AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0864550


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0864550 MtrunA17_Chr5g0447101 94.118 238 14 0 1 238 1 238 1.94e-169 466
Msa0864550 MtrunA17_Chr8g0381351 30.918 207 142 1 33 238 188 394 1.31e-33 124
Msa0864550 MtrunA17_Chr8g0369721 24.615 195 139 6 44 234 8 198 3.47e-13 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0864550 AT4G26490.1 44.175 206 115 0 33 238 63 268 4.29e-65 203
Msa0864550 AT5G56050.1 42.060 233 124 4 6 238 61 282 3.14e-62 196
Msa0864550 AT1G13050.1 32.632 190 127 1 50 238 128 317 4.20e-28 108
Msa0864550 AT1G13050.3 32.704 159 106 1 81 238 27 185 1.71e-27 104
Msa0864550 AT1G13050.2 32.704 159 106 1 81 238 27 185 1.71e-27 104
Msa0864550 AT3G26350.2 31.579 190 129 1 50 238 152 341 8.15e-27 106
Msa0864550 AT3G26350.1 31.579 190 129 1 50 238 167 356 1.08e-26 105

Find 38 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCTTTGGCTTCTGAGTAAA+AGG 0.201329 5_4:+64955519 None:intergenic
AGCTTTACACTTATCTTCTT+TGG 0.214240 5_4:-64955771 Msa0864550:CDS
CTATGCAAAGGGAACATTTA+AGG 0.223322 5_4:-64955394 Msa0864550:CDS
AGTCAAAATTTACAACATTT+AGG 0.299761 5_4:+64955679 None:intergenic
GCATTAGAAATATCAAATAA+AGG 0.310217 5_4:+64955705 None:intergenic
GGTTGCTTGGTTTGAGTGTA+AGG 0.338313 5_4:+64955727 None:intergenic
AAGAAAGTTGGCAATACTTA+AGG 0.339972 5_4:-64955856 Msa0864550:CDS
TTTGATATGATAGGTTGTTC+AGG 0.370467 5_4:+64955918 None:intergenic
GTTTGATATCTAGTTTCCTT+TGG 0.377149 5_4:+64955504 None:intergenic
AAAGGGAGTTGCAAAACAAT+AGG 0.383249 5_4:-64955425 Msa0864550:CDS
CATTAGAAATATCAAATAAA+GGG 0.385546 5_4:+64955706 None:intergenic
CTTGATGATCTTGTTCTAAG+AGG 0.391536 5_4:+64955876 None:intergenic
AAAAGACCAAACCAATTGTA+TGG 0.403433 5_4:-64955821 Msa0864550:CDS
TTCTGAGGGTGGAGATGTGT+TGG 0.412326 5_4:+64955962 None:intergenic
AGCAAACCATACAATTGGTT+TGG 0.414083 5_4:+64955815 None:intergenic
GACTCAAAGCAATACTTCAA+TGG 0.427271 5_4:-64955660 Msa0864550:CDS
ATTGCAGCAAACCATACAAT+TGG 0.442844 5_4:+64955810 None:intergenic
ATATCAAATAAAGGGTTGCT+TGG 0.463721 5_4:+64955714 None:intergenic
AACAAGATCATCAAGAAAGT+TGG 0.467969 5_4:-64955868 Msa0864550:CDS
TTAAGGTGAAGGTTAATATG+TGG 0.477400 5_4:-64955377 Msa0864550:CDS
TTCAATATTAGTTTGTTCTG+AGG 0.495171 5_4:+64955947 None:intergenic
TCAATATTAGTTTGTTCTGA+GGG 0.505732 5_4:+64955948 None:intergenic
TCTGAGGGTGGAGATGTGTT+GGG 0.505757 5_4:+64955963 None:intergenic
GTGGACCAGTCATCTCAATC+TGG 0.507976 5_4:+64955319 None:intergenic
CTAGCTACAAGAGAACCATT+TGG 0.518577 5_4:+64955297 None:intergenic
GAGATGACTGGTCCACCAAA+TGG 0.523109 5_4:-64955312 Msa0864550:CDS
AAAGGAAACTAGATATCAAA+CGG 0.532877 5_4:-64955502 Msa0864550:CDS
AAACTAGATATCAAACGGTA+AGG 0.546166 5_4:-64955497 Msa0864550:CDS
AAAGGGAACATTTAAGGTGA+AGG 0.548043 5_4:-64955388 Msa0864550:CDS
TAGGTTGAGTTGCTATGCAA+AGG 0.548893 5_4:-64955406 Msa0864550:CDS
AGGTTGAGTTGCTATGCAAA+GGG 0.552779 5_4:-64955405 Msa0864550:CDS
AAGTTGGTGTGAAACTTCAA+AGG 0.555056 5_4:-64955443 Msa0864550:CDS
ATATTAGTTTGTTCTGAGGG+TGG 0.577316 5_4:+64955951 None:intergenic
GCTACAAGAGAACCATTTGG+TGG 0.579822 5_4:+64955300 None:intergenic
AGTTTCACACCAACTTCTTG+AGG 0.595238 5_4:+64955450 None:intergenic
AGTTGGTGTGAAACTTCAAA+GGG 0.596723 5_4:-64955442 Msa0864550:CDS
CCAATAGAAAAGTTCATGTG+AGG 0.604027 5_4:-64955605 Msa0864550:CDS
GTGTGCCAGATTGAGATGAC+TGG 0.624651 5_4:-64955324 Msa0864550:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CATTAGAAATATCAAATAAA+GGG + chr5_4:64955541-64955560 None:intergenic 15.0%
!! GCATTAGAAATATCAAATAA+AGG + chr5_4:64955542-64955561 None:intergenic 20.0%
!! AGTCAAAATTTACAACATTT+AGG + chr5_4:64955568-64955587 None:intergenic 20.0%
!!! TCAATATTAGTTTGTTCTGA+GGG + chr5_4:64955299-64955318 None:intergenic 25.0%
!!! TTCAATATTAGTTTGTTCTG+AGG + chr5_4:64955300-64955319 None:intergenic 25.0%
!!! TTGGTTTGTTTTGATATGAT+AGG + chr5_4:64955338-64955357 None:intergenic 25.0%
!! TTCAACTTTTCTACTCAAAT+AGG - chr5_4:64955678-64955697 Msa0864550:CDS 25.0%
! AAAGGAAACTAGATATCAAA+CGG - chr5_4:64955742-64955761 Msa0864550:CDS 25.0%
!! GGATTATACATTCATCTTTT+TGG - chr5_4:64955888-64955907 Msa0864550:CDS 25.0%
TTTGATATGATAGGTTGTTC+AGG + chr5_4:64955329-64955348 None:intergenic 30.0%
!!! TCTAAGAGGATGTTGATTTT+TGG + chr5_4:64955357-64955376 None:intergenic 30.0%
AACAAGATCATCAAGAAAGT+TGG - chr5_4:64955376-64955395 Msa0864550:CDS 30.0%
AAGAAAGTTGGCAATACTTA+AGG - chr5_4:64955388-64955407 Msa0864550:CDS 30.0%
AAAAGACCAAACCAATTGTA+TGG - chr5_4:64955423-64955442 Msa0864550:CDS 30.0%
AGCTTTACACTTATCTTCTT+TGG - chr5_4:64955473-64955492 Msa0864550:CDS 30.0%
ATATCAAATAAAGGGTTGCT+TGG + chr5_4:64955533-64955552 None:intergenic 30.0%
! CTCACATGAACTTTTCTATT+GGG + chr5_4:64955641-64955660 None:intergenic 30.0%
! GTTTGATATCTAGTTTCCTT+TGG + chr5_4:64955743-64955762 None:intergenic 30.0%
AAACTAGATATCAAACGGTA+AGG - chr5_4:64955747-64955766 Msa0864550:CDS 30.0%
! ATTTTTATGCCTCAAGAAGT+TGG - chr5_4:64955785-64955804 Msa0864550:CDS 30.0%
TTAAGGTGAAGGTTAATATG+TGG - chr5_4:64955867-64955886 Msa0864550:CDS 30.0%
!! ATATTAGTTTGTTCTGAGGG+TGG + chr5_4:64955296-64955315 None:intergenic 35.0%
! CTTGATGATCTTGTTCTAAG+AGG + chr5_4:64955371-64955390 None:intergenic 35.0%
!!! CAATTGGTTTGGTCTTTTGT+TGG + chr5_4:64955421-64955440 None:intergenic 35.0%
AGCAAACCATACAATTGGTT+TGG + chr5_4:64955432-64955451 None:intergenic 35.0%
ATTGCAGCAAACCATACAAT+TGG + chr5_4:64955437-64955456 None:intergenic 35.0%
GACTCAAAGCAATACTTCAA+TGG - chr5_4:64955584-64955603 Msa0864550:CDS 35.0%
! CCTCACATGAACTTTTCTAT+TGG + chr5_4:64955642-64955661 None:intergenic 35.0%
CCAATAGAAAAGTTCATGTG+AGG - chr5_4:64955639-64955658 Msa0864550:CDS 35.0%
!! AAGTTGGTGTGAAACTTCAA+AGG - chr5_4:64955801-64955820 Msa0864550:CDS 35.0%
! AGTTGGTGTGAAACTTCAAA+GGG - chr5_4:64955802-64955821 Msa0864550:CDS 35.0%
AAAGGGAGTTGCAAAACAAT+AGG - chr5_4:64955819-64955838 Msa0864550:CDS 35.0%
CTATGCAAAGGGAACATTTA+AGG - chr5_4:64955850-64955869 Msa0864550:CDS 35.0%
! AAAGGGAACATTTAAGGTGA+AGG - chr5_4:64955856-64955875 Msa0864550:CDS 35.0%
! TCCTTTGGCTTCTGAGTAAA+AGG + chr5_4:64955728-64955747 None:intergenic 40.0%
AGTTTCACACCAACTTCTTG+AGG + chr5_4:64955797-64955816 None:intergenic 40.0%
! TAGGTTGAGTTGCTATGCAA+AGG - chr5_4:64955838-64955857 Msa0864550:CDS 40.0%
! AGGTTGAGTTGCTATGCAAA+GGG - chr5_4:64955839-64955858 Msa0864550:CDS 40.0%
CTAGCTACAAGAGAACCATT+TGG + chr5_4:64955950-64955969 None:intergenic 40.0%
! GGTTGCTTGGTTTGAGTGTA+AGG + chr5_4:64955520-64955539 None:intergenic 45.0%
! GCCTTTTACTCAGAAGCCAA+AGG - chr5_4:64955724-64955743 Msa0864550:CDS 45.0%
GCTACAAGAGAACCATTTGG+TGG + chr5_4:64955947-64955966 None:intergenic 45.0%
TCTGAGGGTGGAGATGTGTT+GGG + chr5_4:64955284-64955303 None:intergenic 50.0%
! TTCTGAGGGTGGAGATGTGT+TGG + chr5_4:64955285-64955304 None:intergenic 50.0%
GTGTGCCAGATTGAGATGAC+TGG - chr5_4:64955920-64955939 Msa0864550:CDS 50.0%
GTGGACCAGTCATCTCAATC+TGG + chr5_4:64955928-64955947 None:intergenic 50.0%
! GAGATGACTGGTCCACCAAA+TGG - chr5_4:64955932-64955951 Msa0864550:CDS 50.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 64955275 64955991 64955275 ID=Msa0864550;Name=Msa0864550
chr5_4 mRNA 64955275 64955991 64955275 ID=Msa0864550-mRNA-1;Parent=Msa0864550;Name=Msa0864550-mRNA-1;_AED=0.13;_eAED=0.13;_QI=0|-1|0|1|-1|1|1|0|238
chr5_4 exon 64955275 64955991 64955275 ID=Msa0864550-mRNA-1:exon:20456;Parent=Msa0864550-mRNA-1
chr5_4 CDS 64955275 64955991 64955275 ID=Msa0864550-mRNA-1:cds;Parent=Msa0864550-mRNA-1
Gene Sequence

>Msa0864550

ATGCTTCCCAACACATCTCCACCCTCAGAACAAACTAATATTGAAATTTCTCCTGAACAACCTATCATATCAAAACAAACCAAAAATCAACATCCTCTTAGAACAAGATCATCAAGAAAGTTGGCAATACTTAAGGTTGATGACCAACAAAAGACCAAACCAATTGTATGGTTTGCTGCAATACTATGTTTCATATTCAGCTTTACACTTATCTTCTTTGGAATTGCAACAATAATTTGTTACCTTACACTCAAACCAAGCAACCCTTTATTTGATATTTCTAATGCAAGCCTAAATGTTGTAAATTTTGACTCAAAGCAATACTTCAATGGTGATTTTGCTCTTCAAACAAAATTTTCTAATCCCAATAGAAAAGTTCATGTGAGGTTTGAGTCTTTATATATTCAACTTTTCTACTCAAATAGGCTCATATCATCACAATCAATCAAGCCTTTTACTCAGAAGCCAAAGGAAACTAGATATCAAACGGTAAGGTTTATATCAACTTTGATTTTTATGCCTCAAGAAGTTGGTGTGAAACTTCAAAGGGAGTTGCAAAACAATAGGTTGAGTTGCTATGCAAAGGGAACATTTAAGGTGAAGGTTAATATGTGGATTATACATTCATCTTTTTGGCTTCATAGTGTGTGCCAGATTGAGATGACTGGTCCACCAAATGGTTCTCTTGTAGCTAGACAATGTATAACAACTCGATGA

Protein sequence

>Msa0864550

MLPNTSPPSEQTNIEISPEQPIISKQTKNQHPLRTRSSRKLAILKVDDQQKTKPIVWFAAILCFIFSFTLIFFGIATIICYLTLKPSNPLFDISNASLNVVNFDSKQYFNGDFALQTKFSNPNRKVHVRFESLYIQLFYSNRLISSQSIKPFTQKPKETRYQTVRFISTLIFMPQEVGVKLQRELQNNRLSCYAKGTFKVKVNMWIIHSSFWLHSVCQIEMTGPPNGSLVARQCITTR*