AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1231520


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1231520 MtrunA17_Chr8g0340421 95.855 193 7 1 1 193 3 194 2.26e-135 376
Msa1231520 MtrunA17_Chr2g0331111 66.332 199 58 5 1 193 1 196 1.69e-84 248
Msa1231520 MtrunA17_Chr8g0344381 46.212 132 58 5 59 183 29 154 3.33e-31 111
Msa1231520 MtrunA17_Chr1g0205251 47.778 90 39 3 60 146 2 86 2.60e-23 89.7
Msa1231520 MtrunA17_Chr3g0136441 59.091 66 26 1 57 121 8 73 2.98e-22 87.4
Msa1231520 MtrunA17_Chr5g0394601 43.750 96 45 3 60 152 2 91 1.57e-21 85.1
Msa1231520 MtrunA17_Chr3g0140381 34.211 152 87 4 29 177 4 145 4.69e-19 79.7
Msa1231520 MtrunA17_Chr4g0070371 37.234 94 52 2 60 146 24 117 9.70e-18 76.3
Msa1231520 MtrunA17_Chr4g0070351 40.860 93 50 3 33 121 1 92 1.05e-17 75.5
Msa1231520 MtrunA17_Chr1g0150711 40.217 92 47 2 45 132 1 88 6.64e-16 71.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1231520 AT5G25840.1 50.543 184 54 5 33 193 4 173 2.46e-53 168
Msa1231520 AT1G79770.1 52.903 155 59 3 33 187 27 167 1.09e-46 151
Msa1231520 AT4G14819.1 42.727 110 51 3 60 169 2 99 1.54e-23 90.1
Msa1231520 AT2G25780.1 36.774 155 83 4 33 182 7 151 1.97e-22 89.0
Msa1231520 AT3G22540.1 40.449 89 50 1 60 148 2 87 1.80e-21 85.1
Msa1231520 AT1G72510.1 39.706 136 67 7 60 183 33 165 1.08e-20 84.7
Msa1231520 AT1G72510.2 39.706 136 67 7 60 183 33 165 1.08e-20 84.7
Msa1231520 AT1G54095.1 39.706 136 69 5 59 183 14 147 3.52e-19 80.5
Msa1231520 AT5G20670.1 33.582 134 82 3 57 183 19 152 4.49e-19 80.1
Msa1231520 AT2G09970.1 34.058 138 73 7 60 183 33 166 4.22e-16 72.8

Find 41 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTAACATGGATGGGAAAATT+AGG 0.194429 8_2:+7706863 Msa1231520:CDS
CGACATTTCCTTCGAGTTGA+TGG 0.257929 8_2:+7706531 Msa1231520:CDS
CCTCCTCCTTTCTTGTCCCT+TGG 0.275546 8_2:-7706901 None:intergenic
AAAATAGATAGATAGTTAAT+TGG 0.284549 8_2:-7706992 None:intergenic
TGTGTTAAGTTTAACAAATA+TGG 0.300385 8_2:+7706784 Msa1231520:CDS
GCTTGTGCTTGAAACAAAAC+TGG 0.379794 8_2:-7706817 None:intergenic
GACAAGAAAGGAGGAGGAGG+AGG 0.400333 8_2:+7706907 Msa1231520:CDS
GAAAGTTTCGTTGGTTTGTT+TGG 0.408422 8_2:-7706478 None:intergenic
TAACATGGATGGGAAAATTA+GGG 0.434099 8_2:+7706864 Msa1231520:CDS
ATTTGTGTGCGGTTTATGTT+CGG 0.438573 8_2:+7706687 Msa1231520:CDS
TTGATCTCTCTTGTAAGTGC+TGG 0.461637 8_2:-7706955 None:intergenic
ACACTTTGCATCTTCAACTT+CGG 0.466067 8_2:-7706593 None:intergenic
TGTCGGAGACCGTTCTTTGA+AGG 0.474473 8_2:-7706513 None:intergenic
TTAAGTTTAACAAATATGGT+AGG 0.490124 8_2:+7706788 Msa1231520:CDS
AGGGACAAGAAAGGAGGAGG+AGG 0.494514 8_2:+7706904 Msa1231520:CDS
TGTTGTCAAGTTCATTCTCA+AGG 0.519029 8_2:+7706440 Msa1231520:CDS
TTCTTTCGCCATCAACTCGA+AGG 0.530628 8_2:-7706539 None:intergenic
TAAGTTTAACAAATATGGTA+GGG 0.538103 8_2:+7706789 Msa1231520:CDS
TCGGAAGTTGAAAGTTTCGT+TGG 0.539469 8_2:-7706487 None:intergenic
GGAGGCGGTGAAAGAAGAGT+TGG 0.546775 8_2:+7706708 Msa1231520:CDS
GACCGTTCTTTGAAGGTGGT+CGG 0.559329 8_2:-7706506 None:intergenic
ATCATGGTTATGGCACCTCA+TGG 0.562684 8_2:+7706409 None:intergenic
CCAAGGGACAAGAAAGGAGG+AGG 0.566147 8_2:+7706901 Msa1231520:CDS
CGGAGACCGTTCTTTGAAGG+TGG 0.567308 8_2:-7706510 None:intergenic
GGGCTAAGTCAATTAGTCCA+AGG 0.570684 8_2:+7706884 Msa1231520:CDS
ATTAGTCCAAGGGACAAGAA+AGG 0.576487 8_2:+7706895 Msa1231520:CDS
ACGAACACGATCTATGTACT+CGG 0.578833 8_2:-7706647 None:intergenic
CGTGTTCGTAACAAGTTCGA+AGG 0.581435 8_2:+7706661 Msa1231520:CDS
ACAAGAAAGGAGGAGGAGGA+GGG 0.591395 8_2:+7706908 Msa1231520:CDS
GGCTAAGTCAATTAGTCCAA+GGG 0.598516 8_2:+7706885 Msa1231520:CDS
TGTGTGCGGTTTATGTTCGG+AGG 0.599984 8_2:+7706690 Msa1231520:CDS
TTCCGACCACCTTCAAAGAA+CGG 0.607623 8_2:+7706504 Msa1231520:CDS
CATCAACTCGAAGGAAATGT+CGG 0.632792 8_2:-7706530 None:intergenic
TCTTCAACTTCGGATATCGA+TGG 0.633325 8_2:-7706583 None:intergenic
GTGTTCGTAACAAGTTCGAA+GGG 0.639090 8_2:+7706662 Msa1231520:CDS
TTCGAAGGGAAATTTGTGTG+CGG 0.644656 8_2:+7706676 Msa1231520:CDS
CGAACACGATCTATGTACTC+GGG 0.649900 8_2:-7706646 None:intergenic
GTGCGGTTTATGTTCGGAGG+CGG 0.662587 8_2:+7706693 Msa1231520:CDS
GATGCAAAGTGTGAGTGTTG+TGG 0.665594 8_2:+7706604 Msa1231520:CDS
AGTCCAAGGGACAAGAAAGG+AGG 0.666513 8_2:+7706898 Msa1231520:CDS
GACAACAAACATTCTCCATG+AGG 0.716500 8_2:-7706424 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTGTTAAGTTTAACAAATA+TGG + chr8_2:7706784-7706803 Msa1231520:CDS 20.0%
!! TTAAGTTTAACAAATATGGT+AGG + chr8_2:7706788-7706807 Msa1231520:CDS 20.0%
!! TAAGTTTAACAAATATGGTA+GGG + chr8_2:7706789-7706808 Msa1231520:CDS 20.0%
! AATGTTGAAAAAGAGTAACA+TGG + chr8_2:7706849-7706868 Msa1231520:CDS 25.0%
AAAGAAGAGTTGGAGAAAAA+TGG + chr8_2:7706718-7706737 Msa1231520:CDS 30.0%
TTGAAAAAGAGTAACATGGA+TGG + chr8_2:7706853-7706872 Msa1231520:CDS 30.0%
TGAAAAAGAGTAACATGGAT+GGG + chr8_2:7706854-7706873 Msa1231520:CDS 30.0%
TAACATGGATGGGAAAATTA+GGG + chr8_2:7706864-7706883 Msa1231520:CDS 30.0%
TGTTGTCAAGTTCATTCTCA+AGG + chr8_2:7706440-7706459 Msa1231520:CDS 35.0%
!! GAAAGTTTCGTTGGTTTGTT+TGG - chr8_2:7706481-7706500 None:intergenic 35.0%
ACACTTTGCATCTTCAACTT+CGG - chr8_2:7706596-7706615 None:intergenic 35.0%
ATTTGTGTGCGGTTTATGTT+CGG + chr8_2:7706687-7706706 Msa1231520:CDS 35.0%
AAGAGTTGGAGAAAAATGGT+GGG + chr8_2:7706722-7706741 Msa1231520:CDS 35.0%
GTAACATGGATGGGAAAATT+AGG + chr8_2:7706863-7706882 Msa1231520:CDS 35.0%
GACAACAAACATTCTCCATG+AGG - chr8_2:7706427-7706446 None:intergenic 40.0%
TCGGAAGTTGAAAGTTTCGT+TGG - chr8_2:7706490-7706509 None:intergenic 40.0%
CATCAACTCGAAGGAAATGT+CGG - chr8_2:7706533-7706552 None:intergenic 40.0%
TCTTCAACTTCGGATATCGA+TGG - chr8_2:7706586-7706605 None:intergenic 40.0%
ACGAACACGATCTATGTACT+CGG - chr8_2:7706650-7706669 None:intergenic 40.0%
GTGTTCGTAACAAGTTCGAA+GGG + chr8_2:7706662-7706681 Msa1231520:CDS 40.0%
TTCGAAGGGAAATTTGTGTG+CGG + chr8_2:7706676-7706695 Msa1231520:CDS 40.0%
GAAGAGTTGGAGAAAAATGG+TGG + chr8_2:7706721-7706740 Msa1231520:CDS 40.0%
GCTTGTGCTTGAAACAAAAC+TGG - chr8_2:7706820-7706839 None:intergenic 40.0%
GGCTAAGTCAATTAGTCCAA+GGG + chr8_2:7706885-7706904 Msa1231520:CDS 40.0%
ATTAGTCCAAGGGACAAGAA+AGG + chr8_2:7706895-7706914 Msa1231520:CDS 40.0%
TTGATCTCTCTTGTAAGTGC+TGG - chr8_2:7706958-7706977 None:intergenic 40.0%
TTCCGACCACCTTCAAAGAA+CGG + chr8_2:7706504-7706523 Msa1231520:CDS 45.0%
!! CGACATTTCCTTCGAGTTGA+TGG + chr8_2:7706531-7706550 Msa1231520:CDS 45.0%
TTCTTTCGCCATCAACTCGA+AGG - chr8_2:7706542-7706561 None:intergenic 45.0%
! GATGCAAAGTGTGAGTGTTG+TGG + chr8_2:7706604-7706623 Msa1231520:CDS 45.0%
CGAACACGATCTATGTACTC+GGG - chr8_2:7706649-7706668 None:intergenic 45.0%
CGTGTTCGTAACAAGTTCGA+AGG + chr8_2:7706661-7706680 Msa1231520:CDS 45.0%
GGGCTAAGTCAATTAGTCCA+AGG + chr8_2:7706884-7706903 Msa1231520:CDS 45.0%
! GACCGTTCTTTGAAGGTGGT+CGG - chr8_2:7706509-7706528 None:intergenic 50.0%
TGTCGGAGACCGTTCTTTGA+AGG - chr8_2:7706516-7706535 None:intergenic 50.0%
TGTGTGCGGTTTATGTTCGG+AGG + chr8_2:7706690-7706709 Msa1231520:CDS 50.0%
AGTCCAAGGGACAAGAAAGG+AGG + chr8_2:7706898-7706917 Msa1231520:CDS 50.0%
ACAAGAAAGGAGGAGGAGGA+GGG + chr8_2:7706908-7706927 Msa1231520:CDS 50.0%
! CGGAGACCGTTCTTTGAAGG+TGG - chr8_2:7706513-7706532 None:intergenic 55.0%
GTGCGGTTTATGTTCGGAGG+CGG + chr8_2:7706693-7706712 Msa1231520:CDS 55.0%
GGAGGCGGTGAAAGAAGAGT+TGG + chr8_2:7706708-7706727 Msa1231520:CDS 55.0%
CCTCCTCCTTTCTTGTCCCT+TGG - chr8_2:7706904-7706923 None:intergenic 55.0%
CCAAGGGACAAGAAAGGAGG+AGG + chr8_2:7706901-7706920 Msa1231520:CDS 55.0%
AGGGACAAGAAAGGAGGAGG+AGG + chr8_2:7706904-7706923 Msa1231520:CDS 55.0%
GACAAGAAAGGAGGAGGAGG+AGG + chr8_2:7706907-7706926 Msa1231520:CDS 55.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 7706418 7706999 7706418 ID=Msa1231520;Name=Msa1231520
chr8_2 mRNA 7706418 7706999 7706418 ID=Msa1231520-mRNA-1;Parent=Msa1231520;Name=Msa1231520-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|193
chr8_2 exon 7706418 7706999 7706418 ID=Msa1231520-mRNA-1:exon:2874;Parent=Msa1231520-mRNA-1
chr8_2 CDS 7706418 7706999 7706418 ID=Msa1231520-mRNA-1:cds;Parent=Msa1231520-mRNA-1
Gene Sequence

>Msa1231520

ATGGCACCTCATGGAGAATGTTTGTTGTCAAGTTCATTCTCAAGGAACAACAACAACACACCAAACAAACCAACGAAACTTTCAACTTCCGACCACCTTCAAAGAACGGTCTCCGACATTTCCTTCGAGTTGATGGCGAAAGAAGCAATCGATAATTTAAAACTACCATCGATATCCGAAGTTGAAGATGCAAAGTGTGAGTGTTGTGGCATGTCTGAAGAGTGCACACCCGAGTACATAGATCGTGTTCGTAACAAGTTCGAAGGGAAATTTGTGTGCGGTTTATGTTCGGAGGCGGTGAAAGAAGAGTTGGAGAAAAATGGTGGGAAAAAATTAGAAGAAGCTTTAAACACACATATGAATGCATGTGTTAAGTTTAACAAATATGGTAGGGCTTTTCCAGTTTTGTTTCAAGCACAAGCTATGAAAGAAATGTTGAAAAAGAGTAACATGGATGGGAAAATTAGGGCTAAGTCAATTAGTCCAAGGGACAAGAAAGGAGGAGGAGGAGGGCTTGCTCGTAGTACAAGTTGTATTCCAGCACTTACAAGAGAGATCAACAATATCAAAATAGCCAATTAA

Protein sequence

>Msa1231520

MAPHGECLLSSSFSRNNNNTPNKPTKLSTSDHLQRTVSDISFELMAKEAIDNLKLPSISEVEDAKCECCGMSEECTPEYIDRVRNKFEGKFVCGLCSEAVKEELEKNGGKKLEEALNTHMNACVKFNKYGRAFPVLFQAQAMKEMLKKSNMDGKIRAKSISPRDKKGGGGGLARSTSCIPALTREINNIKIAN*