AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1335720


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1335720 MtrunA17_Chr1g0153661 79.461 297 15 3 1 293 1 255 9.31e-156 434
Msa1335720 MtrunA17_Chr3g0133811 46.377 276 109 11 31 291 43 294 1.00e-31 119
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1335720 AT5G42750.1 36.943 314 154 12 10 284 17 325 2.29e-19 87.0

Find 41 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGGACTTATTGTTATTATT+AGG 0.149195 tig0000674:+12569 None:intergenic
TCTGAGAATAATTCTCTTAT+AGG 0.206112 tig0000674:+12392 None:intergenic
GGAATTATGTGAAGATAATT+TGG 0.215579 tig0000674:+12550 None:intergenic
TGGACTTATTGTTATTATTA+GGG 0.253926 tig0000674:+12570 None:intergenic
GGGAAGAGGATTGTGAATTT+TGG 0.259584 tig0000674:+12645 None:intergenic
TCTTGTTTATTTCTAGTTCT+AGG 0.261211 tig0000674:+12056 None:intergenic
AAGGGAAGTGTGAGAAGATT+TGG 0.268332 tig0000674:+12465 None:intergenic
TTATCATTAAGTTCAAATAA+AGG 0.298290 tig0000674:-12254 Msa1335720:CDS
CTGAGAATAATTCTCTTATA+GGG 0.331590 tig0000674:+12393 None:intergenic
TATCATTAAGTTCAAATAAA+GGG 0.343051 tig0000674:-12253 Msa1335720:CDS
TCCTCCTAGTGATAGTAGTA+TGG 0.363665 tig0000674:-11925 Msa1335720:CDS
ATTAGGGAATGTTGTGTTGA+AGG 0.417429 tig0000674:+12586 None:intergenic
AGTTCAAATAAAGGGACAAA+AGG 0.423209 tig0000674:-12245 Msa1335720:CDS
AAAAGAACACCACTGTTTGA+TGG 0.436121 tig0000674:+11966 None:intergenic
AACAAGAATTGATGAAAGGT+TGG 0.450874 tig0000674:-12040 Msa1335720:CDS
TGAAGGAAAATTCATGAGAA+GGG 0.465614 tig0000674:+12624 None:intergenic
TGGTGTGAACATGGTTGTGA+TGG 0.479025 tig0000674:+12665 None:intergenic
AAATTCATGAGAAGGGGAAG+AGG 0.485413 tig0000674:+12631 None:intergenic
GTTCAAATAAAGGGACAAAA+GGG 0.497754 tig0000674:-12244 Msa1335720:CDS
CTATCACTAGGAGGAGTAAG+AGG 0.500454 tig0000674:+11933 None:intergenic
CACAGCACTTGATTTATCAC+CGG 0.503814 tig0000674:-12525 Msa1335720:CDS
GAACGAGGCGATATCGATGA+AGG 0.509000 tig0000674:+12446 None:intergenic
GTGAAGGAAAATTCATGAGA+AGG 0.523242 tig0000674:+12623 None:intergenic
TGATAAATCAAGTGCTGTGA+AGG 0.533555 tig0000674:+12529 None:intergenic
TCGTTCTTCGACAAATTCCA+TGG 0.546869 tig0000674:-12429 Msa1335720:CDS
GGAGAAGTTCTCATTGATGC+TGG 0.584601 tig0000674:+11987 None:intergenic
AATAAACAAGAATTGATGAA+AGG 0.588793 tig0000674:-12044 Msa1335720:CDS
AGGGAGGGTGAAACTATCCA+TGG 0.597551 tig0000674:+12412 None:intergenic
TGGAAGAAAATATCATCAGC+CGG 0.598474 tig0000674:+12506 None:intergenic
AAGTGTGAGAAGATTTGGAG+AGG 0.598817 tig0000674:+12470 None:intergenic
AAAGGTTGGAGTATGAAACT+AGG 0.604735 tig0000674:-12026 Msa1335720:CDS
AGAATAATTCTCTTATAGGG+AGG 0.614827 tig0000674:+12396 None:intergenic
ATGGAATTTGTCGAAGAACG+AGG 0.618111 tig0000674:+12431 None:intergenic
GAATAATTCTCTTATAGGGA+GGG 0.624482 tig0000674:+12397 None:intergenic
GAAGGAAAATTCATGAGAAG+GGG 0.624850 tig0000674:+12625 None:intergenic
AACGAGGCGATATCGATGAA+GGG 0.633590 tig0000674:+12447 None:intergenic
TCTTCCATACTACTATCACT+AGG 0.641134 tig0000674:+11921 None:intergenic
GGAGAGGAAGTAAATGACCA+TGG 0.661995 tig0000674:+12486 None:intergenic
TCCATACTACTATCACTAGG+AGG 0.675840 tig0000674:+11924 None:intergenic
GGAATTGTGTGAGATTGTGA+AGG 0.688265 tig0000674:+12607 None:intergenic
AGAACTTCTCCATCAAACAG+TGG 0.700411 tig0000674:-11975 Msa1335720:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATATAGAATCATCAAAAA+AGG - tig0000674:12246-12265 Msa1335720:CDS 15.0%
!! TAATGATAAAAATGAAAACT+TGG + tig0000674:12284-12303 None:intergenic 15.0%
!! TTATCATTAAGTTCAAATAA+AGG - tig0000674:12295-12314 Msa1335720:CDS 15.0%
!! TATCATTAAGTTCAAATAAA+GGG - tig0000674:12296-12315 Msa1335720:CDS 15.0%
!!! ATTTTCTCTATTTTGAAAAA+TGG + tig0000674:12430-12449 None:intergenic 15.0%
!! AAATATAGAATCATCAAAAA+AGG - tig0000674:12246-12265 Msa1335720:CDS 15.0%
!! TAATGATAAAAATGAAAACT+TGG + tig0000674:12284-12303 None:intergenic 15.0%
!! TTATCATTAAGTTCAAATAA+AGG - tig0000674:12295-12314 Msa1335720:CDS 15.0%
!! TATCATTAAGTTCAAATAAA+GGG - tig0000674:12296-12315 Msa1335720:CDS 15.0%
!!! ATTTTCTCTATTTTGAAAAA+TGG + tig0000674:12430-12449 None:intergenic 15.0%
!!! TGGACTTATTGTTATTATTA+GGG + tig0000674:11982-12001 None:intergenic 20.0%
!!! TTGGACTTATTGTTATTATT+AGG + tig0000674:11983-12002 None:intergenic 20.0%
!!! AAAAAGTCTTATTCTTATTC+AGG - tig0000674:12460-12479 Msa1335720:CDS 20.0%
!! AATAAACAAGAATTGATGAA+AGG - tig0000674:12505-12524 Msa1335720:CDS 20.0%
!!! TGGACTTATTGTTATTATTA+GGG + tig0000674:11982-12001 None:intergenic 20.0%
!!! TTGGACTTATTGTTATTATT+AGG + tig0000674:11983-12002 None:intergenic 20.0%
!!! AAAAAGTCTTATTCTTATTC+AGG - tig0000674:12460-12479 Msa1335720:CDS 20.0%
!! AATAAACAAGAATTGATGAA+AGG - tig0000674:12505-12524 Msa1335720:CDS 20.0%
! GGAATTATGTGAAGATAATT+TGG + tig0000674:12002-12021 None:intergenic 25.0%
! CTGAGAATAATTCTCTTATA+GGG + tig0000674:12159-12178 None:intergenic 25.0%
! TCTGAGAATAATTCTCTTAT+AGG + tig0000674:12160-12179 None:intergenic 25.0%
!!! AGTGAAAAAGTACTTAAGAA+AGG - tig0000674:12399-12418 Msa1335720:CDS 25.0%
!!! TCTTGTTTATTTCTAGTTCT+AGG + tig0000674:12496-12515 None:intergenic 25.0%
! GGAATTATGTGAAGATAATT+TGG + tig0000674:12002-12021 None:intergenic 25.0%
! CTGAGAATAATTCTCTTATA+GGG + tig0000674:12159-12178 None:intergenic 25.0%
! TCTGAGAATAATTCTCTTAT+AGG + tig0000674:12160-12179 None:intergenic 25.0%
!!! AGTGAAAAAGTACTTAAGAA+AGG - tig0000674:12399-12418 Msa1335720:CDS 25.0%
!!! TCTTGTTTATTTCTAGTTCT+AGG + tig0000674:12496-12515 None:intergenic 25.0%
TGAAGGAAAATTCATGAGAA+GGG + tig0000674:11928-11947 None:intergenic 30.0%
GAATAATTCTCTTATAGGGA+GGG + tig0000674:12155-12174 None:intergenic 30.0%
AGAATAATTCTCTTATAGGG+AGG + tig0000674:12156-12175 None:intergenic 30.0%
AGAATCATCAAAAAAGGTAG+AGG - tig0000674:12252-12271 Msa1335720:CDS 30.0%
GAATCATCAAAAAAGGTAGA+GGG - tig0000674:12253-12272 Msa1335720:CDS 30.0%
AGTTCAAATAAAGGGACAAA+AGG - tig0000674:12304-12323 Msa1335720:CDS 30.0%
GTTCAAATAAAGGGACAAAA+GGG - tig0000674:12305-12324 Msa1335720:CDS 30.0%
AACAAGAATTGATGAAAGGT+TGG - tig0000674:12509-12528 Msa1335720:CDS 30.0%
TGAAGGAAAATTCATGAGAA+GGG + tig0000674:11928-11947 None:intergenic 30.0%
GAATAATTCTCTTATAGGGA+GGG + tig0000674:12155-12174 None:intergenic 30.0%
AGAATAATTCTCTTATAGGG+AGG + tig0000674:12156-12175 None:intergenic 30.0%
AGAATCATCAAAAAAGGTAG+AGG - tig0000674:12252-12271 Msa1335720:CDS 30.0%
GAATCATCAAAAAAGGTAGA+GGG - tig0000674:12253-12272 Msa1335720:CDS 30.0%
AGTTCAAATAAAGGGACAAA+AGG - tig0000674:12304-12323 Msa1335720:CDS 30.0%
GTTCAAATAAAGGGACAAAA+GGG - tig0000674:12305-12324 Msa1335720:CDS 30.0%
AACAAGAATTGATGAAAGGT+TGG - tig0000674:12509-12528 Msa1335720:CDS 30.0%
!! TGTGAATTTTGGTGTGAACA+TGG + tig0000674:11896-11915 None:intergenic 35.0%
GAAGGAAAATTCATGAGAAG+GGG + tig0000674:11927-11946 None:intergenic 35.0%
GTGAAGGAAAATTCATGAGA+AGG + tig0000674:11929-11948 None:intergenic 35.0%
ATTAGGGAATGTTGTGTTGA+AGG + tig0000674:11966-11985 None:intergenic 35.0%
! TGATAAATCAAGTGCTGTGA+AGG + tig0000674:12023-12042 None:intergenic 35.0%
TGGAAGAAAATATCATCAGC+CGG + tig0000674:12046-12065 None:intergenic 35.0%
! GCTGATGATATTTTCTTCCA+TGG - tig0000674:12046-12065 Msa1335720:CDS 35.0%
AAAGGTTGGAGTATGAAACT+AGG - tig0000674:12523-12542 Msa1335720:CDS 35.0%
AAAAGAACACCACTGTTTGA+TGG + tig0000674:12586-12605 None:intergenic 35.0%
TCTTCCATACTACTATCACT+AGG + tig0000674:12631-12650 None:intergenic 35.0%
!! TGTGAATTTTGGTGTGAACA+TGG + tig0000674:11896-11915 None:intergenic 35.0%
GAAGGAAAATTCATGAGAAG+GGG + tig0000674:11927-11946 None:intergenic 35.0%
GTGAAGGAAAATTCATGAGA+AGG + tig0000674:11929-11948 None:intergenic 35.0%
ATTAGGGAATGTTGTGTTGA+AGG + tig0000674:11966-11985 None:intergenic 35.0%
! TGATAAATCAAGTGCTGTGA+AGG + tig0000674:12023-12042 None:intergenic 35.0%
TGGAAGAAAATATCATCAGC+CGG + tig0000674:12046-12065 None:intergenic 35.0%
! GCTGATGATATTTTCTTCCA+TGG - tig0000674:12046-12065 Msa1335720:CDS 35.0%
AAAGGTTGGAGTATGAAACT+AGG - tig0000674:12523-12542 Msa1335720:CDS 35.0%
AAAAGAACACCACTGTTTGA+TGG + tig0000674:12586-12605 None:intergenic 35.0%
TCTTCCATACTACTATCACT+AGG + tig0000674:12631-12650 None:intergenic 35.0%
! GGGAAGAGGATTGTGAATTT+TGG + tig0000674:11907-11926 None:intergenic 40.0%
AAATTCATGAGAAGGGGAAG+AGG + tig0000674:11921-11940 None:intergenic 40.0%
GGAATTGTGTGAGATTGTGA+AGG + tig0000674:11945-11964 None:intergenic 40.0%
CACAGCACTTGATTTATCAC+CGG - tig0000674:12024-12043 Msa1335720:CDS 40.0%
AAGTGTGAGAAGATTTGGAG+AGG + tig0000674:12082-12101 None:intergenic 40.0%
! AAGGGAAGTGTGAGAAGATT+TGG + tig0000674:12087-12106 None:intergenic 40.0%
ATGGAATTTGTCGAAGAACG+AGG + tig0000674:12121-12140 None:intergenic 40.0%
TCGTTCTTCGACAAATTCCA+TGG - tig0000674:12120-12139 Msa1335720:CDS 40.0%
AGAACTTCTCCATCAAACAG+TGG - tig0000674:12574-12593 Msa1335720:CDS 40.0%
TCCTCCTAGTGATAGTAGTA+TGG - tig0000674:12624-12643 Msa1335720:CDS 40.0%
TCCATACTACTATCACTAGG+AGG + tig0000674:12628-12647 None:intergenic 40.0%
! GGGAAGAGGATTGTGAATTT+TGG + tig0000674:11907-11926 None:intergenic 40.0%
AAATTCATGAGAAGGGGAAG+AGG + tig0000674:11921-11940 None:intergenic 40.0%
GGAATTGTGTGAGATTGTGA+AGG + tig0000674:11945-11964 None:intergenic 40.0%
CACAGCACTTGATTTATCAC+CGG - tig0000674:12024-12043 Msa1335720:CDS 40.0%
AAGTGTGAGAAGATTTGGAG+AGG + tig0000674:12082-12101 None:intergenic 40.0%
! AAGGGAAGTGTGAGAAGATT+TGG + tig0000674:12087-12106 None:intergenic 40.0%
ATGGAATTTGTCGAAGAACG+AGG + tig0000674:12121-12140 None:intergenic 40.0%
TCGTTCTTCGACAAATTCCA+TGG - tig0000674:12120-12139 Msa1335720:CDS 40.0%
AGAACTTCTCCATCAAACAG+TGG - tig0000674:12574-12593 Msa1335720:CDS 40.0%
TCCTCCTAGTGATAGTAGTA+TGG - tig0000674:12624-12643 Msa1335720:CDS 40.0%
TCCATACTACTATCACTAGG+AGG + tig0000674:12628-12647 None:intergenic 40.0%
TGGTGTGAACATGGTTGTGA+TGG + tig0000674:11887-11906 None:intergenic 45.0%
GGAGAGGAAGTAAATGACCA+TGG + tig0000674:12066-12085 None:intergenic 45.0%
AACGAGGCGATATCGATGAA+GGG + tig0000674:12105-12124 None:intergenic 45.0%
! TGCTGCTACTGTCTTTTGTG+GGG + tig0000674:12201-12220 None:intergenic 45.0%
! CTGCTGCTACTGTCTTTTGT+GGG + tig0000674:12202-12221 None:intergenic 45.0%
GGAGAAGTTCTCATTGATGC+TGG + tig0000674:12565-12584 None:intergenic 45.0%
CTATCACTAGGAGGAGTAAG+AGG + tig0000674:12619-12638 None:intergenic 45.0%
TGGTGTGAACATGGTTGTGA+TGG + tig0000674:11887-11906 None:intergenic 45.0%
GGAGAGGAAGTAAATGACCA+TGG + tig0000674:12066-12085 None:intergenic 45.0%
AACGAGGCGATATCGATGAA+GGG + tig0000674:12105-12124 None:intergenic 45.0%
! TGCTGCTACTGTCTTTTGTG+GGG + tig0000674:12201-12220 None:intergenic 45.0%
! CTGCTGCTACTGTCTTTTGT+GGG + tig0000674:12202-12221 None:intergenic 45.0%
GGAGAAGTTCTCATTGATGC+TGG + tig0000674:12565-12584 None:intergenic 45.0%
CTATCACTAGGAGGAGTAAG+AGG + tig0000674:12619-12638 None:intergenic 45.0%
GAACGAGGCGATATCGATGA+AGG + tig0000674:12106-12125 None:intergenic 50.0%
AGGGAGGGTGAAACTATCCA+TGG + tig0000674:12140-12159 None:intergenic 50.0%
! GCTGCTGCTACTGTCTTTTG+TGG + tig0000674:12203-12222 None:intergenic 50.0%
GAACGAGGCGATATCGATGA+AGG + tig0000674:12106-12125 None:intergenic 50.0%
AGGGAGGGTGAAACTATCCA+TGG + tig0000674:12140-12159 None:intergenic 50.0%
! GCTGCTGCTACTGTCTTTTG+TGG + tig0000674:12203-12222 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0000674 gene 11845 12726 11845 ID=Msa1335720;Name=Msa1335720
tig0000674 mRNA 11845 12726 11845 ID=Msa1335720-mRNA-1;Parent=Msa1335720;Name=Msa1335720-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|293
tig0000674 exon 11845 12726 11845 ID=Msa1335720-mRNA-1:exon:365;Parent=Msa1335720-mRNA-1
tig0000674 CDS 11845 12726 11845 ID=Msa1335720-mRNA-1:cds;Parent=Msa1335720-mRNA-1
Gene Sequence

>Msa1335720

ATGGAAAAACAAATTGAAGTAGAAAATCAACAACAAAAACCATCACAACCATGTTCACACCAAAATTCACAATCCTCTTCCCCTTCTCATGAATTTTCCTTCACAATCTCACACAATTCCTTCAACACAACATTCCCTAATAATAACAATAAGTCCAAATTATCTTCACATAATTCCTTCACAGCACTTGATTTATCACCGGCTGATGATATTTTCTTCCATGGTCATTTACTTCCTCTCCAAATCTTCTCACACTTCCCTTCATCGATATCGCCTCGTTCTTCGACAAATTCCATGGATAGTTTCACCCTCCCTATAAGAGAATTATTCTCAGAAGATGATGATGAAAATCTCCCCACAAAAGACAGTAGCAGCAGCAGCAACAGCAACAATAGCAGCAAAAATATAGAATCATCAAAAAAGGTAGAGGGTAAGTCCAAGTTTTCATTTTTATCATTAAGTTCAAATAAAGGGACAAAAGGGTGTATTAAAGAGAAAGAAGATAAAGTGAAGAATAAGAAGAAGCTGAGATTTGATTTTGATGTGTTACATGCAGTGAAAAAGTACTTAAGAAAGGTGAAGCCATTTTTCAAAATAGAGAAAATTAGAGAACATAAAAAGTCTTATTCTTATTCAGGAAATGTAACACCTAGAACTAGAAATAAACAAGAATTGATGAAAGGTTGGAGTATGAAACTAGGACAATATTATTCAGCACCAGCATCAATGAGAACTTCTCCATCAAACAGTGGTGTTCTTTTTGCTACTGCACCTCTTACTCCTCCTAGTGATAGTAGTATGGAAGATTTACAAGCTGCTATTCAATCTGCAATTGCTCATTGCAAAAATTCATATTCAAAAGAAGAGAAACTCAATTGCTGA

Protein sequence

>Msa1335720

MEKQIEVENQQQKPSQPCSHQNSQSSSPSHEFSFTISHNSFNTTFPNNNNKSKLSSHNSFTALDLSPADDIFFHGHLLPLQIFSHFPSSISPRSSTNSMDSFTLPIRELFSEDDDENLPTKDSSSSSNSNNSSKNIESSKKVEGKSKFSFLSLSSNKGTKGCIKEKEDKVKNKKKLRFDFDVLHAVKKYLRKVKPFFKIEKIREHKKSYSYSGNVTPRTRNKQELMKGWSMKLGQYYSAPASMRTSPSNSGVLFATAPLTPPSDSSMEDLQAAIQSAIAHCKNSYSKEEKLNC*