AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0974340

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0974340 MtrunA17_Chr6g0452991 96.117 206 8 0 9 214 170 375 9.66e-145 408
Msa0974340 MtrunA17_Chr6g0452971 94.660 206 11 0 9 214 170 375 1.92e-141 399
Msa0974340 MtrunA17_Chr7g0217021 69.697 198 57 1 9 206 166 360 8.53e-99 291
Msa0974340 MtrunA17_Chr4g0060521 53.846 195 85 2 9 203 166 355 9.71e-67 209
Msa0974340 MtrunA17_Chr6g0478501 48.990 198 97 2 9 206 146 339 1.04e-61 196
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0974340 AT3G47800.1 52.525 198 85 3 9 204 166 356 8.67e-69 214
Msa0974340 AT5G15140.1 51.000 200 92 3 5 204 294 487 6.16e-64 206
Msa0974340 AT3G17940.1 45.178 197 105 2 9 205 148 341 6.86e-56 181
Msa0974340 AT3G01260.1 43.655 197 95 5 8 204 243 423 1.85e-41 145

Find 32 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTAGTTAACCATGCTTAT+TGG 0.207837 6_4:-7335806 Msa0974340:CDS
AACAACATAACATGCTTATA+AGG 0.235997 6_4:+7335318 None:intergenic
ACAATAGTTGAAGGAAAATT+AGG 0.263993 6_4:+7335354 None:intergenic
TTGCTTGCATAATTATTGTT+AGG 0.265306 6_4:+7335856 None:intergenic
TTACTGGTGTAGGTTTGTTT+AGG 0.267070 6_4:+7335829 None:intergenic
TACTGGTGTAGGTTTGTTTA+GGG 0.287587 6_4:+7335830 None:intergenic
CTTCTGATGATGCAGCTTCT+AGG 0.304583 6_4:-7335888 Msa0974340:CDS
GCATGGTTAACTAAATTTAC+TGG 0.313208 6_4:+7335813 None:intergenic
CTAAAATGTTGCCACTGTTA+TGG 0.321628 6_4:+7335772 None:intergenic
ATTAACTATGTGCTTAATAA+AGG 0.334398 6_4:-7335588 Msa0974340:CDS
ACCACGTTCAGCACTTTGTT+TGG 0.345777 6_4:-7335409 Msa0974340:CDS
GACAATAACCTTATTCCAAC+TGG 0.357944 6_4:-7335708 Msa0974340:CDS
TTCCTAAAACCACAAATTGT+TGG 0.359831 6_4:-7335651 Msa0974340:CDS
TTAGGATGATTAACAGAATC+AGG 0.363742 6_4:+7335372 None:intergenic
GGAATAAGGTTATTGTCAAT+AGG 0.410891 6_4:+7335714 None:intergenic
ATTCTTGTACCAACAATTTG+TGG 0.418307 6_4:+7335642 None:intergenic
TGCTTGCATAATTATTGTTA+GGG 0.423747 6_4:+7335857 None:intergenic
GCACTATAAAATTGCAATCC+AGG 0.428333 6_4:+7335477 None:intergenic
AACCATGCTTATTGGAACTT+AGG 0.428402 6_4:-7335798 Msa0974340:CDS
AGAGAACAAAGAAGGATTAA+CGG 0.450183 6_4:-7335559 Msa0974340:CDS
ATAGTGATGGATAAGAAATC+AGG 0.452035 6_4:-7335528 Msa0974340:CDS
GTGAAGAATGATAAGGGAAA+AGG 0.455139 6_4:-7335447 Msa0974340:CDS
AAGCTTAGTACTAATGCTCC+TGG 0.469025 6_4:-7335495 Msa0974340:CDS
GGAAAATTAGAGAACAAAGA+AGG 0.503162 6_4:-7335567 Msa0974340:CDS
TTAACTAAATTTACTGGTGT+AGG 0.514196 6_4:+7335819 None:intergenic
AAGAATGATAAGGGAAAAGG+AGG 0.537569 6_4:-7335444 Msa0974340:CDS
TTCCTAAGTTCCAATAAGCA+TGG 0.549621 6_4:+7335796 None:intergenic
AACGGTTGCATCTATAGTGA+TGG 0.565533 6_4:-7335541 Msa0974340:CDS
AAAAGCATGTGGAACTTTGG+TGG 0.603729 6_4:+7335287 None:intergenic
TCCAAACAAAGTGCTGAACG+TGG 0.666017 6_4:+7335408 None:intergenic
AGAATGATAAGGGAAAAGGA+GGG 0.703237 6_4:-7335443 Msa0974340:CDS
AACTTAGGAAACCATAACAG+TGG 0.715250 6_4:-7335783 Msa0974340:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAACTATGTGCTTAATAA+AGG - chr6_4:7335584-7335603 Msa0974340:CDS 20.0%
!!! AAATTTTGTGAAGAATGATA+AGG - chr6_4:7335718-7335737 Msa0974340:CDS 20.0%
!!! AATTTTGTGAAGAATGATAA+GGG - chr6_4:7335719-7335738 Msa0974340:CDS 20.0%
! TGCTTGCATAATTATTGTTA+GGG + chr6_4:7335318-7335337 None:intergenic 25.0%
! TTGCTTGCATAATTATTGTT+AGG + chr6_4:7335319-7335338 None:intergenic 25.0%
! TTAACTAAATTTACTGGTGT+AGG + chr6_4:7335356-7335375 None:intergenic 25.0%
! ATTTAGTTAACCATGCTTAT+TGG - chr6_4:7335366-7335385 Msa0974340:CDS 25.0%
!! GATGAAGTTGTTCAAATTTT+TGG - chr6_4:7335422-7335441 Msa0974340:CDS 25.0%
!! AAAATTTTCCAGTTGGAATA+AGG + chr6_4:7335475-7335494 None:intergenic 25.0%
! AACCAATTACCAAAAACAAA+TGG - chr6_4:7335554-7335573 Msa0974340:CDS 25.0%
!!! AACCATTTGTTTTTGGTAAT+TGG + chr6_4:7335559-7335578 None:intergenic 25.0%
!!! ATGTCATAACCATTTGTTTT+TGG + chr6_4:7335566-7335585 None:intergenic 25.0%
! ACAATAGTTGAAGGAAAATT+AGG + chr6_4:7335821-7335840 None:intergenic 25.0%
!! TCTTTTGTAACAATAGTTGA+AGG + chr6_4:7335830-7335849 None:intergenic 25.0%
! AACAACATAACATGCTTATA+AGG + chr6_4:7335857-7335876 None:intergenic 25.0%
GCATGGTTAACTAAATTTAC+TGG + chr6_4:7335362-7335381 None:intergenic 30.0%
GGAATAAGGTTATTGTCAAT+AGG + chr6_4:7335461-7335480 None:intergenic 30.0%
! TCCAACTGGAAAATTTTCAT+CGG - chr6_4:7335478-7335497 Msa0974340:CDS 30.0%
!!! TGTGGTTTTAGGAAATCATA+TGG + chr6_4:7335515-7335534 None:intergenic 30.0%
TTCCTAAAACCACAAATTGT+TGG - chr6_4:7335521-7335540 Msa0974340:CDS 30.0%
! TACCAACAATTTGTGGTTTT+AGG + chr6_4:7335526-7335545 None:intergenic 30.0%
ATTCTTGTACCAACAATTTG+TGG + chr6_4:7335533-7335552 None:intergenic 30.0%
GGAAAATTAGAGAACAAAGA+AGG - chr6_4:7335605-7335624 Msa0974340:CDS 30.0%
AGAGAACAAAGAAGGATTAA+CGG - chr6_4:7335613-7335632 Msa0974340:CDS 30.0%
!! ATAGTGATGGATAAGAAATC+AGG - chr6_4:7335644-7335663 Msa0974340:CDS 30.0%
TTAGGATGATTAACAGAATC+AGG + chr6_4:7335803-7335822 None:intergenic 30.0%
! TAGAATTGTGAAAAAGCATG+TGG + chr6_4:7335899-7335918 None:intergenic 30.0%
! TACTGGTGTAGGTTTGTTTA+GGG + chr6_4:7335345-7335364 None:intergenic 35.0%
! TTACTGGTGTAGGTTTGTTT+AGG + chr6_4:7335346-7335365 None:intergenic 35.0%
AACCATGCTTATTGGAACTT+AGG - chr6_4:7335374-7335393 Msa0974340:CDS 35.0%
TTCCTAAGTTCCAATAAGCA+TGG + chr6_4:7335379-7335398 None:intergenic 35.0%
AACTTAGGAAACCATAACAG+TGG - chr6_4:7335389-7335408 Msa0974340:CDS 35.0%
CTAAAATGTTGCCACTGTTA+TGG + chr6_4:7335403-7335422 None:intergenic 35.0%
GACAATAACCTTATTCCAAC+TGG - chr6_4:7335464-7335483 Msa0974340:CDS 35.0%
! ACCGATGAAAATTTTCCAGT+TGG + chr6_4:7335482-7335501 None:intergenic 35.0%
GCACTATAAAATTGCAATCC+AGG + chr6_4:7335698-7335717 None:intergenic 35.0%
GTGAAGAATGATAAGGGAAA+AGG - chr6_4:7335725-7335744 Msa0974340:CDS 35.0%
AAGAATGATAAGGGAAAAGG+AGG - chr6_4:7335728-7335747 Msa0974340:CDS 35.0%
AGAATGATAAGGGAAAAGGA+GGG - chr6_4:7335729-7335748 Msa0974340:CDS 35.0%
! TGAAAAAGCATGTGGAACTT+TGG + chr6_4:7335891-7335910 None:intergenic 35.0%
! GGAAAATTTTCATCGGTCGA+AGG - chr6_4:7335485-7335504 Msa0974340:CDS 40.0%
AACGGTTGCATCTATAGTGA+TGG - chr6_4:7335631-7335650 Msa0974340:CDS 40.0%
AAGCTTAGTACTAATGCTCC+TGG - chr6_4:7335677-7335696 Msa0974340:CDS 40.0%
! AAAAGCATGTGGAACTTTGG+TGG + chr6_4:7335888-7335907 None:intergenic 40.0%
! CTTCTGATGATGCAGCTTCT+AGG - chr6_4:7335284-7335303 Msa0974340:CDS 45.0%
ACCACGTTCAGCACTTTGTT+TGG - chr6_4:7335763-7335782 Msa0974340:CDS 45.0%
!! TCCAAACAAAGTGCTGAACG+TGG + chr6_4:7335767-7335786 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 7335275 7335919 7335275 ID=Msa0974340;Name=Msa0974340
chr6_4 mRNA 7335275 7335919 7335275 ID=Msa0974340-mRNA-1;Parent=Msa0974340;Name=Msa0974340-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|214
chr6_4 exon 7335275 7335919 7335275 ID=Msa0974340-mRNA-1:exon:2872;Parent=Msa0974340-mRNA-1
chr6_4 CDS 7335275 7335919 7335275 ID=Msa0974340-mRNA-1:cds;Parent=Msa0974340-mRNA-1
Gene Sequence

>Msa0974340

ATGAGGCAGCTTCTGATGATGCAGCTTCTAGGAAAAAACTCCCTAACAATAATTATGCAAGCAAAAGCCCTAAACAAACCTACACCAGTAAATTTAGTTAACCATGCTTATTGGAACTTAGGAAACCATAACAGTGGCAACATTTTAGATGAAGTTGTTCAAATTTTTGGATCAAAATTCACACCTATTGACAATAACCTTATTCCAACTGGAAAATTTTCATCGGTCGAAGGAACGCCATATGATTTCCTAAAACCACAAATTGTTGGTACAAGAATTAACCAATTACCAAAAACAAATGGTTATGACATTAACTATGTGCTTAATAAAGGAAAATTAGAGAACAAAGAAGGATTAACGGTTGCATCTATAGTGATGGATAAGAAATCAGGAAGAGTTATGAAGCTTAGTACTAATGCTCCTGGATTGCAATTTTATAGTGCAAATTTTGTGAAGAATGATAAGGGAAAAGGAGGGTTTGTTTATCAACCACGTTCAGCACTTTGTTTGGAGAGTCAAGCTTTTCCTGATTCTGTTAATCATCCTAATTTTCCTTCAACTATTGTTACAAAAGAAAAGCCTTATAAGCATGTTATGTTGTTGAAGTTTTCCACCAAAGTTCCACATGCTTTTTCACAATTCTAA
Protein sequence

>Msa0974340

MRQLLMMQLLGKNSLTIIMQAKALNKPTPVNLVNHAYWNLGNHNSGNILDEVVQIFGSKFTPIDNNLIPTGKFSSVEGTPYDFLKPQIVGTRINQLPKTNGYDINYVLNKGKLENKEGLTVASIVMDKKSGRVMKLSTNAPGLQFYSANFVKNDKGKGGFVYQPRSALCLESQAFPDSVNHPNFPSTIVTKEKPYKHVMLLKFSTKVPHAFSQF*