AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0309980


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0309980 MtrunA17_Chr2g0278621 98.585 212 3 0 1 212 1 212 3.94e-153 423
Msa0309980 MtrunA17_Chr6g0479471 98.113 212 4 0 1 212 1 212 2.04e-152 421
Msa0309980 MtrunA17_Chr1g0202031 69.565 184 51 1 29 207 29 212 1.36e-85 252
Msa0309980 MtrunA17_Chr6g0463641 66.154 195 56 2 23 207 11 205 3.54e-77 230
Msa0309980 MtrunA17_Chr4g0050831 60.938 192 66 1 27 209 30 221 2.32e-75 226
Msa0309980 MtrunA17_Chr4g0050821 60.938 192 66 1 27 209 30 221 2.47e-75 226
Msa0309980 MtrunA17_Chr4g0050841 61.579 190 64 1 27 207 30 219 2.88e-75 226
Msa0309980 MtrunA17_Chr4g0050811 56.279 215 83 3 1 209 27 236 2.24e-72 219
Msa0309980 MtrunA17_Chr4g0050851 52.232 224 83 3 11 210 5 228 9.52e-64 197
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0309980 AT3G43660.1 68.205 195 58 2 14 207 2 193 3.06e-91 266
Msa0309980 AT3G43630.1 71.277 188 50 2 21 207 8 192 1.19e-84 249
Msa0309980 AT1G21140.1 69.792 192 54 2 17 207 7 195 2.85e-83 246
Msa0309980 AT1G76800.1 69.519 187 53 1 21 207 9 191 2.30e-79 236
Msa0309980 AT3G25190.1 59.000 200 67 3 21 207 15 212 1.25e-63 197

Find 41 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGCTATGTCTCTTACTTT+TGG 0.225220 2_4:+4810668 Msa0309980:CDS
AGCCTTGCTTTGTTTGCTTT+TGG 0.248729 2_4:+4810575 Msa0309980:CDS
GAAGCAAAGGCAGCATAATA+AGG 0.258027 2_4:-4810455 None:intergenic
GGCTCCAACACCCATCATTA+AGG 0.342144 2_4:-4810264 None:intergenic
TGTTCTTGGGAAAGCTCCTT+TGG 0.348881 2_4:+4810610 Msa0309980:CDS
TTTGGTGAAGTCTTCTTTGA+GGG 0.356177 2_4:+4810628 Msa0309980:CDS
GGATTGTTGAGTGCTGTTCT+TGG 0.377078 2_4:+4810596 Msa0309980:CDS
GTTAAGACAATGATTCTAAC+AGG 0.391005 2_4:+4810299 Msa0309980:CDS
CTCAAAGAGCACAATGGCTT+AGG 0.396117 2_4:+4810198 Msa0309980:CDS
TTATTATGCTGCCTTTGCTT+CGG 0.407157 2_4:+4810457 Msa0309980:CDS
CTTTGGTGAAGTCTTCTTTG+AGG 0.408112 2_4:+4810627 Msa0309980:CDS
GATTGTTGAGTGCTGTTCTT+GGG 0.419290 2_4:+4810597 Msa0309980:CDS
GGCGCCTTTGTGCCGCTACT+CGG 0.427583 2_4:+4810497 Msa0309980:CDS
CTCAACAGCATCCTTAATGA+TGG 0.435656 2_4:+4810253 Msa0309980:CDS
ATGATTCTAACAGGAATTGC+TGG 0.440222 2_4:+4810308 Msa0309980:CDS
TAAAGACTATAAGATGAGGT+TGG 0.456281 2_4:+4810532 Msa0309980:CDS
AAAAGCGATGGCCGAAGCAA+AGG 0.483514 2_4:-4810468 None:intergenic
TAAGATGAGGTTGGGAGTTG+TGG 0.484406 2_4:+4810541 Msa0309980:CDS
AAAGACTATAAGATGAGGTT+GGG 0.489210 2_4:+4810533 Msa0309980:CDS
GGAATTGCTGGTCTTGTAGC+TGG 0.491668 2_4:+4810320 Msa0309980:CDS
TCAAAGAGCACAATGGCTTA+GGG 0.493819 2_4:+4810199 Msa0309980:CDS
AAGCAAAGGCAGCATAATAA+GGG 0.516802 2_4:-4810454 None:intergenic
GGCGCCGACCGCAAAAGCGA+TGG 0.528738 2_4:-4810480 None:intergenic
ATGAGGTTGGGAGTTGTGGT+TGG 0.534054 2_4:+4810545 Msa0309980:CDS
GCATCCTTAATGATGGGTGT+TGG 0.549500 2_4:+4810260 Msa0309980:CDS
ATCCAAAAGCAAACAAAGCA+AGG 0.566512 2_4:-4810577 None:intergenic
AAGGCAGCATAATAAGGGTT+AGG 0.567356 2_4:-4810449 None:intergenic
CGCGCCGAGTAGCGGCACAA+AGG 0.568749 2_4:-4810501 None:intergenic
GGTGCATGTAGCATGGCAAT+TGG 0.569674 2_4:+4810341 Msa0309980:CDS
TCAACAGCATCCTTAATGAT+GGG 0.587391 2_4:+4810254 Msa0309980:CDS
ACAAACGCCGCGCCGAGTAG+CGG 0.601438 2_4:-4810509 None:intergenic
TTGTTAAAGACTATAAGATG+AGG 0.623966 2_4:+4810528 Msa0309980:CDS
CTCAAAGAAGACTTCACCAA+AGG 0.626739 2_4:-4810626 None:intergenic
TGTAGCTGGTGCATGTAGCA+TGG 0.629799 2_4:+4810334 Msa0309980:CDS
CTTTGTGCCGCTACTCGGCG+CGG 0.645709 2_4:+4810502 Msa0309980:CDS
TACGTGCTAGTGTAGCTGCA+TGG 0.662565 2_4:-4810106 None:intergenic
ATTATACTCAAAGAGCACAA+TGG 0.665811 2_4:+4810192 Msa0309980:CDS
TGAATCAAAAGTGTACAACA+TGG 0.690093 2_4:+4810130 Msa0309980:CDS
TTTGCACAAATGAAAAGACA+AGG 0.695332 2_4:+4810401 Msa0309980:CDS
AAAATGATCAAACTACAACA+TGG 0.718736 2_4:-4810709 None:intergenic
GTGCTAGTGTAGCTGCATGG+TGG 0.751494 2_4:-4810103 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AACATGGATGTTGAAAAAAA+AGG + chr2_4:4810146-4810165 Msa0309980:CDS 25.0%
!! TGTCTTAACATCTTTTGTAA+CGG - chr2_4:4810288-4810307 None:intergenic 25.0%
! TTGTTAAAGACTATAAGATG+AGG + chr2_4:4810528-4810547 Msa0309980:CDS 25.0%
! TGAATCAAAAGTGTACAACA+TGG + chr2_4:4810130-4810149 Msa0309980:CDS 30.0%
! ATTATACTCAAAGAGCACAA+TGG + chr2_4:4810192-4810211 Msa0309980:CDS 30.0%
GTTAAGACAATGATTCTAAC+AGG + chr2_4:4810299-4810318 Msa0309980:CDS 30.0%
TTTGCACAAATGAAAAGACA+AGG + chr2_4:4810401-4810420 Msa0309980:CDS 30.0%
TAAAGACTATAAGATGAGGT+TGG + chr2_4:4810532-4810551 Msa0309980:CDS 30.0%
AAAGACTATAAGATGAGGTT+GGG + chr2_4:4810533-4810552 Msa0309980:CDS 30.0%
TCAACAGCATCCTTAATGAT+GGG + chr2_4:4810254-4810273 Msa0309980:CDS 35.0%
ATGATTCTAACAGGAATTGC+TGG + chr2_4:4810308-4810327 Msa0309980:CDS 35.0%
AAGCAAAGGCAGCATAATAA+GGG - chr2_4:4810457-4810476 None:intergenic 35.0%
TTATTATGCTGCCTTTGCTT+CGG + chr2_4:4810457-4810476 Msa0309980:CDS 35.0%
ATCCAAAAGCAAACAAAGCA+AGG - chr2_4:4810580-4810599 None:intergenic 35.0%
TTTGGTGAAGTCTTCTTTGA+GGG + chr2_4:4810628-4810647 Msa0309980:CDS 35.0%
!! TCTTCTTTGAGGGTTTTGAT+TGG + chr2_4:4810638-4810657 Msa0309980:CDS 35.0%
!! CTTGCTATGTCTCTTACTTT+TGG + chr2_4:4810668-4810687 Msa0309980:CDS 35.0%
! TCAAAGAGCACAATGGCTTA+GGG + chr2_4:4810199-4810218 Msa0309980:CDS 40.0%
!! GCTGTTTTAGGTGCTAATGA+TGG + chr2_4:4810224-4810243 Msa0309980:CDS 40.0%
CTCAACAGCATCCTTAATGA+TGG + chr2_4:4810253-4810272 Msa0309980:CDS 40.0%
AAGGCAGCATAATAAGGGTT+AGG - chr2_4:4810452-4810471 None:intergenic 40.0%
GAAGCAAAGGCAGCATAATA+AGG - chr2_4:4810458-4810477 None:intergenic 40.0%
!!! AGCCTTGCTTTGTTTGCTTT+TGG + chr2_4:4810575-4810594 Msa0309980:CDS 40.0%
! GATTGTTGAGTGCTGTTCTT+GGG + chr2_4:4810597-4810616 Msa0309980:CDS 40.0%
CTCAAAGAAGACTTCACCAA+AGG - chr2_4:4810629-4810648 None:intergenic 40.0%
CTTTGGTGAAGTCTTCTTTG+AGG + chr2_4:4810627-4810646 Msa0309980:CDS 40.0%
!!! TCTTTGAGGGTTTTGATTGG+TGG + chr2_4:4810641-4810660 Msa0309980:CDS 40.0%
! CTCAAAGAGCACAATGGCTT+AGG + chr2_4:4810198-4810217 Msa0309980:CDS 45.0%
!! GCATCCTTAATGATGGGTGT+TGG + chr2_4:4810260-4810279 Msa0309980:CDS 45.0%
TAAGATGAGGTTGGGAGTTG+TGG + chr2_4:4810541-4810560 Msa0309980:CDS 45.0%
! GGATTGTTGAGTGCTGTTCT+TGG + chr2_4:4810596-4810615 Msa0309980:CDS 45.0%
TGTTCTTGGGAAAGCTCCTT+TGG + chr2_4:4810610-4810629 Msa0309980:CDS 45.0%
!!! TGAGGGTTTTGATTGGTGGA+TGG + chr2_4:4810645-4810664 Msa0309980:CDS 45.0%
TACGTGCTAGTGTAGCTGCA+TGG - chr2_4:4810109-4810128 None:intergenic 50.0%
!! TGGCTTAGGGCAGCTGTTTT+AGG + chr2_4:4810212-4810231 Msa0309980:CDS 50.0%
GGCTCCAACACCCATCATTA+AGG - chr2_4:4810267-4810286 None:intergenic 50.0%
!! GGAATTGCTGGTCTTGTAGC+TGG + chr2_4:4810320-4810339 Msa0309980:CDS 50.0%
TGTAGCTGGTGCATGTAGCA+TGG + chr2_4:4810334-4810353 Msa0309980:CDS 50.0%
GGTGCATGTAGCATGGCAAT+TGG + chr2_4:4810341-4810360 Msa0309980:CDS 50.0%
AAAAGCGATGGCCGAAGCAA+AGG - chr2_4:4810471-4810490 None:intergenic 50.0%
ATGAGGTTGGGAGTTGTGGT+TGG + chr2_4:4810545-4810564 Msa0309980:CDS 50.0%
GTGCTAGTGTAGCTGCATGG+TGG - chr2_4:4810106-4810125 None:intergenic 55.0%
!! TGCTTCGGCCATCGCTTTTG+CGG + chr2_4:4810472-4810491 Msa0309980:CDS 55.0%
!! TCGGCCATCGCTTTTGCGGT+CGG + chr2_4:4810476-4810495 Msa0309980:CDS 60.0%
! GGCGCCTTTGTGCCGCTACT+CGG + chr2_4:4810497-4810516 Msa0309980:CDS 65.0%
! CTTTGTGCCGCTACTCGGCG+CGG + chr2_4:4810502-4810521 Msa0309980:CDS 65.0%
ACAAACGCCGCGCCGAGTAG+CGG - chr2_4:4810512-4810531 None:intergenic 65.0%
!! GGCGCCGACCGCAAAAGCGA+TGG - chr2_4:4810483-4810502 None:intergenic 70.0%
CGCGCCGAGTAGCGGCACAA+AGG - chr2_4:4810504-4810523 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 4810086 4810724 4810086 ID=Msa0309980;Name=Msa0309980
chr2_4 mRNA 4810086 4810724 4810086 ID=Msa0309980-mRNA-1;Parent=Msa0309980;Name=Msa0309980-mRNA-1;_AED=0.05;_eAED=0.05;_QI=0|-1|0|1|-1|1|1|0|212
chr2_4 exon 4810086 4810724 4810086 ID=Msa0309980-mRNA-1:exon:1637;Parent=Msa0309980-mRNA-1
chr2_4 CDS 4810086 4810724 4810086 ID=Msa0309980-mRNA-1:cds;Parent=Msa0309980-mRNA-1
Gene Sequence

>Msa0309980

ATGGCAGAAATTCAGCACCACCATGCAGCTACACTAGCACGTAGTGAATCAAAAGTGTACAACATGGATGTTGAAAAAAAAGGAGAAGAAGAAAATCATGAAAAAGATTATACTCAAAGAGCACAATGGCTTAGGGCAGCTGTTTTAGGTGCTAATGATGGTTTACTCTCAACAGCATCCTTAATGATGGGTGTTGGAGCCGTTACAAAAGATGTTAAGACAATGATTCTAACAGGAATTGCTGGTCTTGTAGCTGGTGCATGTAGCATGGCAATTGGTGAATTTGTGTCTGTTTATTCACAATATGATATTGAATTTGCACAAATGAAAAGACAAGGAAACATTTCTCAAAAAGATAAATTGCCTAACCCTTATTATGCTGCCTTTGCTTCGGCCATCGCTTTTGCGGTCGGCGCCTTTGTGCCGCTACTCGGCGCGGCGTTTGTTAAAGACTATAAGATGAGGTTGGGAGTTGTGGTTGGTGTTGTTAGCCTTGCTTTGTTTGCTTTTGGATTGTTGAGTGCTGTTCTTGGGAAAGCTCCTTTGGTGAAGTCTTCTTTGAGGGTTTTGATTGGTGGATGGCTTGCTATGTCTCTTACTTTTGGTTTAACTAAGCTTGTAAACCATGTTGTAGTTTGA

Protein sequence

>Msa0309980

MAEIQHHHAATLARSESKVYNMDVEKKGEEENHEKDYTQRAQWLRAAVLGANDGLLSTASLMMGVGAVTKDVKTMILTGIAGLVAGACSMAIGEFVSVYSQYDIEFAQMKRQGNISQKDKLPNPYYAAFASAIAFAVGAFVPLLGAAFVKDYKMRLGVVVGVVSLALFAFGLLSAVLGKAPLVKSSLRVLIGGWLAMSLTFGLTKLVNHVVV*