AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0783620


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0783620 MtrunA17_Chr5g0437991 96.648 179 6 0 1 179 1 179 4.59e-113 319
Msa0783620 MtrunA17_Chr3g0106861 46.835 158 82 1 25 180 1 158 2.12e-45 147
Msa0783620 MtrunA17_Chr7g0244441 59.350 123 49 1 51 173 6 127 1.79e-43 141
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0783620 AT2G40435.1 64.103 156 54 2 25 179 1 155 1.83e-67 203
Msa0783620 AT3G56220.1 57.419 155 63 3 25 177 1 154 9.23e-57 176
Msa0783620 AT2G40435.2 65.354 127 43 1 25 150 1 127 1.93e-55 172
Msa0783620 AT2G40435.3 65.354 127 43 1 25 150 1 127 2.06e-55 171
Msa0783620 AT3G56220.2 58.594 128 46 4 25 148 1 125 1.00e-42 140
Msa0783620 AT1G29270.1 34.752 141 83 6 25 159 1 138 1.31e-11 60.1

Find 26 sgRNAs with CRISPR-Local

Find 117 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGTTCTGAGGCCATTTAAA+AGG 0.297363 5_2:-67772133 None:intergenic
CTCAATTACCATAGGCAAGT+TGG 0.394555 5_2:-67772980 None:intergenic
AGAAAACACATGAGATCATA+TGG 0.396404 5_2:+67772089 None:intergenic
GCCTCAGAACTCATCAGAAT+TGG 0.404408 5_2:+67772144 Msa0783620:CDS
TCAATTACCATAGGCAAGTT+GGG 0.413845 5_2:-67772979 None:intergenic
TACAGTGGAAACCCTAGAAA+AGG 0.442701 5_2:+67773576 Msa0783620:CDS
GCTTACTGTGCTGGAAGCTA+GGG 0.457026 5_2:+67773678 Msa0783620:CDS
CTTTGCAATTTACACTTGAT+CGG 0.474337 5_2:-67774252 None:intergenic
TATTGAAAATCTAAAGGAAA+AGG 0.484456 5_2:+67772903 Msa0783620:CDS
AGAGATGAGGCTTACTGTGC+TGG 0.485736 5_2:+67773669 Msa0783620:CDS
GGCTTACTGTGCTGGAAGCT+AGG 0.491888 5_2:+67773677 Msa0783620:CDS
CCACAATCCCAACTTGCCTA+TGG 0.504234 5_2:+67772972 Msa0783620:CDS
AAAGTATATTGAAAATCTAA+AGG 0.516255 5_2:+67772897 Msa0783620:CDS
AGTAAGCCTCATCTCTTCAA+TGG 0.521158 5_2:-67773662 None:intergenic
CCATAGGCAAGTTGGGATTG+TGG 0.527764 5_2:-67772972 None:intergenic
ACAGTGGAAACCCTAGAAAA+GGG 0.541907 5_2:+67773577 Msa0783620:CDS
TTACCTCTCCTCCAACAGCT+TGG 0.548657 5_2:-67773726 None:intergenic
TTTCCAAGCTGTTGGAGGAG+AGG 0.549162 5_2:+67773723 Msa0783620:CDS
TTGAAGCCATTGAAGAGATG+AGG 0.583640 5_2:+67773656 Msa0783620:CDS
TGATGCATCGATTACGATCG+AGG 0.609202 5_2:-67772875 None:intergenic
GTATTGAAACAAGCATACCT+TGG 0.629414 5_2:-67773633 None:intergenic
ACCAATTCTGATGAGTTCTG+AGG 0.646466 5_2:-67772145 None:intergenic
CAAGCTGTGAAACAAGCAGT+GGG 0.658275 5_2:+67774200 Msa0783620:CDS
TGGACTTGTGCAGGTTACAG+TGG 0.658893 5_2:+67773561 Msa0783620:intron
CTTATGTAGAGTGAAGATCA+AGG 0.661626 5_2:+67774161 Msa0783620:intron
ACAAGCTGTGAAACAAGCAG+TGG 0.701888 5_2:+67774199 Msa0783620:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATAAAAAAAATATATAAAT+GGG - chr5_2:67773019-67773038 None:intergenic 0.0%
!! ATTAATTCCAATAATAAAAA+TGG - chr5_2:67772439-67772458 None:intergenic 10.0%
!! ACTTTCTTAATAAAAAATAT+TGG - chr5_2:67773045-67773064 None:intergenic 10.0%
!! AAGACTATATATTATTATTA+GGG - chr5_2:67774034-67774053 None:intergenic 10.0%
!!! GAATATTCTTTTATAGAATT+GGG - chr5_2:67772379-67772398 None:intergenic 15.0%
!!! TGAATATTCTTTTATAGAAT+TGG - chr5_2:67772380-67772399 None:intergenic 15.0%
!! AAAGTATATTGAAAATCTAA+AGG + chr5_2:67772897-67772916 Msa0783620:CDS 15.0%
!! AACTTATAAACAATTAAACA+CGG + chr5_2:67773237-67773256 Msa0783620:intron 15.0%
!! GAAGACTATATATTATTATT+AGG - chr5_2:67774035-67774054 None:intergenic 15.0%
!!! GCATATATTTTCATTAAAAT+TGG - chr5_2:67774414-67774433 None:intergenic 15.0%
!!! ATTTTAATGAAAATATATGC+CGG + chr5_2:67774414-67774433 Msa0783620:intron 15.0%
!! AAAGAGAAAACACAAAAAAA+TGG + chr5_2:67772194-67772213 Msa0783620:CDS 20.0%
!! TTTCATTGAGAATATATTGA+TGG - chr5_2:67772353-67772372 None:intergenic 20.0%
!! ACTAAAAAAAATAGCAAACT+TGG - chr5_2:67772466-67772485 None:intergenic 20.0%
!!! TTTTCTAATACTTCTTCTTA+TGG + chr5_2:67772818-67772837 Msa0783620:intron 20.0%
!! TATTGAAAATCTAAAGGAAA+AGG + chr5_2:67772903-67772922 Msa0783620:CDS 20.0%
!!! GAAATTTGAAATGGATTTTA+TGG + chr5_2:67773537-67773556 Msa0783620:intron 20.0%
!!! GCATATCAATTAAATTTTCA+TGG + chr5_2:67773818-67773837 Msa0783620:intron 20.0%
!!! GAGTAACGTTTTTATATAAA+GGG - chr5_2:67773922-67773941 None:intergenic 20.0%
!!! TGAGTAACGTTTTTATATAA+AGG - chr5_2:67773923-67773942 None:intergenic 20.0%
!! ATATAAAAACGTTACTCATT+TGG + chr5_2:67773925-67773944 Msa0783620:intron 20.0%
!! TATAAAAACGTTACTCATTT+GGG + chr5_2:67773926-67773945 Msa0783620:intron 20.0%
!! TTATTATTAGGGTTAAGATT+AGG - chr5_2:67774023-67774042 None:intergenic 20.0%
!!! TTTATCAAGCTTTATTTTGT+TGG + chr5_2:67774333-67774352 Msa0783620:three_prime_UTR 20.0%
!! TCATAACTCTTCCTTTTAAA+TGG + chr5_2:67772122-67772141 Msa0783620:exon 25.0%
! AACACAAAAAAATGGTTTCT+AGG + chr5_2:67772202-67772221 Msa0783620:CDS 25.0%
! ACACAAAAAAATGGTTTCTA+GGG + chr5_2:67772203-67772222 Msa0783620:CDS 25.0%
! AATGGAAAGAAAAGAAAGAT+AGG - chr5_2:67772320-67772339 None:intergenic 25.0%
!! TATCTTTCTTTTCTTTCCAT+TGG + chr5_2:67772319-67772338 Msa0783620:intron 25.0%
!!! TTTGGGTCCATTTTTATTAT+TGG + chr5_2:67772429-67772448 Msa0783620:intron 25.0%
! GCAGAAAGAATGAATTAATA+AGG - chr5_2:67772540-67772559 None:intergenic 25.0%
!! GTAATTTTCTCAATTACCAT+AGG - chr5_2:67772991-67773010 None:intergenic 25.0%
!! TTTTCGTTAACTATCTTGAA+GGG + chr5_2:67773192-67773211 Msa0783620:intron 25.0%
!!! GTCTCTTTGAATTGTTTTAT+TGG - chr5_2:67773332-67773351 None:intergenic 25.0%
!! ATTCTGCTTCAAGTTATTTA+GGG - chr5_2:67773389-67773408 None:intergenic 25.0%
!! AATTCTGCTTCAAGTTATTT+AGG - chr5_2:67773390-67773409 None:intergenic 25.0%
!!! TTCACTTTTTTTCTTCTTCT+TGG + chr5_2:67773412-67773431 Msa0783620:intron 25.0%
!!! TCACTTTTTTTCTTCTTCTT+GGG + chr5_2:67773413-67773432 Msa0783620:intron 25.0%
! TGCAAGTATGAAATTTGAAA+TGG + chr5_2:67773528-67773547 Msa0783620:intron 25.0%
!!! TTTGAAATGGATTTTATGGA+TGG + chr5_2:67773541-67773560 Msa0783620:intron 25.0%
!! TATAAGAAATCCCTTTTCTA+GGG - chr5_2:67773590-67773609 None:intergenic 25.0%
!! TTATAAGAAATCCCTTTTCT+AGG - chr5_2:67773591-67773610 None:intergenic 25.0%
! ACAAAAATATTGACAAGTGA+AGG - chr5_2:67773885-67773904 None:intergenic 25.0%
! ATAAAAACGTTACTCATTTG+GGG + chr5_2:67773927-67773946 Msa0783620:intron 25.0%
! GTACATTGAATCATTGATAT+TGG + chr5_2:67773976-67773995 Msa0783620:intron 25.0%
! TTAAGATTAGGCATCATTTA+TGG - chr5_2:67774011-67774030 None:intergenic 25.0%
!!! AGCTTTATTTTGTTGGTTTA+AGG + chr5_2:67774340-67774359 Msa0783620:three_prime_UTR 25.0%
!!! GGTTTTATGAAATTTATGTG+TGG + chr5_2:67774486-67774505 Msa0783620:intron 25.0%
TATACTCTTGTTCCTGATTT+GGG + chr5_2:67772412-67772431 Msa0783620:intron 30.0%
AATAAAAATGGACCCAAATC+AGG - chr5_2:67772427-67772446 None:intergenic 30.0%
GCTGATAAGAATATAGGATA+AGG - chr5_2:67772764-67772783 None:intergenic 30.0%
CACATAGCTGATAAGAATAT+AGG - chr5_2:67772770-67772789 None:intergenic 30.0%
CTATATTCTTATCAGCTATG+TGG + chr5_2:67772768-67772787 Msa0783620:intron 30.0%
TATGTGGAGCTTATTTGATA+TGG + chr5_2:67772784-67772803 Msa0783620:intron 30.0%
! CTTCTTATGGTTTTTATGCA+TGG + chr5_2:67772831-67772850 Msa0783620:intron 30.0%
! TATGGTTTTTATGCATGGTT+TGG + chr5_2:67772836-67772855 Msa0783620:intron 30.0%
! AATCAGAATTTGACTGCTTT+TGG + chr5_2:67773075-67773094 Msa0783620:intron 30.0%
! GTTTTCGTTAACTATCTTGA+AGG + chr5_2:67773191-67773210 Msa0783620:intron 30.0%
!!! TTTTCTAGGATAGATAGACA+AGG - chr5_2:67773358-67773377 None:intergenic 30.0%
!! AATTTTTGTTTCCAAGCTGT+TGG + chr5_2:67773715-67773734 Msa0783620:CDS 30.0%
TGGGACAAGCAATAAAAAAT+TGG + chr5_2:67774219-67774238 Msa0783620:CDS 30.0%
CTTTGCAATTTACACTTGAT+CGG - chr5_2:67774255-67774274 None:intergenic 30.0%
AAATATATGCCGGTAGTAAA+TGG + chr5_2:67774424-67774443 Msa0783620:intron 30.0%
TATGGATATTATGTGTATGC+TGG - chr5_2:67774514-67774533 None:intergenic 30.0%
TGTGTGTGTGTGTATATATA+TGG - chr5_2:67774532-67774551 None:intergenic 30.0%
GATAGGAGATAGAAAATGCA+GGG - chr5_2:67772303-67772322 None:intergenic 35.0%
AGATAGGAGATAGAAAATGC+AGG - chr5_2:67772304-67772323 None:intergenic 35.0%
ATTGATGGAGAGAAATCCAA+TGG - chr5_2:67772338-67772357 None:intergenic 35.0%
CTATACTCTTGTTCCTGATT+TGG + chr5_2:67772411-67772430 Msa0783620:intron 35.0%
! GGATGAGAGCATAAAAGTAT+AGG - chr5_2:67772574-67772593 None:intergenic 35.0%
TTTGAACCTAGATATGCATG+TGG - chr5_2:67772595-67772614 None:intergenic 35.0%
AGGATACACATACACTACTA+TGG - chr5_2:67772744-67772763 None:intergenic 35.0%
TCAATTACCATAGGCAAGTT+GGG - chr5_2:67772982-67773001 None:intergenic 35.0%
TTGTTAATATCGCGAGCTAA+TGG - chr5_2:67773275-67773294 None:intergenic 35.0%
TTAACAATCTCACAAGCGTT+AGG + chr5_2:67773288-67773307 Msa0783620:intron 35.0%
!! TTAGGGTCAAGACTTTTTCT+AGG - chr5_2:67773372-67773391 None:intergenic 35.0%
GTATTGAAACAAGCATACCT+TGG - chr5_2:67773636-67773655 None:intergenic 35.0%
TGATTCAATGTACAGCAACT+CGG - chr5_2:67773969-67773988 None:intergenic 35.0%
TCGTTATTGATGAACTTAGC+TGG - chr5_2:67774084-67774103 None:intergenic 35.0%
CTTATGTAGAGTGAAGATCA+AGG + chr5_2:67774161-67774180 Msa0783620:intron 35.0%
ATTGGCAGAACTTGAAGATT+TGG - chr5_2:67774396-67774415 None:intergenic 35.0%
!! GAGTTTTGACCATTTACTAC+CGG - chr5_2:67774436-67774455 None:intergenic 35.0%
GTAGTAAATGGTCAAAACTC+AGG + chr5_2:67774436-67774455 Msa0783620:intron 35.0%
!! GAGTTCTGAGGCCATTTAAA+AGG - chr5_2:67772136-67772155 None:intergenic 40.0%
ACCAATTCTGATGAGTTCTG+AGG - chr5_2:67772148-67772167 None:intergenic 40.0%
! GAGCATAAAAGTATAGGCAG+TGG - chr5_2:67772568-67772587 None:intergenic 40.0%
TCTCATCCACATGCATATCT+AGG + chr5_2:67772586-67772605 Msa0783620:intron 40.0%
CTCAATTACCATAGGCAAGT+TGG - chr5_2:67772983-67773002 None:intergenic 40.0%
CTAGGATAGATAGACAAGGA+TGG - chr5_2:67773354-67773373 None:intergenic 40.0%
!! TTTTATGGATGGACTTGTGC+AGG + chr5_2:67773552-67773571 Msa0783620:intron 40.0%
TACAGTGGAAACCCTAGAAA+AGG + chr5_2:67773576-67773595 Msa0783620:CDS 40.0%
ACAGTGGAAACCCTAGAAAA+GGG + chr5_2:67773577-67773596 Msa0783620:CDS 40.0%
! TTTTCAGCAAAAAGCAGCCA+AGG + chr5_2:67773616-67773635 Msa0783620:CDS 40.0%
TTGAAGCCATTGAAGAGATG+AGG + chr5_2:67773656-67773675 Msa0783620:CDS 40.0%
AGTAAGCCTCATCTCTTCAA+TGG - chr5_2:67773665-67773684 None:intergenic 40.0%
!! TTTTGTTTCCAAGCTGTTGG+AGG + chr5_2:67773718-67773737 Msa0783620:CDS 40.0%
! ATTTGGGGTTCTCGAGAAAA+GGG + chr5_2:67773942-67773961 Msa0783620:intron 40.0%
CCATCATTCTCATGCATGAT+GGG - chr5_2:67774128-67774147 None:intergenic 40.0%
TCCATCATTCTCATGCATGA+TGG - chr5_2:67774129-67774148 None:intergenic 40.0%
GTTAATGAGTAGATGCACGA+TGG + chr5_2:67774465-67774484 Msa0783620:intron 40.0%
GCCTCAGAACTCATCAGAAT+TGG + chr5_2:67772144-67772163 Msa0783620:CDS 45.0%
!! TGATGCATCGATTACGATCG+AGG - chr5_2:67772878-67772897 None:intergenic 45.0%
CTCACAAGCGTTAGGTTAGT+AGG + chr5_2:67773296-67773315 Msa0783620:intron 45.0%
! CATTTGGGGTTCTCGAGAAA+AGG + chr5_2:67773941-67773960 Msa0783620:intron 45.0%
CCCATCATGCATGAGAATGA+TGG + chr5_2:67774125-67774144 Msa0783620:intron 45.0%
ACAAGCTGTGAAACAAGCAG+TGG + chr5_2:67774199-67774218 Msa0783620:CDS 45.0%
CAAGCTGTGAAACAAGCAGT+GGG + chr5_2:67774200-67774219 Msa0783620:CDS 45.0%
!! CTATAAAAAAAATATATAAA+TGG - chr5_2:67773020-67773039 None:intergenic 5.0%
!! AAGAAAAATAATAATAAATA+TGG - chr5_2:67774306-67774325 None:intergenic 5.0%
! CCATAGGCAAGTTGGGATTG+TGG - chr5_2:67772975-67772994 None:intergenic 50.0%
CCACAATCCCAACTTGCCTA+TGG + chr5_2:67772972-67772991 Msa0783620:CDS 50.0%
TGGACTTGTGCAGGTTACAG+TGG + chr5_2:67773561-67773580 Msa0783620:intron 50.0%
AGAGATGAGGCTTACTGTGC+TGG + chr5_2:67773669-67773688 Msa0783620:CDS 50.0%
GCTTACTGTGCTGGAAGCTA+GGG + chr5_2:67773678-67773697 Msa0783620:CDS 50.0%
TTTCCAAGCTGTTGGAGGAG+AGG + chr5_2:67773723-67773742 Msa0783620:CDS 50.0%
TTACCTCTCCTCCAACAGCT+TGG - chr5_2:67773729-67773748 None:intergenic 50.0%
GGCTTACTGTGCTGGAAGCT+AGG + chr5_2:67773677-67773696 Msa0783620:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 67772099 67774601 67772099 ID=Msa0783620;Name=Msa0783620
chr5_2 mRNA 67772099 67774601 67772099 ID=Msa0783620-mRNA-1;Parent=Msa0783620;Name=Msa0783620-mRNA-1;_AED=0.13;_eAED=0.13;_QI=42|1|1|1|0.75|0.6|5|139|181
chr5_2 exon 67772099 67772290 67772099 ID=Msa0783620-mRNA-1:exon:20281;Parent=Msa0783620-mRNA-1
chr5_2 exon 67772865 67772993 67772865 ID=Msa0783620-mRNA-1:exon:20282;Parent=Msa0783620-mRNA-1
chr5_2 exon 67773574 67773744 67773574 ID=Msa0783620-mRNA-1:exon:20283;Parent=Msa0783620-mRNA-1
chr5_2 exon 67774170 67774380 67774170 ID=Msa0783620-mRNA-1:exon:20284;Parent=Msa0783620-mRNA-1
chr5_2 exon 67774578 67774601 67774578 ID=Msa0783620-mRNA-1:exon:20285;Parent=Msa0783620-mRNA-1
chr5_2 five_prime_UTR 67772099 67772140 67772099 ID=Msa0783620-mRNA-1:five_prime_utr;Parent=Msa0783620-mRNA-1
chr5_2 CDS 67772141 67772290 67772141 ID=Msa0783620-mRNA-1:cds;Parent=Msa0783620-mRNA-1
chr5_2 CDS 67772865 67772993 67772865 ID=Msa0783620-mRNA-1:cds;Parent=Msa0783620-mRNA-1
chr5_2 CDS 67773574 67773744 67773574 ID=Msa0783620-mRNA-1:cds;Parent=Msa0783620-mRNA-1
chr5_2 CDS 67774170 67774265 67774170 ID=Msa0783620-mRNA-1:cds;Parent=Msa0783620-mRNA-1
chr5_2 three_prime_UTR 67774266 67774380 67774266 ID=Msa0783620-mRNA-1:three_prime_utr;Parent=Msa0783620-mRNA-1
chr5_2 three_prime_UTR 67774578 67774601 67774578 ID=Msa0783620-mRNA-1:three_prime_utr;Parent=Msa0783620-mRNA-1
Gene Sequence

>Msa0783620

ATGGCCTCAGAACTCATCAGAATTGGTAGCAAAAGAAAAAGAGAGAGATATAGAAAGAGAAAACACAAAAAAATGGTTTCTAGGGAGCAAAAGAGAGCAGCACTGCATGAGAAGCTGCAACTTCTTCGTTCTGTTACTAACTCTCATGCTCTAAATGATACCTCGATCGTAATCGATGCATCAAAGTATATTGAAAATCTAAAGGAAAAGGTAGAACGACTGAACGAAGAAATAGCTTCTGCAGAAAGTTCAAGTGTCCACAATCCCAACTTGCCTATGGTTACAGTGGAAACCCTAGAAAAGGGATTTCTTATAAACGTTTTTTCAGCAAAAAGCAGCCAAGGTATGCTTGTTTCAATACTTGAAGCCATTGAAGAGATGAGGCTTACTGTGCTGGAAGCTAGGGTTTCTTGTACAGACAATTTTTGTTTCCAAGCTGTTGGAGGAGAGAGTGAAGATCAAGGTGAAACTATTGATGCACAAGCTGTGAAACAAGCAGTGGGACAAGCAATAAAAAATTGGAGTGAAAGTTCCGATCAAGTGTAA

Protein sequence

>Msa0783620

MASELIRIGSKRKRERYRKRKHKKMVSREQKRAALHEKLQLLRSVTNSHALNDTSIVIDASKYIENLKEKVERLNEEIASAESSSVHNPNLPMVTVETLEKGFLINVFSAKSSQGMLVSILEAIEEMRLTVLEARVSCTDNFCFQAVGGESEDQGETIDAQAVKQAVGQAIKNWSESSDQV*