AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1431270

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1431270 MtrunA17_Chr1g0179561 85.922 206 20 3 1 206 1 197 3.27e-105 311
Msa1431270 MtrunA17_Chr7g0265561 57.212 208 55 4 2 206 1 177 4.43e-70 220
Msa1431270 MtrunA17_Chr1g0201951 40.984 183 86 5 39 206 24 199 4.68e-34 125
Msa1431270 MtrunA17_Chr2g0328901 49.600 125 58 2 86 206 64 187 5.82e-32 120
Msa1431270 MtrunA17_Chr6g0463911 64.773 88 30 1 119 206 106 192 1.19e-29 114
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1431270 AT3G10040.1 44.796 221 73 6 2 206 1 188 1.02e-35 130
Msa1431270 AT1G21200.1 51.639 122 52 2 89 206 71 189 8.30e-34 125
Msa1431270 AT1G21200.2 51.639 122 52 2 89 206 71 189 8.30e-34 125
Msa1431270 AT1G76870.2 44.853 136 66 2 71 206 28 154 2.34e-32 120
Msa1431270 AT1G76870.1 44.853 136 66 2 71 206 28 154 2.34e-32 120
Msa1431270 AT1G76870.3 44.853 136 66 2 71 206 28 154 2.34e-32 120

Find 41 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTCTTCAGCTTGAAAATT+TGG 0.110218 tig0026815:+7393 None:intergenic
CTGTTGTTGATGTTTGTTCT+TGG 0.169378 tig0026815:+7452 None:intergenic
TCAAGGGCTATGATGGAAAA+AGG 0.210514 tig0026815:-7186 Msa1431270:CDS
AGTTTAATGATTTGAATAAA+AGG 0.261559 tig0026815:-7131 Msa1431270:CDS
ATCACTCCTTCTGGTTTGTT+AGG 0.338445 tig0026815:-7687 Msa1431270:CDS
TTGTTCTTGGATGAAGAAAA+TGG 0.352317 tig0026815:+7465 None:intergenic
GTTGTTGTTGTTGGTGTAAA+GGG 0.380586 tig0026815:+7649 None:intergenic
AATGGTAAGGCTATTGATAA+TGG 0.397789 tig0026815:-7310 Msa1431270:CDS
TGTGTCAGTGTCATGATGTT+GGG 0.401350 tig0026815:+7530 None:intergenic
ATCTGTTTCAAGGGCTATGA+TGG 0.408066 tig0026815:-7193 Msa1431270:CDS
CACCATGGCAAAGAATGAAA+TGG 0.442437 tig0026815:-7341 Msa1431270:CDS
GAAAGTGGAAATCTGTTTCA+AGG 0.446222 tig0026815:-7203 Msa1431270:CDS
TGTTGTTGTTGTTGGTGTAA+AGG 0.459607 tig0026815:+7648 None:intergenic
TCTTGAATGATGGAAGCTAA+TGG 0.466883 tig0026815:-7723 None:intergenic
TAGTGGGTTGTTACAGAAGA+AGG 0.473118 tig0026815:-7226 Msa1431270:CDS
GTCCATTTCATTCTTTGCCA+TGG 0.478175 tig0026815:+7339 None:intergenic
TTTCAAGCTGAAGAAAGCTC+TGG 0.499001 tig0026815:-7387 Msa1431270:CDS
ATTTGAATAAAAGGTATAAG+AGG 0.507384 tig0026815:-7122 Msa1431270:CDS
CATCATCATTCAATGAAACA+TGG 0.509386 tig0026815:-7495 Msa1431270:CDS
TATTACATTGGTGATGAAGC+TGG 0.519299 tig0026815:-7282 Msa1431270:CDS
GTGTGTCAGTGTCATGATGT+TGG 0.523565 tig0026815:+7529 None:intergenic
AATGAAATGGACTGATACAA+TGG 0.534079 tig0026815:-7328 Msa1431270:CDS
AACTTATCTTCACATTGTTG+AGG 0.538324 tig0026815:+7150 None:intergenic
TGTTACAGAAGAAGGGAAAG+TGG 0.544015 tig0026815:-7218 Msa1431270:CDS
ATAATGGCTGTTTATTACAT+TGG 0.545685 tig0026815:-7294 Msa1431270:CDS
GGGGAGCATAGGAAACAACT+TGG 0.576375 tig0026815:+7550 None:intergenic
GTCATGATGTTGGGGAGCAT+AGG 0.579377 tig0026815:+7539 None:intergenic
ATCATCATTCAATGAAACAT+GGG 0.582829 tig0026815:-7494 Msa1431270:CDS
CAAGCTGAAGAAAGCTCTGG+TGG 0.582867 tig0026815:-7384 Msa1431270:CDS
TCTTGGATGAAGAAAATGGA+GGG 0.591048 tig0026815:+7469 None:intergenic
AAAGTGGAAATCTGTTTCAA+GGG 0.595878 tig0026815:-7202 Msa1431270:CDS
CATAGGAAACAACTTGGGAA+TGG 0.599175 tig0026815:+7556 None:intergenic
AATGGACTGATACAATGGTA+AGG 0.602489 tig0026815:-7323 Msa1431270:CDS
AGTGGGTTGTTACAGAAGAA+GGG 0.604261 tig0026815:-7225 Msa1431270:CDS
GTGTCAGTGTCATGATGTTG+GGG 0.613275 tig0026815:+7531 None:intergenic
TTCTTGGATGAAGAAAATGG+AGG 0.615525 tig0026815:+7468 None:intergenic
TAACAAACCAGAAGGAGTGA+TGG 0.616326 tig0026815:+7689 None:intergenic
CAAACCAGAAGGAGTGATGG+TGG 0.618353 tig0026815:+7692 None:intergenic
ACTACTCCTAACAAACCAGA+AGG 0.660583 tig0026815:+7681 None:intergenic
GGGAGCATAGGAAACAACTT+GGG 0.683513 tig0026815:+7551 None:intergenic
TGGGAATGGTGCAAATGATG+AGG 0.685441 tig0026815:+7570 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTTTAATGATTTGAATAAA+AGG - tig0026815:7705-7724 Msa1431270:CDS 15.0%
!!! ATTTGAATAAAAGGTATAAG+AGG - tig0026815:7714-7733 Msa1431270:CDS 20.0%
! ATCATCATTCAATGAAACAT+GGG - tig0026815:7342-7361 Msa1431270:CDS 25.0%
! ATAATGGCTGTTTATTACAT+TGG - tig0026815:7542-7561 Msa1431270:CDS 25.0%
! CAAATAAGAAAAAGACTAGT+GGG - tig0026815:7594-7613 Msa1431270:CDS 25.0%
! TGTTGTTGTTGTTGTTGATT+AGG + tig0026815:7242-7261 None:intergenic 30.0%
CATCATCATTCAATGAAACA+TGG - tig0026815:7341-7360 Msa1431270:CDS 30.0%
TTGTTCTTGGATGAAGAAAA+TGG + tig0026815:7374-7393 None:intergenic 30.0%
CTTTCTTCAGCTTGAAAATT+TGG + tig0026815:7446-7465 None:intergenic 30.0%
! CATGGTGAAATCTTTCTTTT+TGG + tig0026815:7482-7501 None:intergenic 30.0%
CAAAAAGAAAGATTTCACCA+TGG - tig0026815:7480-7499 Msa1431270:CDS 30.0%
!! AATGAAATGGACTGATACAA+TGG - tig0026815:7508-7527 Msa1431270:CDS 30.0%
AATGGTAAGGCTATTGATAA+TGG - tig0026815:7526-7545 Msa1431270:CDS 30.0%
!!! CCACTAGTCTTTTTCTTATT+TGG + tig0026815:7596-7615 None:intergenic 30.0%
CCAAATAAGAAAAAGACTAG+TGG - tig0026815:7593-7612 Msa1431270:CDS 30.0%
AAAGTGGAAATCTGTTTCAA+GGG - tig0026815:7634-7653 Msa1431270:CDS 30.0%
AACTTATCTTCACATTGTTG+AGG + tig0026815:7689-7708 None:intergenic 30.0%
! GTTGTTGTTGTTGGTGTAAA+GGG + tig0026815:7190-7209 None:intergenic 35.0%
! TGTTGTTGTTGTTGGTGTAA+AGG + tig0026815:7191-7210 None:intergenic 35.0%
! GTTGTTGTTGTTGTTGTTGT+TGG + tig0026815:7199-7218 None:intergenic 35.0%
TCTTGGATGAAGAAAATGGA+GGG + tig0026815:7370-7389 None:intergenic 35.0%
TTCTTGGATGAAGAAAATGG+AGG + tig0026815:7371-7390 None:intergenic 35.0%
CTGTTGTTGATGTTTGTTCT+TGG + tig0026815:7387-7406 None:intergenic 35.0%
!! AATGGACTGATACAATGGTA+AGG - tig0026815:7513-7532 Msa1431270:CDS 35.0%
!! TATTACATTGGTGATGAAGC+TGG - tig0026815:7554-7573 Msa1431270:CDS 35.0%
GAAAGTGGAAATCTGTTTCA+AGG - tig0026815:7633-7652 Msa1431270:CDS 35.0%
TAACAAACCAGAAGGAGTGA+TGG + tig0026815:7150-7169 None:intergenic 40.0%
!! ATCACTCCTTCTGGTTTGTT+AGG - tig0026815:7149-7168 Msa1431270:CDS 40.0%
ACTACTCCTAACAAACCAGA+AGG + tig0026815:7158-7177 None:intergenic 40.0%
CATAGGAAACAACTTGGGAA+TGG + tig0026815:7283-7302 None:intergenic 40.0%
TGTGTCAGTGTCATGATGTT+GGG + tig0026815:7309-7328 None:intergenic 40.0%
TTTCAAGCTGAAGAAAGCTC+TGG - tig0026815:7449-7468 Msa1431270:CDS 40.0%
CACCATGGCAAAGAATGAAA+TGG - tig0026815:7495-7514 Msa1431270:CDS 40.0%
GTCCATTTCATTCTTTGCCA+TGG + tig0026815:7500-7519 None:intergenic 40.0%
!! TAGTGGGTTGTTACAGAAGA+AGG - tig0026815:7610-7629 Msa1431270:CDS 40.0%
!! AGTGGGTTGTTACAGAAGAA+GGG - tig0026815:7611-7630 Msa1431270:CDS 40.0%
TGTTACAGAAGAAGGGAAAG+TGG - tig0026815:7618-7637 Msa1431270:CDS 40.0%
ATCTGTTTCAAGGGCTATGA+TGG - tig0026815:7643-7662 Msa1431270:CDS 40.0%
! TCAAGGGCTATGATGGAAAA+AGG - tig0026815:7650-7669 Msa1431270:CDS 40.0%
! CAAGGGCTATGATGGAAAAA+GGG - tig0026815:7651-7670 Msa1431270:CDS 40.0%
! TTTTCCACCATCACTCCTTC+TGG - tig0026815:7140-7159 Msa1431270:CDS 45.0%
TGGGAATGGTGCAAATGATG+AGG + tig0026815:7269-7288 None:intergenic 45.0%
! GGGAGCATAGGAAACAACTT+GGG + tig0026815:7288-7307 None:intergenic 45.0%
GTGTCAGTGTCATGATGTTG+GGG + tig0026815:7308-7327 None:intergenic 45.0%
GTGTGTCAGTGTCATGATGT+TGG + tig0026815:7310-7329 None:intergenic 45.0%
CAAACCAGAAGGAGTGATGG+TGG + tig0026815:7147-7166 None:intergenic 50.0%
! GGGGAGCATAGGAAACAACT+TGG + tig0026815:7289-7308 None:intergenic 50.0%
! GTCATGATGTTGGGGAGCAT+AGG + tig0026815:7300-7319 None:intergenic 50.0%
! CAAGCTGAAGAAAGCTCTGG+TGG - tig0026815:7452-7471 Msa1431270:CDS 50.0%
Chromosome Type Strat End Strand Name
tig0026815 gene 7119 7739 7119 ID=Msa1431270;Name=Msa1431270
tig0026815 mRNA 7119 7739 7119 ID=Msa1431270-mRNA-1;Parent=Msa1431270;Name=Msa1431270-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|1|1|0|206
tig0026815 exon 7119 7739 7119 ID=Msa1431270-mRNA-1:exon:7489;Parent=Msa1431270-mRNA-1
tig0026815 CDS 7119 7739 7119 ID=Msa1431270-mRNA-1:cds;Parent=Msa1431270-mRNA-1
Gene Sequence

>Msa1431270

ATGATGGAAGCTAATGGCATGTTTTCCACCATCACTCCTTCTGGTTTGTTAGGAGTAGTTGATAATATCCCTTTACACCAACAACAACAACAACAACAACAACAAAAACAACAGAATCTTCCTAATCAACAACAACAACAACAAAATCCTCATCATTTGCACCATTCCCAAGTTGTTTCCTATGCTCCCCAACATCATGACACTGACACACATCAACAACAACATCATCATTCAATGAAACATGGGTTCCCTCCATTTTCTTCATCCAAGAACAAACATCAACAACAGCAGCAACAAAGTTCTCAGATGAGTGATGAAGATGAACCAAATTTTCAAGCTGAAGAAAGCTCTGGTGGCGATCCAAAAAGAAAGATTTCACCATGGCAAAGAATGAAATGGACTGATACAATGGTAAGGCTATTGATAATGGCTGTTTATTACATTGGTGATGAAGCTGGTTCTGAAGTGACTGATCCAAATAAGAAAAAGACTAGTGGGTTGTTACAGAAGAAGGGAAAGTGGAAATCTGTTTCAAGGGCTATGATGGAAAAAGGGTTTTATGTGTCACCTCAACAATGTGAAGATAAGTTTAATGATTTGAATAAAAGGTATAAGAGGTGA
Protein sequence

>Msa1431270

MMEANGMFSTITPSGLLGVVDNIPLHQQQQQQQQQKQQNLPNQQQQQQNPHHLHHSQVVSYAPQHHDTDTHQQQHHHSMKHGFPPFSSSKNKHQQQQQQSSQMSDEDEPNFQAEESSGGDPKRKISPWQRMKWTDTMVRLLIMAVYYIGDEAGSEVTDPNKKKTSGLLQKKGKWKSVSRAMMEKGFYVSPQQCEDKFNDLNKRYKR*