AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1407670


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1407670 MtrunA17_Chr3g0126341 98.413 63 1 0 1 63 1 63 3.12e-38 120
Msa1407670 MtrunA17_Chr1g0159001 76.271 59 12 1 7 63 4 62 1.81e-18 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1407670 AT2G46330.1 63.462 52 19 0 12 63 11 62 1.02e-18 72.4
Msa1407670 AT3G61640.1 56.667 60 26 0 4 63 3 62 1.41e-17 69.3
Msa1407670 AT5G53250.1 58.182 55 23 0 9 63 9 63 2.33e-15 63.5
Msa1407670 AT5G24105.1 63.492 63 23 0 1 63 1 63 5.03e-11 52.4

Find 20 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGTTTCATGTGCTTCATTC+AGG 0.175879 tig0023322:+21384 Msa1407670:CDS
TGTTCTAATGCTTGTGGCTT+TGG 0.292333 tig0023322:+22222 Msa1407670:CDS
TTCAGGGTGGTTGCCTTCCT+TGG 0.296499 tig0023322:+21401 Msa1407670:CDS
GATAAATTAATGAATGATAT+AGG 0.396044 tig0023322:-22251 None:intergenic
GAATATTTACCATCGCTTGT+AGG 0.408971 tig0023322:-21485 None:intergenic
TGTTTCATGTGCTTCATTCA+GGG 0.448362 tig0023322:+21385 Msa1407670:CDS
TTACCATCGCTTGTAGGAGC+AGG 0.455603 tig0023322:-21479 None:intergenic
AGGAGCAGGGGCAGGTGCAA+TGG 0.532358 tig0023322:-21465 None:intergenic
TTATGCAACACTTATTTCTG+TGG 0.538882 tig0023322:+21430 Msa1407670:CDS
TACCATCGCTTGTAGGAGCA+GGG 0.542274 tig0023322:-21478 None:intergenic
AAATAAGTGTTGCATAAATG+AGG 0.548157 tig0023322:-21424 None:intergenic
TGCATGTGTTCTAATGCTTG+TGG 0.551000 tig0023322:+22216 Msa1407670:CDS
TCGCTTGTAGGAGCAGGGGC+AGG 0.566771 tig0023322:-21473 None:intergenic
TGCATAAATGAGGCCAAGGA+AGG 0.567934 tig0023322:-21414 None:intergenic
TTAGAACACATGCAATCGCT+TGG 0.574241 tig0023322:-22207 None:intergenic
TGCAATCGCTTGGTCAATTG+TGG 0.581446 tig0023322:-22197 None:intergenic
GTGTTGCATAAATGAGGCCA+AGG 0.582795 tig0023322:-21418 None:intergenic
GCCCCTGCTCCTACAAGCGA+TGG 0.595947 tig0023322:+21476 Msa1407670:CDS
ACCATCGCTTGTAGGAGCAG+GGG 0.636251 tig0023322:-21477 None:intergenic
TTCATGTGCTTCATTCAGGG+TGG 0.668781 tig0023322:+21388 Msa1407670:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAAAAATAAATTAAAATGG+AGG - tig0023322:21601-21620 None:intergenic 15.0%
!!! TTTATTTTCAGAGATTAAAT+TGG - tig0023322:21641-21660 None:intergenic 15.0%
!!! AATCATTTCATAAATCTTTT+TGG + tig0023322:21795-21814 Msa1407670:intron 15.0%
!! TAATGATTATAAAACAAATG+TGG + tig0023322:21920-21939 Msa1407670:intron 15.0%
!! AACAAATTGAAAATCAAATA+TGG - tig0023322:22085-22104 None:intergenic 15.0%
!! TGAAAAATAAATTAAAATGG+AGG - tig0023322:21601-21620 None:intergenic 15.0%
!!! TTTATTTTCAGAGATTAAAT+TGG - tig0023322:21641-21660 None:intergenic 15.0%
!!! AATCATTTCATAAATCTTTT+TGG + tig0023322:21795-21814 Msa1407670:intron 15.0%
!! TAATGATTATAAAACAAATG+TGG + tig0023322:21920-21939 Msa1407670:intron 15.0%
!! AACAAATTGAAAATCAAATA+TGG - tig0023322:22085-22104 None:intergenic 15.0%
!! AAGTGATGAAACATTAATAA+GGG - tig0023322:21540-21559 None:intergenic 20.0%
!! AAAGTGATGAAACATTAATA+AGG - tig0023322:21541-21560 None:intergenic 20.0%
!!! AAAACACCTTATACTTTTTA+AGG + tig0023322:21837-21856 Msa1407670:intron 20.0%
!!! ATTTAGCCTTAAAAAGTATA+AGG - tig0023322:21846-21865 None:intergenic 20.0%
!! GCTAAAAGTTAAGTAAAATT+TGG - tig0023322:22002-22021 None:intergenic 20.0%
!!! AATTGTTGTTTATAATATGC+AGG + tig0023322:22172-22191 Msa1407670:intron 20.0%
!! AAGTGATGAAACATTAATAA+GGG - tig0023322:21540-21559 None:intergenic 20.0%
!! AAAGTGATGAAACATTAATA+AGG - tig0023322:21541-21560 None:intergenic 20.0%
!!! AAAACACCTTATACTTTTTA+AGG + tig0023322:21837-21856 Msa1407670:intron 20.0%
!!! ATTTAGCCTTAAAAAGTATA+AGG - tig0023322:21846-21865 None:intergenic 20.0%
!! GCTAAAAGTTAAGTAAAATT+TGG - tig0023322:22002-22021 None:intergenic 20.0%
!!! AATTGTTGTTTATAATATGC+AGG + tig0023322:22172-22191 Msa1407670:intron 20.0%
!! AAATAAGTGTTGCATAAATG+AGG - tig0023322:21427-21446 None:intergenic 25.0%
!! GATTAAATTGGTGATTCATT+TGG - tig0023322:21629-21648 None:intergenic 25.0%
!!! CTTTCAATCACATTAGTTTT+CGG - tig0023322:21766-21785 None:intergenic 25.0%
!!! AAACTCACATATATTTTGAG+AGG - tig0023322:21878-21897 None:intergenic 25.0%
! TGGACTAATATCCATATAAA+CGG + tig0023322:21940-21959 Msa1407670:intron 25.0%
! TAATATCCATATAAACGGTT+AGG + tig0023322:21945-21964 Msa1407670:intron 25.0%
!! ATCAAATATGGAGATGTTTT+TGG - tig0023322:22073-22092 None:intergenic 25.0%
! TCTTTATGAGCATTATTGAT+AGG + tig0023322:22123-22142 Msa1407670:intron 25.0%
!! AAATAAGTGTTGCATAAATG+AGG - tig0023322:21427-21446 None:intergenic 25.0%
!! GATTAAATTGGTGATTCATT+TGG - tig0023322:21629-21648 None:intergenic 25.0%
!!! CTTTCAATCACATTAGTTTT+CGG - tig0023322:21766-21785 None:intergenic 25.0%
!!! AAACTCACATATATTTTGAG+AGG - tig0023322:21878-21897 None:intergenic 25.0%
! TGGACTAATATCCATATAAA+CGG + tig0023322:21940-21959 Msa1407670:intron 25.0%
! TAATATCCATATAAACGGTT+AGG + tig0023322:21945-21964 Msa1407670:intron 25.0%
!! ATCAAATATGGAGATGTTTT+TGG - tig0023322:22073-22092 None:intergenic 25.0%
! TCTTTATGAGCATTATTGAT+AGG + tig0023322:22123-22142 Msa1407670:intron 25.0%
!! TTATGCAACACTTATTTCTG+TGG + tig0023322:21430-21449 Msa1407670:CDS 30.0%
GCTCATAAAGAATAATAGCA+TGG - tig0023322:22114-22133 None:intergenic 30.0%
!! TTATGCAACACTTATTTCTG+TGG + tig0023322:21430-21449 Msa1407670:CDS 30.0%
GCTCATAAAGAATAATAGCA+TGG - tig0023322:22114-22133 None:intergenic 30.0%
TGTTTCATGTGCTTCATTCA+GGG + tig0023322:21385-21404 Msa1407670:CDS 35.0%
GAATATTTACCATCGCTTGT+AGG - tig0023322:21488-21507 None:intergenic 35.0%
GTTCTTCCTAACCGTTTATA+TGG - tig0023322:21954-21973 None:intergenic 35.0%
TGTTTCATGTGCTTCATTCA+GGG + tig0023322:21385-21404 Msa1407670:CDS 35.0%
GAATATTTACCATCGCTTGT+AGG - tig0023322:21488-21507 None:intergenic 35.0%
GTTCTTCCTAACCGTTTATA+TGG - tig0023322:21954-21973 None:intergenic 35.0%
CTGTTTCATGTGCTTCATTC+AGG + tig0023322:21384-21403 Msa1407670:CDS 40.0%
ATAAACGGTTAGGAAGAACC+TGG + tig0023322:21955-21974 Msa1407670:intron 40.0%
TAAACGGTTAGGAAGAACCT+GGG + tig0023322:21956-21975 Msa1407670:intron 40.0%
AAGATTGTTCGTACAAACCC+AGG - tig0023322:21976-21995 None:intergenic 40.0%
TCCCATTCCCTAGAACTAAA+GGG + tig0023322:22041-22060 Msa1407670:intron 40.0%
!! ACCCTTTAGTTCTAGGGAAT+GGG - tig0023322:22045-22064 None:intergenic 40.0%
!! AACCCTTTAGTTCTAGGGAA+TGG - tig0023322:22046-22065 None:intergenic 40.0%
TTAGAACACATGCAATCGCT+TGG - tig0023322:22210-22229 None:intergenic 40.0%
TGCATGTGTTCTAATGCTTG+TGG + tig0023322:22216-22235 Msa1407670:CDS 40.0%
TGTTCTAATGCTTGTGGCTT+TGG + tig0023322:22222-22241 Msa1407670:CDS 40.0%
CTGTTTCATGTGCTTCATTC+AGG + tig0023322:21384-21403 Msa1407670:CDS 40.0%
ATAAACGGTTAGGAAGAACC+TGG + tig0023322:21955-21974 Msa1407670:intron 40.0%
TAAACGGTTAGGAAGAACCT+GGG + tig0023322:21956-21975 Msa1407670:intron 40.0%
AAGATTGTTCGTACAAACCC+AGG - tig0023322:21976-21995 None:intergenic 40.0%
TCCCATTCCCTAGAACTAAA+GGG + tig0023322:22041-22060 Msa1407670:intron 40.0%
!! ACCCTTTAGTTCTAGGGAAT+GGG - tig0023322:22045-22064 None:intergenic 40.0%
!! AACCCTTTAGTTCTAGGGAA+TGG - tig0023322:22046-22065 None:intergenic 40.0%
TTAGAACACATGCAATCGCT+TGG - tig0023322:22210-22229 None:intergenic 40.0%
TGCATGTGTTCTAATGCTTG+TGG + tig0023322:22216-22235 Msa1407670:CDS 40.0%
TGTTCTAATGCTTGTGGCTT+TGG + tig0023322:22222-22241 Msa1407670:CDS 40.0%
TTCATGTGCTTCATTCAGGG+TGG + tig0023322:21388-21407 Msa1407670:CDS 45.0%
TGCATAAATGAGGCCAAGGA+AGG - tig0023322:21417-21436 None:intergenic 45.0%
GTGTTGCATAAATGAGGCCA+AGG - tig0023322:21421-21440 None:intergenic 45.0%
!! TAGTTCTAGGGAATGGGACA+TGG - tig0023322:22039-22058 None:intergenic 45.0%
GTCCCATTCCCTAGAACTAA+AGG + tig0023322:22040-22059 Msa1407670:intron 45.0%
TCCCTAGAACTAAAGGGTTG+TGG + tig0023322:22047-22066 Msa1407670:intron 45.0%
!! GCCACAACCCTTTAGTTCTA+GGG - tig0023322:22051-22070 None:intergenic 45.0%
TGCAATCGCTTGGTCAATTG+TGG - tig0023322:22200-22219 None:intergenic 45.0%
TTCATGTGCTTCATTCAGGG+TGG + tig0023322:21388-21407 Msa1407670:CDS 45.0%
TGCATAAATGAGGCCAAGGA+AGG - tig0023322:21417-21436 None:intergenic 45.0%
GTGTTGCATAAATGAGGCCA+AGG - tig0023322:21421-21440 None:intergenic 45.0%
!! TAGTTCTAGGGAATGGGACA+TGG - tig0023322:22039-22058 None:intergenic 45.0%
GTCCCATTCCCTAGAACTAA+AGG + tig0023322:22040-22059 Msa1407670:intron 45.0%
TCCCTAGAACTAAAGGGTTG+TGG + tig0023322:22047-22066 Msa1407670:intron 45.0%
!! GCCACAACCCTTTAGTTCTA+GGG - tig0023322:22051-22070 None:intergenic 45.0%
TGCAATCGCTTGGTCAATTG+TGG - tig0023322:22200-22219 None:intergenic 45.0%
!! TATTGAAAAATAAATTAAAA+TGG - tig0023322:21604-21623 None:intergenic 5.0%
!! TATTGAAAAATAAATTAAAA+TGG - tig0023322:21604-21623 None:intergenic 5.0%
TACCATCGCTTGTAGGAGCA+GGG - tig0023322:21481-21500 None:intergenic 50.0%
TTACCATCGCTTGTAGGAGC+AGG - tig0023322:21482-21501 None:intergenic 50.0%
!! GGCCACAACCCTTTAGTTCT+AGG - tig0023322:22052-22071 None:intergenic 50.0%
TACCATCGCTTGTAGGAGCA+GGG - tig0023322:21481-21500 None:intergenic 50.0%
TTACCATCGCTTGTAGGAGC+AGG - tig0023322:21482-21501 None:intergenic 50.0%
!! GGCCACAACCCTTTAGTTCT+AGG - tig0023322:22052-22071 None:intergenic 50.0%
TTCAGGGTGGTTGCCTTCCT+TGG + tig0023322:21401-21420 Msa1407670:CDS 55.0%
ACCATCGCTTGTAGGAGCAG+GGG - tig0023322:21480-21499 None:intergenic 55.0%
TTCAGGGTGGTTGCCTTCCT+TGG + tig0023322:21401-21420 Msa1407670:CDS 55.0%
ACCATCGCTTGTAGGAGCAG+GGG - tig0023322:21480-21499 None:intergenic 55.0%
AGGAGCAGGGGCAGGTGCAA+TGG - tig0023322:21468-21487 None:intergenic 65.0%
TCGCTTGTAGGAGCAGGGGC+AGG - tig0023322:21476-21495 None:intergenic 65.0%
GCCCCTGCTCCTACAAGCGA+TGG + tig0023322:21476-21495 Msa1407670:CDS 65.0%
AGGAGCAGGGGCAGGTGCAA+TGG - tig0023322:21468-21487 None:intergenic 65.0%
TCGCTTGTAGGAGCAGGGGC+AGG - tig0023322:21476-21495 None:intergenic 65.0%
GCCCCTGCTCCTACAAGCGA+TGG + tig0023322:21476-21495 Msa1407670:CDS 65.0%
Chromosome Type Strat End Strand Name
tig0023322 gene 21380 22267 21380 ID=Msa1407670;Name=Msa1407670
tig0023322 mRNA 21380 22267 21380 ID=Msa1407670-mRNA-1;Parent=Msa1407670;Name=Msa1407670-mRNA-1;_AED=0.20;_eAED=0.20;_QI=0|0|0|0.5|1|1|2|0|63
tig0023322 exon 21380 21497 21380 ID=Msa1407670-mRNA-1:exon:25234;Parent=Msa1407670-mRNA-1
tig0023322 exon 22194 22267 22194 ID=Msa1407670-mRNA-1:exon:25235;Parent=Msa1407670-mRNA-1
tig0023322 CDS 21380 21497 21380 ID=Msa1407670-mRNA-1:cds;Parent=Msa1407670-mRNA-1
tig0023322 CDS 22194 22267 22194 ID=Msa1407670-mRNA-1:cds;Parent=Msa1407670-mRNA-1
Gene Sequence

>Msa1407670

ATGGCTGTTTCATGTGCTTCATTCAGGGTGGTTGCCTTCCTTGGCCTCATTTATGCAACACTTATTTCTGTGGCTTGTTCACAATCCATTGCACCTGCCCCTGCTCCTACAAGCGATGGCACCACAATTGACCAAGCGATTGCATGTGTTCTAATGCTTGTGGCTTTGGTGTTGACCTATATCATTCATTAA

Protein sequence

>Msa1407670

MAVSCASFRVVAFLGLIYATLISVACSQSIAPAPAPTSDGTTIDQAIACVLMLVALVLTYIIH*