AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1460340


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1460340 MtrunA17_Chr3g0146001 80.889 225 20 1 1 202 1 225 1.17e-126 362
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1460340 AT4G35250.1 95.092 163 8 0 40 202 65 227 5.05e-115 333

Find 66 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGAACTTCCTCCGTGATTC+TGG 0.246351 tig0040842:+17361 Msa1460340:CDS
AGCTGACTTCCTTCGTGATT+GGG 0.252587 tig0040842:+17090 Msa1460340:CDS
CAGCTGACTTCCTTCGTGAT+TGG 0.278974 tig0040842:+17089 Msa1460340:CDS
AGTATACTTGTTGGCCTAAC+AGG 0.305613 tig0040842:-16968 Msa1460340:intergenic
TGGCTGTTGGTAACCTCATC+AGG 0.328407 tig0040842:-16758 Msa1460340:intergenic
GTTGGAGCCACGGGGACTTT+GGG 0.335711 tig0040842:+16995 Msa1460340:CDS
CTTTGGGAAGGCAGATTGTT+CGG 0.350602 tig0040842:+17011 Msa1460340:CDS
CGGGATGTTTGTCGCAGTTA+TGG 0.356296 tig0040842:-17306 Msa1460340:intergenic
ACTATTCCTGCTACATTAGT+TGG 0.362432 tig0040842:+17151 Msa1460340:CDS
GGTTGGAGCCACGGGGACTT+TGG 0.381360 tig0040842:+16994 Msa1460340:CDS
GCCTATCAAAACAGTTGATT+GGG 0.393639 tig0040842:+17216 Msa1460340:CDS
AGCCTATCAAAACAGTTGAT+TGG 0.402139 tig0040842:+17215 Msa1460340:CDS
AGGATACGACGTCCGGTGTC+TGG 0.418347 tig0040842:+17048 Msa1460340:CDS
AGAGAAGAAGATTATTAGAG+TGG 0.430290 tig0040842:+16868 Msa1460340:CDS
ATACTTGTGGTTGGAGCCAC+GGG 0.432518 tig0040842:+16986 Msa1460340:CDS
TCAGAGAGGGCAGTGAATCT+TGG 0.438962 tig0040842:+16935 Msa1460340:CDS
CACATTGTCATCCGTTTATG+TGG 0.441513 tig0040842:+17391 Msa1460340:CDS
ACTGTTATTGACTGCGCCAC+TGG 0.449162 tig0040842:+17181 Msa1460340:CDS
ATCTCCATGAGTGGGACCTC+GGG 0.452186 tig0040842:-17325 Msa1460340:intergenic
CTTGCATGAAACCACATAAA+CGG 0.459989 tig0040842:-17402 Msa1460340:intergenic
TTGGACCAGGGACACCTGTT+AGG 0.469779 tig0040842:+16954 Msa1460340:CDS
GTTGGCCTAACAGGTGTCCC+TGG 0.478236 tig0040842:-16959 Msa1460340:intergenic
ATTCAATGTGCTAAAGCAAT+GGG 0.487829 tig0040842:+17256 Msa1460340:CDS
AAGTCAGCTGGAGCAGGCCT+CGG 0.491663 tig0040842:-17076 Msa1460340:intergenic
CGAAGGAAGTCAGCTGGAGC+AGG 0.509309 tig0040842:-17082 Msa1460340:intergenic
GAGAAGAAGATTATTAGAGT+GGG 0.514706 tig0040842:+16869 Msa1460340:CDS
TATTCAATGTGCTAAAGCAA+TGG 0.515599 tig0040842:+17255 Msa1460340:CDS
ACGACGTCCGGTGTCTGGTA+AGG 0.516950 tig0040842:+17053 Msa1460340:CDS
GCAGATTGTTCGGAGGGCAC+TGG 0.517013 tig0040842:+17021 Msa1460340:CDS
TCCGGTGTCTGGTAAGGCCG+AGG 0.517171 tig0040842:+17059 Msa1460340:CDS
TGAACTCCAACTAATGTAGC+AGG 0.522361 tig0040842:-17157 Msa1460340:intergenic
GATCTCCATGAGTGGGACCT+CGG 0.525916 tig0040842:-17326 Msa1460340:intergenic
CCAACCACAAGTATACTTGT+TGG 0.527488 tig0040842:-16977 Msa1460340:intergenic
GCTGACTTCCTTCGTGATTG+GGG 0.529696 tig0040842:+17091 Msa1460340:CDS
ATGTTTGTCGCAGTTATGGA+TGG 0.531609 tig0040842:-17302 Msa1460340:intergenic
GAGCCACGGGGACTTTGGGA+AGG 0.531810 tig0040842:+16999 Msa1460340:CDS
CAATCACGAAGGAAGTCAGC+TGG 0.537462 tig0040842:-17088 Msa1460340:intergenic
TATACTTGTGGTTGGAGCCA+CGG 0.537842 tig0040842:+16985 Msa1460340:CDS
AATGTAGCAGGAATAGTCTC+AGG 0.539300 tig0040842:-17145 Msa1460340:intergenic
ACATCCCGAGGTCCCACTCA+TGG 0.539781 tig0040842:+17321 Msa1460340:CDS
AGGCTCTTCAGGACGGCCAG+TGG 0.567494 tig0040842:-17197 Msa1460340:intergenic
ACCCTACCAGGTGTGGCTGT+TGG 0.574945 tig0040842:-16771 Msa1460340:intergenic
GGGAAGGCAGATTGTTCGGA+GGG 0.578906 tig0040842:+17015 Msa1460340:CDS
AGGGCAGTGAATCTTGGACC+AGG 0.579063 tig0040842:+16941 Msa1460340:CDS
TGGACGAAGGATACGACGTC+CGG 0.585255 tig0040842:+17041 Msa1460340:CDS
CGTCACCACCCTACCAGGTG+TGG 0.587901 tig0040842:-16778 Msa1460340:intergenic
TGAAAATGGCGACCCTGATG+AGG 0.599647 tig0040842:+16745 Msa1460340:CDS
ATCAAAACAGTTGATTGGGA+AGG 0.599943 tig0040842:+17220 Msa1460340:CDS
AGGTTACCAACAGCCACACC+TGG 0.599991 tig0040842:+16765 Msa1460340:CDS
CCAACAAGTATACTTGTGGT+TGG 0.608034 tig0040842:+16977 Msa1460340:CDS
CAATACTTGATCTCCATGAG+TGG 0.630169 tig0040842:-17334 Msa1460340:intergenic
TGGGAAGGCAGATTGTTCGG+AGG 0.630372 tig0040842:+17014 Msa1460340:CDS
GTTCGGAGGGCACTGGACGA+AGG 0.631129 tig0040842:+17028 Msa1460340:CDS
TGTGATTGAGTCCAGAATCA+CGG 0.632628 tig0040842:-17372 Msa1460340:intergenic
TAGGCCAACAAGTATACTTG+TGG 0.636061 tig0040842:+16973 Msa1460340:CDS
GGGCAGTGAATCTTGGACCA+GGG 0.636252 tig0040842:+16942 Msa1460340:CDS
GGCTGTTGGTAACCTCATCA+GGG 0.639067 tig0040842:-16757 Msa1460340:intergenic
TAGCAATAGCAATTCAGAGA+GGG 0.647837 tig0040842:+16922 Msa1460340:CDS
GCCTCGGCCTTACCAGACAC+CGG 0.648299 tig0040842:-17060 Msa1460340:intergenic
AATACTTGATCTCCATGAGT+GGG 0.653716 tig0040842:-17333 Msa1460340:intergenic
CTGCCTTCCCAAAGTCCCCG+TGG 0.669955 tig0040842:-17002 Msa1460340:intergenic
TAACTGCGACAAACATCCCG+AGG 0.701969 tig0040842:+17309 Msa1460340:CDS
CAGTTGCTCCCCAATCACGA+AGG 0.720142 tig0040842:-17099 Msa1460340:intergenic
ATAGCAATAGCAATTCAGAG+AGG 0.747554 tig0040842:+16921 Msa1460340:CDS
TACTTGTGGTTGGAGCCACG+GGG 0.774798 tig0040842:+16987 Msa1460340:CDS
GATTGAGTCCAGAATCACGG+AGG 0.804340 tig0040842:-17369 Msa1460330:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AACTCAACAAAATGATGACT+AGG - tig0040842:16833-16852 Msa1460340:intergenic 30.0%
! CATTTTGTTGAGTTTTGCAA+AGG + tig0040842:16839-16858 Msa1460340:intron 30.0%
AGAGAAGAAGATTATTAGAG+TGG + tig0040842:16868-16887 Msa1460340:CDS 30.0%
GAGAAGAAGATTATTAGAGT+GGG + tig0040842:16869-16888 Msa1460340:CDS 30.0%
TATTCAATGTGCTAAAGCAA+TGG + tig0040842:17255-17274 Msa1460340:CDS 30.0%
ATTCAATGTGCTAAAGCAAT+GGG + tig0040842:17256-17275 Msa1460340:CDS 30.0%
TGATGACTAGGATAAAGAAC+AGG - tig0040842:16821-16840 Msa1460340:intergenic 35.0%
! TTTGTTGAGTTTTGCAAAGG+TGG + tig0040842:16842-16861 Msa1460340:intron 35.0%
ATAGCAATAGCAATTCAGAG+AGG + tig0040842:16921-16940 Msa1460340:CDS 35.0%
TAGCAATAGCAATTCAGAGA+GGG + tig0040842:16922-16941 Msa1460340:CDS 35.0%
ACTATTCCTGCTACATTAGT+TGG + tig0040842:17151-17170 Msa1460340:CDS 35.0%
AGCCTATCAAAACAGTTGAT+TGG + tig0040842:17215-17234 Msa1460340:CDS 35.0%
GCCTATCAAAACAGTTGATT+GGG + tig0040842:17216-17235 Msa1460340:CDS 35.0%
!!! TCCCAATCAACTGTTTTGAT+AGG - tig0040842:17220-17239 Msa1460340:intergenic 35.0%
ATCAAAACAGTTGATTGGGA+AGG + tig0040842:17220-17239 Msa1460340:CDS 35.0%
AATACTTGATCTCCATGAGT+GGG - tig0040842:17336-17355 Msa1460340:intergenic 35.0%
! AGTATACTTGTTGGCCTAAC+AGG - tig0040842:16971-16990 Msa1460340:intergenic 40.0%
TAGGCCAACAAGTATACTTG+TGG + tig0040842:16973-16992 Msa1460340:CDS 40.0%
CCAACCACAAGTATACTTGT+TGG - tig0040842:16980-16999 Msa1460340:intergenic 40.0%
CCAACAAGTATACTTGTGGT+TGG + tig0040842:16977-16996 Msa1460340:CDS 40.0%
AATGTAGCAGGAATAGTCTC+AGG - tig0040842:17148-17167 Msa1460340:intergenic 40.0%
TGAACTCCAACTAATGTAGC+AGG - tig0040842:17160-17179 Msa1460340:intergenic 40.0%
! TTTTGATAGGCTCTTCAGGA+CGG - tig0040842:17207-17226 Msa1460340:intergenic 40.0%
!!! ACTGTTTTGATAGGCTCTTC+AGG - tig0040842:17211-17230 Msa1460340:intergenic 40.0%
ATGTTTGTCGCAGTTATGGA+TGG - tig0040842:17305-17324 Msa1460340:intergenic 40.0%
CAATACTTGATCTCCATGAG+TGG - tig0040842:17337-17356 Msa1460340:intergenic 40.0%
TGTGATTGAGTCCAGAATCA+CGG - tig0040842:17375-17394 Msa1460340:intergenic 40.0%
CACATTGTCATCCGTTTATG+TGG + tig0040842:17391-17410 Msa1460340:CDS 40.0%
TATACTTGTGGTTGGAGCCA+CGG + tig0040842:16985-17004 Msa1460340:CDS 45.0%
! CTTTGGGAAGGCAGATTGTT+CGG + tig0040842:17011-17030 Msa1460340:CDS 45.0%
! AGCTGACTTCCTTCGTGATT+GGG + tig0040842:17090-17109 Msa1460340:CDS 45.0%
TGAAAATGGCGACCCTGATG+AGG + tig0040842:16745-16764 Msa1460340:CDS 50.0%
!! GGCTGTTGGTAACCTCATCA+GGG - tig0040842:16760-16779 Msa1460340:intergenic 50.0%
!! TGGCTGTTGGTAACCTCATC+AGG - tig0040842:16761-16780 Msa1460340:intergenic 50.0%
TCAGAGAGGGCAGTGAATCT+TGG + tig0040842:16935-16954 Msa1460340:CDS 50.0%
ATACTTGTGGTTGGAGCCAC+GGG + tig0040842:16986-17005 Msa1460340:CDS 50.0%
CAATCACGAAGGAAGTCAGC+TGG - tig0040842:17091-17110 Msa1460340:intergenic 50.0%
! CAGCTGACTTCCTTCGTGAT+TGG + tig0040842:17089-17108 Msa1460340:CDS 50.0%
! GCTGACTTCCTTCGTGATTG+GGG + tig0040842:17091-17110 Msa1460340:CDS 50.0%
! ACTGTTATTGACTGCGCCAC+TGG + tig0040842:17181-17200 Msa1460340:CDS 50.0%
CGGGATGTTTGTCGCAGTTA+TGG - tig0040842:17309-17328 Msa1460340:intergenic 50.0%
TAACTGCGACAAACATCCCG+AGG + tig0040842:17309-17328 Msa1460340:CDS 50.0%
GAGAACTTCCTCCGTGATTC+TGG + tig0040842:17361-17380 Msa1460340:CDS 50.0%
GATTGAGTCCAGAATCACGG+AGG - tig0040842:17372-17391 Msa1460340:intergenic 50.0%
AGGTTACCAACAGCCACACC+TGG + tig0040842:16765-16784 Msa1460340:CDS 55.0%
TACCAACAGCCACACCTGGT+AGG + tig0040842:16769-16788 Msa1460340:intron 55.0%
ACCAACAGCCACACCTGGTA+GGG + tig0040842:16770-16789 Msa1460340:intron 55.0%
AGGGCAGTGAATCTTGGACC+AGG + tig0040842:16941-16960 Msa1460340:CDS 55.0%
GGGCAGTGAATCTTGGACCA+GGG + tig0040842:16942-16961 Msa1460340:CDS 55.0%
TTGGACCAGGGACACCTGTT+AGG + tig0040842:16954-16973 Msa1460340:CDS 55.0%
TACTTGTGGTTGGAGCCACG+GGG + tig0040842:16987-17006 Msa1460340:CDS 55.0%
TGGGAAGGCAGATTGTTCGG+AGG + tig0040842:17014-17033 Msa1460340:CDS 55.0%
GGGAAGGCAGATTGTTCGGA+GGG + tig0040842:17015-17034 Msa1460340:CDS 55.0%
TGGACGAAGGATACGACGTC+CGG + tig0040842:17041-17060 Msa1460340:CDS 55.0%
CAGTTGCTCCCCAATCACGA+AGG - tig0040842:17102-17121 Msa1460340:intergenic 55.0%
ATCTCCATGAGTGGGACCTC+GGG - tig0040842:17328-17347 Msa1460340:intergenic 55.0%
GATCTCCATGAGTGGGACCT+CGG - tig0040842:17329-17348 Msa1460340:intergenic 55.0%
ACCCTACCAGGTGTGGCTGT+TGG - tig0040842:16774-16793 Msa1460340:intergenic 60.0%
AACAGCCACACCTGGTAGGG+TGG + tig0040842:16773-16792 Msa1460340:intron 60.0%
! GTTGGCCTAACAGGTGTCCC+TGG - tig0040842:16962-16981 Msa1460340:intergenic 60.0%
GTTGGAGCCACGGGGACTTT+GGG + tig0040842:16995-17014 Msa1460340:CDS 60.0%
! GCAGATTGTTCGGAGGGCAC+TGG + tig0040842:17021-17040 Msa1460340:CDS 60.0%
AGGATACGACGTCCGGTGTC+TGG + tig0040842:17048-17067 Msa1460340:CDS 60.0%
ACGACGTCCGGTGTCTGGTA+AGG + tig0040842:17053-17072 Msa1460340:CDS 60.0%
AAGTCAGCTGGAGCAGGCCT+CGG - tig0040842:17079-17098 Msa1460340:intergenic 60.0%
CGAAGGAAGTCAGCTGGAGC+AGG - tig0040842:17085-17104 Msa1460340:intergenic 60.0%
ACATCCCGAGGTCCCACTCA+TGG + tig0040842:17321-17340 Msa1460340:CDS 60.0%
CGTCACCACCCTACCAGGTG+TGG - tig0040842:16781-16800 Msa1460340:intergenic 65.0%
CGTCTCGTCACCACCCTACC+AGG - tig0040842:16786-16805 Msa1460340:intergenic 65.0%
! GGGTGGTGACGAGACGAGAG+AGG + tig0040842:16790-16809 Msa1460340:intron 65.0%
GGTTGGAGCCACGGGGACTT+TGG + tig0040842:16994-17013 Msa1460340:CDS 65.0%
! GAGCCACGGGGACTTTGGGA+AGG + tig0040842:16999-17018 Msa1460340:CDS 65.0%
CTGCCTTCCCAAAGTCCCCG+TGG - tig0040842:17005-17024 Msa1460340:intergenic 65.0%
!! GTTCGGAGGGCACTGGACGA+AGG + tig0040842:17028-17047 Msa1460340:CDS 65.0%
TCCGGTGTCTGGTAAGGCCG+AGG + tig0040842:17059-17078 Msa1460340:CDS 65.0%
GCCTCGGCCTTACCAGACAC+CGG - tig0040842:17063-17082 Msa1460340:intergenic 65.0%
AGGCTCTTCAGGACGGCCAG+TGG - tig0040842:17200-17219 Msa1460340:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0040842 gene 16744 17423 16744 ID=Msa1460340;Name=Msa1460340
tig0040842 mRNA 16744 17423 16744 ID=Msa1460340-mRNA-1;Parent=Msa1460340;Name=Msa1460340-mRNA-1;_AED=0.07;_eAED=0.11;_QI=0|0|0|1|1|1|2|0|202
tig0040842 exon 16744 16786 16744 ID=Msa1460340-mRNA-1:exon:22675;Parent=Msa1460340-mRNA-1
tig0040842 exon 16861 17423 16861 ID=Msa1460340-mRNA-1:exon:22676;Parent=Msa1460340-mRNA-1
tig0040842 CDS 16744 16786 16744 ID=Msa1460340-mRNA-1:cds;Parent=Msa1460340-mRNA-1
tig0040842 CDS 16861 17423 16861 ID=Msa1460340-mRNA-1:cds;Parent=Msa1460340-mRNA-1
Gene Sequence

>Msa1460340

ATGAAAATGGCGACCCTGATGAGGTTACCAACAGCCACACCTGGTGGAGAAGAGAAGAAGATTATTAGAGTGGGAGTGAAATGCAATATCAACAGCAATAGCAATAGCAATAGCAATTCAGAGAGGGCAGTGAATCTTGGACCAGGGACACCTGTTAGGCCAACAAGTATACTTGTGGTTGGAGCCACGGGGACTTTGGGAAGGCAGATTGTTCGGAGGGCACTGGACGAAGGATACGACGTCCGGTGTCTGGTAAGGCCGAGGCCTGCTCCAGCTGACTTCCTTCGTGATTGGGGAGCAACTGTTGTGAATGCTGATCTTAGTAAACCTGAGACTATTCCTGCTACATTAGTTGGAGTTCATACTGTTATTGACTGCGCCACTGGCCGTCCTGAAGAGCCTATCAAAACAGTTGATTGGGAAGGTAAAGTTGCTCTTATTCAATGTGCTAAAGCAATGGGTATTCAGAAATATGTTTTCTATTCCATCCATAACTGCGACAAACATCCCGAGGTCCCACTCATGGAGATCAAGTATTGCACTGAGAACTTCCTCCGTGATTCTGGACTCAATCACATTGTCATCCGTTTATGTGGTTTCATGCAA

Protein sequence

>Msa1460340

MKMATLMRLPTATPGGEEKKIIRVGVKCNINSNSNSNSNSERAVNLGPGTPVRPTSILVVGATGTLGRQIVRRALDEGYDVRCLVRPRPAPADFLRDWGATVVNADLSKPETIPATLVGVHTVIDCATGRPEEPIKTVDWEGKVALIQCAKAMGIQKYVFYSIHNCDKHPEVPLMEIKYCTENFLRDSGLNHIVIRLCGFMQ