AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0147800


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0147800 MtrunA17_Chr1g0157201 90.365 301 16 4 11 305 30 323 0.0 535
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0147800 AT1G76080.1 64.590 305 92 5 10 305 5 302 2.28e-136 388

Find 48 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTGAGATATACCCTTTCT+TGG 0.236936 1_4:-7850415 Msa0147800:CDS
TGTGGTAGGTATGTTGGTTC+AGG 0.274596 1_4:-7849910 Msa0147800:CDS
TGTTGAGTTTCTTCTTGTTA+TGG 0.292877 1_4:-7850367 Msa0147800:CDS
GAGGGATATGGAAGTTGTTC+AGG 0.305188 1_4:-7849968 Msa0147800:CDS
ACATCACCAACAAGCATATC+TGG 0.321339 1_4:+7850231 None:intergenic
GTTGAGTTTCTTCTTGTTAT+GGG 0.323733 1_4:-7850366 Msa0147800:CDS
TGAGGGTTTGCATATGAAAT+TGG 0.324749 1_4:+7850719 None:intergenic
GAATGAAGGGTAAGGAAGTT+AGG 0.357510 1_4:+7850672 None:intergenic
AGCAGCTGTGCCTGTTGCTT+TGG 0.361080 1_4:+7850569 None:intergenic
AAGCTTATTGTTCTTGATGT+TGG 0.379209 1_4:-7850117 Msa0147800:CDS
TACTACGGTGATAACCATTC+AGG 0.418710 1_4:-7850204 Msa0147800:CDS
CATCGTTACATGTTCGGCTT+AGG 0.421411 1_4:+7850388 None:intergenic
ACATTGTGGGCCATGTGTTA+AGG 0.424051 1_4:-7850088 Msa0147800:CDS
GTGGTAGGTATGTTGGTTCA+GGG 0.432018 1_4:-7849909 Msa0147800:CDS
AACTCATTGGTGAAATTCTC+AGG 0.435220 1_4:-7849879 Msa0147800:CDS
ATTAGAGATGGTAAGATTTG+TGG 0.439626 1_4:-7849928 Msa0147800:CDS
GAAATTGAAGGAGGGATTGA+GGG 0.440827 1_4:+7850702 None:intergenic
CGGCTTAGGTCAACCAAGAA+AGG 0.444183 1_4:+7850402 None:intergenic
AAGATTTGTGGTAGGTATGT+TGG 0.445880 1_4:-7849916 Msa0147800:CDS
TTAGGATGAGTTGAAATTGA+AGG 0.445917 1_4:+7850690 None:intergenic
TGAAATTGAAGGAGGGATTG+AGG 0.455754 1_4:+7850701 None:intergenic
GTTGTTATCACCAAAGCAAC+AGG 0.459253 1_4:-7850579 Msa0147800:CDS
ACTCAACATCGTTACATGTT+CGG 0.469979 1_4:+7850382 None:intergenic
ATTCATGAAGAAGAAGCTAT+TGG 0.470180 1_4:-7850255 Msa0147800:CDS
AAGAAGAACGAAGAGAATGA+AGG 0.480454 1_4:+7850658 None:intergenic
AGGTATGTTGGTTCAGGGAA+AGG 0.482216 1_4:-7849904 Msa0147800:CDS
ATGTTGGTCTTAAACATTGT+GGG 0.490241 1_4:-7850101 Msa0147800:CDS
AGAAGAACGAAGAGAATGAA+GGG 0.507243 1_4:+7850659 None:intergenic
AACGAAGAGAATGAAGGGTA+AGG 0.514490 1_4:+7850664 None:intergenic
AGAACTCTGCAAAAGAGAAA+AGG 0.515029 1_4:-7850322 Msa0147800:CDS
GGATGAGTTGAAATTGAAGG+AGG 0.516103 1_4:+7850693 None:intergenic
AATAAGTAACACGAACTCCT+TGG 0.520146 1_4:+7849854 None:intergenic
TCAGGGAAAGGTGAACTCAT+TGG 0.523543 1_4:-7849892 Msa0147800:CDS
AGTGATTGTAGTAGTAGCCA+TGG 0.525091 1_4:+7850749 None:intergenic
CTTGACAGCTTAATCACTGT+CGG 0.540890 1_4:+7850060 None:intergenic
GATGAGTTGAAATTGAAGGA+GGG 0.552894 1_4:+7850694 None:intergenic
AGATGTTGAGAAACTTATTG+AGG 0.553117 1_4:-7850157 Msa0147800:CDS
ATTCATTCTACTTCTCGGGT+AGG 0.557229 1_4:-7850615 Msa0147800:CDS
ATTGGTCCAGATATGCTTGT+TGG 0.557827 1_4:-7850237 Msa0147800:CDS
GGCTTAGGTCAACCAAGAAA+GGG 0.570139 1_4:+7850403 None:intergenic
GATGTTGGTCTTAAACATTG+TGG 0.582468 1_4:-7850102 Msa0147800:CDS
GTTGGTGATGTGTTATACTA+CGG 0.591943 1_4:-7850219 Msa0147800:CDS
GAAGTTGTACTACACCTGAA+TGG 0.613386 1_4:+7850190 None:intergenic
GAGATGGTAAGATTTGTGGT+AGG 0.631571 1_4:-7849924 Msa0147800:CDS
GTCGGATAAACCTTAACACA+TGG 0.636213 1_4:+7850078 None:intergenic
GTGATTGTAGTAGTAGCCAT+GGG 0.650122 1_4:+7850750 None:intergenic
GGTGAAATTCTCAGGTACCA+AGG 0.658840 1_4:-7849871 Msa0147800:CDS
CTCTTGTAGAAAGTGAAGTG+TGG 0.692063 1_4:+7850288 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! CAAAAATTCATTCTACTTCT+CGG - chr1_4:7849979-7849998 Msa0147800:CDS 25.0%
! AAAAATTCATTCTACTTCTC+GGG - chr1_4:7849980-7849999 Msa0147800:CDS 25.0%
!!! ATGATACTGTTATTTTTGCA+AGG - chr1_4:7850570-7850589 Msa0147800:CDS 25.0%
! TCTCTAATGAACAAAAAAGT+AGG + chr1_4:7850659-7850678 None:intergenic 25.0%
!!! ACTTTTTTGTTCATTAGAGA+TGG - chr1_4:7850659-7850678 Msa0147800:CDS 25.0%
! CAAAAATTCATTCTACTTCT+CGG - chr1_4:7849979-7849998 Msa0147800:CDS 25.0%
! AAAAATTCATTCTACTTCTC+GGG - chr1_4:7849980-7849999 Msa0147800:CDS 25.0%
!!! ATGATACTGTTATTTTTGCA+AGG - chr1_4:7850570-7850589 Msa0147800:CDS 25.0%
! TCTCTAATGAACAAAAAAGT+AGG + chr1_4:7850659-7850678 None:intergenic 25.0%
!!! ACTTTTTTGTTCATTAGAGA+TGG - chr1_4:7850659-7850678 Msa0147800:CDS 25.0%
! TTAGGATGAGTTGAAATTGA+AGG + chr1_4:7849912-7849931 None:intergenic 30.0%
! CGAGAAGTAGAATGAATTTT+TGG + chr1_4:7849981-7850000 None:intergenic 30.0%
TGTTGAGTTTCTTCTTGTTA+TGG - chr1_4:7850232-7850251 Msa0147800:CDS 30.0%
! GTTGAGTTTCTTCTTGTTAT+GGG - chr1_4:7850233-7850252 Msa0147800:CDS 30.0%
ATTCATGAAGAAGAAGCTAT+TGG - chr1_4:7850344-7850363 Msa0147800:CDS 30.0%
AGATGTTGAGAAACTTATTG+AGG - chr1_4:7850442-7850461 Msa0147800:CDS 30.0%
AAGCTTATTGTTCTTGATGT+TGG - chr1_4:7850482-7850501 Msa0147800:CDS 30.0%
!! ATGTTGGTCTTAAACATTGT+GGG - chr1_4:7850498-7850517 Msa0147800:CDS 30.0%
!!! GTTATTTTTGCAAGGATGAA+TGG - chr1_4:7850578-7850597 Msa0147800:CDS 30.0%
! ATAGTTGTATGCAGTTTTTG+AGG - chr1_4:7850612-7850631 Msa0147800:CDS 30.0%
! TAGTTGTATGCAGTTTTTGA+GGG - chr1_4:7850613-7850632 Msa0147800:CDS 30.0%
ATTAGAGATGGTAAGATTTG+TGG - chr1_4:7850671-7850690 Msa0147800:CDS 30.0%
! TTAGGATGAGTTGAAATTGA+AGG + chr1_4:7849912-7849931 None:intergenic 30.0%
! CGAGAAGTAGAATGAATTTT+TGG + chr1_4:7849981-7850000 None:intergenic 30.0%
TGTTGAGTTTCTTCTTGTTA+TGG - chr1_4:7850232-7850251 Msa0147800:CDS 30.0%
! GTTGAGTTTCTTCTTGTTAT+GGG - chr1_4:7850233-7850252 Msa0147800:CDS 30.0%
ATTCATGAAGAAGAAGCTAT+TGG - chr1_4:7850344-7850363 Msa0147800:CDS 30.0%
AGATGTTGAGAAACTTATTG+AGG - chr1_4:7850442-7850461 Msa0147800:CDS 30.0%
AAGCTTATTGTTCTTGATGT+TGG - chr1_4:7850482-7850501 Msa0147800:CDS 30.0%
!! ATGTTGGTCTTAAACATTGT+GGG - chr1_4:7850498-7850517 Msa0147800:CDS 30.0%
!!! GTTATTTTTGCAAGGATGAA+TGG - chr1_4:7850578-7850597 Msa0147800:CDS 30.0%
! ATAGTTGTATGCAGTTTTTG+AGG - chr1_4:7850612-7850631 Msa0147800:CDS 30.0%
! TAGTTGTATGCAGTTTTTGA+GGG - chr1_4:7850613-7850632 Msa0147800:CDS 30.0%
ATTAGAGATGGTAAGATTTG+TGG - chr1_4:7850671-7850690 Msa0147800:CDS 30.0%
TGAGGGTTTGCATATGAAAT+TGG + chr1_4:7849883-7849902 None:intergenic 35.0%
! GATGAGTTGAAATTGAAGGA+GGG + chr1_4:7849908-7849927 None:intergenic 35.0%
AGAAGAACGAAGAGAATGAA+GGG + chr1_4:7849943-7849962 None:intergenic 35.0%
AAGAAGAACGAAGAGAATGA+AGG + chr1_4:7849944-7849963 None:intergenic 35.0%
CATTGAGATATACCCTTTCT+TGG - chr1_4:7850184-7850203 Msa0147800:CDS 35.0%
ACTCAACATCGTTACATGTT+CGG + chr1_4:7850220-7850239 None:intergenic 35.0%
AGAACTCTGCAAAAGAGAAA+AGG - chr1_4:7850277-7850296 Msa0147800:CDS 35.0%
!! GTTGGTGATGTGTTATACTA+CGG - chr1_4:7850380-7850399 Msa0147800:CDS 35.0%
!! GATGTTGGTCTTAAACATTG+TGG - chr1_4:7850497-7850516 Msa0147800:CDS 35.0%
!! TATGCAGTTTTTGAGGGATA+TGG - chr1_4:7850619-7850638 Msa0147800:CDS 35.0%
AAGATTTGTGGTAGGTATGT+TGG - chr1_4:7850683-7850702 Msa0147800:CDS 35.0%
AACTCATTGGTGAAATTCTC+AGG - chr1_4:7850720-7850739 Msa0147800:CDS 35.0%
AATAAGTAACACGAACTCCT+TGG + chr1_4:7850748-7850767 None:intergenic 35.0%
TGAGGGTTTGCATATGAAAT+TGG + chr1_4:7849883-7849902 None:intergenic 35.0%
! GATGAGTTGAAATTGAAGGA+GGG + chr1_4:7849908-7849927 None:intergenic 35.0%
AGAAGAACGAAGAGAATGAA+GGG + chr1_4:7849943-7849962 None:intergenic 35.0%
AAGAAGAACGAAGAGAATGA+AGG + chr1_4:7849944-7849963 None:intergenic 35.0%
CATTGAGATATACCCTTTCT+TGG - chr1_4:7850184-7850203 Msa0147800:CDS 35.0%
ACTCAACATCGTTACATGTT+CGG + chr1_4:7850220-7850239 None:intergenic 35.0%
AGAACTCTGCAAAAGAGAAA+AGG - chr1_4:7850277-7850296 Msa0147800:CDS 35.0%
!! GTTGGTGATGTGTTATACTA+CGG - chr1_4:7850380-7850399 Msa0147800:CDS 35.0%
!! GATGTTGGTCTTAAACATTG+TGG - chr1_4:7850497-7850516 Msa0147800:CDS 35.0%
!! TATGCAGTTTTTGAGGGATA+TGG - chr1_4:7850619-7850638 Msa0147800:CDS 35.0%
AAGATTTGTGGTAGGTATGT+TGG - chr1_4:7850683-7850702 Msa0147800:CDS 35.0%
AACTCATTGGTGAAATTCTC+AGG - chr1_4:7850720-7850739 Msa0147800:CDS 35.0%
AATAAGTAACACGAACTCCT+TGG + chr1_4:7850748-7850767 None:intergenic 35.0%
GAAATTGAAGGAGGGATTGA+GGG + chr1_4:7849900-7849919 None:intergenic 40.0%
TGAAATTGAAGGAGGGATTG+AGG + chr1_4:7849901-7849920 None:intergenic 40.0%
! GGATGAGTTGAAATTGAAGG+AGG + chr1_4:7849909-7849928 None:intergenic 40.0%
GAATGAAGGGTAAGGAAGTT+AGG + chr1_4:7849930-7849949 None:intergenic 40.0%
AACGAAGAGAATGAAGGGTA+AGG + chr1_4:7849938-7849957 None:intergenic 40.0%
ATTCATTCTACTTCTCGGGT+AGG - chr1_4:7849984-7850003 Msa0147800:CDS 40.0%
GTTGTTATCACCAAAGCAAC+AGG - chr1_4:7850020-7850039 Msa0147800:CDS 40.0%
CTCTTGTAGAAAGTGAAGTG+TGG + chr1_4:7850314-7850333 None:intergenic 40.0%
ATTGGTCCAGATATGCTTGT+TGG - chr1_4:7850362-7850381 Msa0147800:CDS 40.0%
ACATCACCAACAAGCATATC+TGG + chr1_4:7850371-7850390 None:intergenic 40.0%
TACTACGGTGATAACCATTC+AGG - chr1_4:7850395-7850414 Msa0147800:CDS 40.0%
GAAGTTGTACTACACCTGAA+TGG + chr1_4:7850412-7850431 None:intergenic 40.0%
GTCGGATAAACCTTAACACA+TGG + chr1_4:7850524-7850543 None:intergenic 40.0%
CTTGACAGCTTAATCACTGT+CGG + chr1_4:7850542-7850561 None:intergenic 40.0%
GAGATGGTAAGATTTGTGGT+AGG - chr1_4:7850675-7850694 Msa0147800:CDS 40.0%
GAAATTGAAGGAGGGATTGA+GGG + chr1_4:7849900-7849919 None:intergenic 40.0%
TGAAATTGAAGGAGGGATTG+AGG + chr1_4:7849901-7849920 None:intergenic 40.0%
! GGATGAGTTGAAATTGAAGG+AGG + chr1_4:7849909-7849928 None:intergenic 40.0%
GAATGAAGGGTAAGGAAGTT+AGG + chr1_4:7849930-7849949 None:intergenic 40.0%
AACGAAGAGAATGAAGGGTA+AGG + chr1_4:7849938-7849957 None:intergenic 40.0%
ATTCATTCTACTTCTCGGGT+AGG - chr1_4:7849984-7850003 Msa0147800:CDS 40.0%
GTTGTTATCACCAAAGCAAC+AGG - chr1_4:7850020-7850039 Msa0147800:CDS 40.0%
CTCTTGTAGAAAGTGAAGTG+TGG + chr1_4:7850314-7850333 None:intergenic 40.0%
ATTGGTCCAGATATGCTTGT+TGG - chr1_4:7850362-7850381 Msa0147800:CDS 40.0%
ACATCACCAACAAGCATATC+TGG + chr1_4:7850371-7850390 None:intergenic 40.0%
TACTACGGTGATAACCATTC+AGG - chr1_4:7850395-7850414 Msa0147800:CDS 40.0%
GAAGTTGTACTACACCTGAA+TGG + chr1_4:7850412-7850431 None:intergenic 40.0%
GTCGGATAAACCTTAACACA+TGG + chr1_4:7850524-7850543 None:intergenic 40.0%
CTTGACAGCTTAATCACTGT+CGG + chr1_4:7850542-7850561 None:intergenic 40.0%
GAGATGGTAAGATTTGTGGT+AGG - chr1_4:7850675-7850694 Msa0147800:CDS 40.0%
GGCTTAGGTCAACCAAGAAA+GGG + chr1_4:7850199-7850218 None:intergenic 45.0%
CATCGTTACATGTTCGGCTT+AGG + chr1_4:7850214-7850233 None:intergenic 45.0%
ACATTGTGGGCCATGTGTTA+AGG - chr1_4:7850511-7850530 Msa0147800:CDS 45.0%
GAGGGATATGGAAGTTGTTC+AGG - chr1_4:7850631-7850650 Msa0147800:CDS 45.0%
!! TGTGGTAGGTATGTTGGTTC+AGG - chr1_4:7850689-7850708 Msa0147800:CDS 45.0%
!! GTGGTAGGTATGTTGGTTCA+GGG - chr1_4:7850690-7850709 Msa0147800:CDS 45.0%
!! AGGTATGTTGGTTCAGGGAA+AGG - chr1_4:7850695-7850714 Msa0147800:CDS 45.0%
TCAGGGAAAGGTGAACTCAT+TGG - chr1_4:7850707-7850726 Msa0147800:CDS 45.0%
GGTGAAATTCTCAGGTACCA+AGG - chr1_4:7850728-7850747 Msa0147800:CDS 45.0%
GGCTTAGGTCAACCAAGAAA+GGG + chr1_4:7850199-7850218 None:intergenic 45.0%
CATCGTTACATGTTCGGCTT+AGG + chr1_4:7850214-7850233 None:intergenic 45.0%
ACATTGTGGGCCATGTGTTA+AGG - chr1_4:7850511-7850530 Msa0147800:CDS 45.0%
GAGGGATATGGAAGTTGTTC+AGG - chr1_4:7850631-7850650 Msa0147800:CDS 45.0%
!! TGTGGTAGGTATGTTGGTTC+AGG - chr1_4:7850689-7850708 Msa0147800:CDS 45.0%
!! GTGGTAGGTATGTTGGTTCA+GGG - chr1_4:7850690-7850709 Msa0147800:CDS 45.0%
!! AGGTATGTTGGTTCAGGGAA+AGG - chr1_4:7850695-7850714 Msa0147800:CDS 45.0%
TCAGGGAAAGGTGAACTCAT+TGG - chr1_4:7850707-7850726 Msa0147800:CDS 45.0%
GGTGAAATTCTCAGGTACCA+AGG - chr1_4:7850728-7850747 Msa0147800:CDS 45.0%
CGGCTTAGGTCAACCAAGAA+AGG + chr1_4:7850200-7850219 None:intergenic 50.0%
CGGCTTAGGTCAACCAAGAA+AGG + chr1_4:7850200-7850219 None:intergenic 50.0%
! AGCAGCTGTGCCTGTTGCTT+TGG + chr1_4:7850033-7850052 None:intergenic 55.0%
! AGCAGCTGTGCCTGTTGCTT+TGG + chr1_4:7850033-7850052 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 7849852 7850769 7849852 ID=Msa0147800;Name=Msa0147800
chr1_4 mRNA 7849852 7850769 7849852 ID=Msa0147800-mRNA-1;Parent=Msa0147800;Name=Msa0147800-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|-1|0|1|-1|1|1|0|305
chr1_4 exon 7849852 7850769 7849852 ID=Msa0147800-mRNA-1:exon:3357;Parent=Msa0147800-mRNA-1
chr1_4 CDS 7849852 7850769 7849852 ID=Msa0147800-mRNA-1:cds;Parent=Msa0147800-mRNA-1
Gene Sequence

>Msa0147800

ATGGCTACTACTACAATCACTCACTGCACCAATTTCATATGCAAACCCTCAATCCCTCCTTCAATTTCAACTCATCCTAACTTCCTTACCCTTCATTCTCTTCGTTCTTCTTCTTCTTCTTCTTTACCAAAAATTCATTCTACTTCTCGGGTAGGACTGCAGAGACGTGTTGTTATCACCAAAGCAACAGGCACAGCTGCTTCAGATGCTAAGAAGAAAAAAGATGAAAGAGTTCAAAGAGTTCACAGCATAGAAGAGTTCGATGCAGCACTTCAATCTGCAAAAGACAAACTCGTTGTTGTTGAGTACGCTACAAGCGACGACTCAGAAAGCATTGAGATATACCCTTTCTTGGTTGACCTAAGCCGAACATGTAACGATGTTGAGTTTCTTCTTGTTATGGGAGATGAATCAGAGAAAACAAAAGAACTCTGCAAAAGAGAAAAGGTTGATAAAGTACCACACTTCACTTTCTACAAGAGCAAAGAGAAGATTCATGAAGAAGAAGCTATTGGTCCAGATATGCTTGTTGGTGATGTGTTATACTACGGTGATAACCATTCAGGTGTAGTACAACTTCACAACAGAGAAGATGTTGAGAAACTTATTGAGGATCATAAGATTGATCATAAGCTTATTGTTCTTGATGTTGGTCTTAAACATTGTGGGCCATGTGTTAAGGTTTATCCGACAGTGATTAAGCTGTCAAGACAAATGAATGATACTGTTATTTTTGCAAGGATGAATGGTGATGAGAATGATAGTTGTATGCAGTTTTTGAGGGATATGGAAGTTGTTCAGGTTCCTACTTTTTTGTTCATTAGAGATGGTAAGATTTGTGGTAGGTATGTTGGTTCAGGGAAAGGTGAACTCATTGGTGAAATTCTCAGGTACCAAGGAGTTCGTGTTACTTATTAA

Protein sequence

>Msa0147800

MATTTITHCTNFICKPSIPPSISTHPNFLTLHSLRSSSSSSLPKIHSTSRVGLQRRVVITKATGTAASDAKKKKDERVQRVHSIEEFDAALQSAKDKLVVVEYATSDDSESIEIYPFLVDLSRTCNDVEFLLVMGDESEKTKELCKREKVDKVPHFTFYKSKEKIHEEEAIGPDMLVGDVLYYGDNHSGVVQLHNREDVEKLIEDHKIDHKLIVLDVGLKHCGPCVKVYPTVIKLSRQMNDTVIFARMNGDENDSCMQFLRDMEVVQVPTFLFIRDGKICGRYVGSGKGELIGEILRYQGVRVTY*