAGCCACACACAGACACGGAGAGGGGGAAGGGTGGAAACCTGGGATCAAGCCCAGATACCTGCATAAAACGTCCACACTCCGAAACACTAGGCTCTAACATCTTGTAGATTTATTTCTGTTCATTCTTGTTCACAAGATTATTCCATTGCATGTTGGTATCCAGCTAAATCTTTTGCAATATTAGTCTTAATATAACGATTAATTGCTATGAAAAGTTGTTGAATTTCTTATCCAGATATCAACCAATATTTGTCTTATTGCATGACTTTCCTATTATATTTTGCTTCCCTTTTCTACAATTCATAATGAAACTTGAGGAAATACAGTCATAACTTTTTTCTTGTTCTCAGTGACCAATTGATGTTTTTCACAGGTTTACATTCAAGGTTATTGTTGAAATGGAGACAGGTAAAGCTTCTAAAAACATAAAGACAAGTGAAGTAACCAAAAACATTGTAGAGGTTTATGGTGCTCCTCATCAAAAAAAGAAAATGGCAGCAGACAATGCAGCCGAGGGTGCATTGTGGTACTTAAAGCATATAGGTTTTGTTTTGAAGAACAAATAA

Protein sequence

>MS.gene067461.t1

MKFQLFHSVICTAEVCLQHYTQYKTWTRAIILLTPPSRVNRTKVYAAKMVKPNLNNQMKMVETVESIVQNPVLKNIDAVQSSVSSSKESVILGKTTTSDEGMKKGCGRSKLYETCAVNHWKPPVFECCKEEGPCHCIMFTFKVIVEMETGKASKNIKTSEVTKNIVEVYGAPHQKKKMAADNAAEGALWYLKHIGFVLKNK