AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1220850


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1220850 MtrunA17_Chr4g0063501 97.059 170 2 3 1 169 1 168 3.73e-117 328
Msa1220850 MtrunA17_Chr4g0003581 66.026 156 51 2 1 156 5 158 1.83e-76 226
Msa1220850 MtrunA17_Chr2g0332851 60.947 169 61 4 1 168 5 169 2.70e-67 202
Msa1220850 MtrunA17_Chr2g0332841 57.738 168 66 4 1 167 5 168 1.50e-62 190
Msa1220850 MtrunA17_Chr2g0277151 60.432 139 53 1 4 142 2 138 1.92e-57 177
Msa1220850 MtrunA17_Chr5g0405171 57.534 146 60 1 2 145 22 167 9.73e-57 177
Msa1220850 MtrunA17_Chr8g0372141 55.556 144 62 1 4 145 12 155 6.66e-55 171
Msa1220850 MtrunA17_Chr4g0020201 52.143 140 65 2 3 140 32 171 2.58e-50 160
Msa1220850 MtrunA17_Chr1g0212241 54.730 148 62 4 20 166 1 144 1.60e-49 156
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1220850 AT1G80160.1 63.804 163 57 2 2 164 6 166 2.44e-73 218
Msa1220850 AT1G80160.3 63.804 163 57 2 2 164 47 207 9.14e-73 218
Msa1220850 AT1G15380.2 62.130 169 59 4 2 167 6 172 6.14e-71 212
Msa1220850 AT1G15380.1 62.130 169 59 4 2 167 6 172 6.14e-71 212
Msa1220850 AT2G28420.1 51.852 135 63 2 7 140 18 151 2.83e-51 162
Msa1220850 AT1G80160.2 62.069 116 42 2 49 164 27 140 4.65e-45 145

Find 29 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTATTCTTGGTCATACTTTC+TGG 0.158615 8_1:+84227600 None:intergenic
TTGATTAGGTTGTTTAATTA+TGG 0.210559 8_1:-84227657 Msa1220850:intron
AAGAACAGAGTAGAGGAAAA+TGG 0.294782 8_1:-84227388 Msa1220850:CDS
ATTAATGTGCACATTATTCT+TGG 0.304684 8_1:+84227587 None:intergenic
CAAATTGTGTTCTCTGATAA+AGG 0.332337 8_1:+84227283 None:intergenic
GATATACTTGGAAAGAAATA+TGG 0.341030 8_1:+84227553 None:intergenic
TTCTCTGATAAAGGTACAAT+TGG 0.358152 8_1:+84227292 None:intergenic
AAAGAAATATGGTTGTCCTT+TGG 0.368432 8_1:+84227564 None:intergenic
AAGGAGGTAGGTCTCTTAAT+AGG 0.373287 8_1:+84227802 None:intergenic
CTTTATCAGAGAACACAATT+TGG 0.412500 8_1:-84227282 Msa1220850:CDS
TTTCTGGATCATCATCTGAT+TGG 0.413129 8_1:+84227616 None:intergenic
TCGTTGCTAGTGTGAAAGTA+TGG 0.421471 8_1:-84227455 Msa1220850:intron
TACGTACCATGCACCATTGA+AGG 0.464268 8_1:+84227777 None:intergenic
ATCATTGAATCACATCTCAT+TGG 0.477448 8_1:-84227881 Msa1220850:CDS
ATTCAATGATTTGAGTTGTA+GGG 0.480431 8_1:+84227894 None:intergenic
ATTTCAATCATAGTGCCATC+TGG 0.481430 8_1:+84227334 None:intergenic
TCATAGTGCCATCTGGATCA+TGG 0.483510 8_1:+84227341 None:intergenic
AGGTTGTTTAATTATGGCAT+TGG 0.497038 8_1:-84227651 Msa1220850:CDS
CCTACCTCCTTAGCCTTCAA+TGG 0.497853 8_1:-84227790 Msa1220850:CDS
GATTCAATGATTTGAGTTGT+AGG 0.509824 8_1:+84227893 None:intergenic
GTGTGAAAGTATGGCAGTAG+TGG 0.540760 8_1:-84227446 Msa1220850:CDS
TTCAATGATTTGAGTTGTAG+GGG 0.553026 8_1:+84227895 None:intergenic
CCATGCACCATTGAAGGCTA+AGG 0.575830 8_1:+84227783 None:intergenic
GTATGTGAAGAACAGAGTAG+AGG 0.586484 8_1:-84227395 Msa1220850:CDS
CCATTGAAGGCTAAGGAGGT+AGG 0.593613 8_1:+84227790 None:intergenic
TTGTTCTTCCATGATCCAGA+TGG 0.596741 8_1:-84227349 Msa1220850:CDS
CCTTAGCCTTCAATGGTGCA+TGG 0.610902 8_1:-84227783 Msa1220850:intron
TAATGTGCACATTAATCCAA+AGG 0.618094 8_1:-84227580 Msa1220850:CDS
TGCACCATTGAAGGCTAAGG+AGG 0.624890 8_1:+84227786 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAACTTATGTTTACATTTT+TGG - chr8_1:84227436-84227455 Msa1220850:CDS 15.0%
!! AAATCACATAATAAGTATAT+AGG + chr8_1:84227638-84227657 None:intergenic 15.0%
!! AACATAAGTTATTCTAACAA+TGG + chr8_1:84227428-84227447 None:intergenic 20.0%
!!! TTTACATTTTTGGTTTGATT+AGG - chr8_1:84227446-84227465 Msa1220850:CDS 20.0%
!!! TTGATTAGGTTGTTTAATTA+TGG - chr8_1:84227460-84227479 Msa1220850:intron 20.0%
!! AAATAATCTACACAAATAGA+GGG + chr8_1:84227595-84227614 None:intergenic 20.0%
!!! ATTCAATGATTTGAGTTGTA+GGG + chr8_1:84227226-84227245 None:intergenic 25.0%
! ATTAATGTGCACATTATTCT+TGG + chr8_1:84227533-84227552 None:intergenic 25.0%
! GATATACTTGGAAAGAAATA+TGG + chr8_1:84227567-84227586 None:intergenic 25.0%
! GAAATAATCTACACAAATAG+AGG + chr8_1:84227596-84227615 None:intergenic 25.0%
!! TTCAATGATTTGAGTTGTAG+GGG + chr8_1:84227225-84227244 None:intergenic 30.0%
!! GATTCAATGATTTGAGTTGT+AGG + chr8_1:84227227-84227246 None:intergenic 30.0%
ATCATTGAATCACATCTCAT+TGG - chr8_1:84227236-84227255 Msa1220850:CDS 30.0%
! GATTTTTACGTCAATGTTCT+TGG - chr8_1:84227285-84227304 Msa1220850:CDS 30.0%
AGGTTGTTTAATTATGGCAT+TGG - chr8_1:84227466-84227485 Msa1220850:intron 30.0%
TTATTCTTGGTCATACTTTC+TGG + chr8_1:84227520-84227539 None:intergenic 30.0%
TAATGTGCACATTAATCCAA+AGG - chr8_1:84227537-84227556 Msa1220850:intron 30.0%
AAAGAAATATGGTTGTCCTT+TGG + chr8_1:84227556-84227575 None:intergenic 30.0%
! TTCTCTGATAAAGGTACAAT+TGG + chr8_1:84227828-84227847 None:intergenic 30.0%
CAAATTGTGTTCTCTGATAA+AGG + chr8_1:84227837-84227856 None:intergenic 30.0%
CTTTATCAGAGAACACAATT+TGG - chr8_1:84227835-84227854 Msa1220850:CDS 30.0%
TTTCTGGATCATCATCTGAT+TGG + chr8_1:84227504-84227523 None:intergenic 35.0%
AAGAACAGAGTAGAGGAAAA+TGG - chr8_1:84227729-84227748 Msa1220850:intron 35.0%
ATTTCAATCATAGTGCCATC+TGG + chr8_1:84227786-84227805 None:intergenic 35.0%
AAGGAGGTAGGTCTCTTAAT+AGG + chr8_1:84227318-84227337 None:intergenic 40.0%
TAGAGGGAGAGAGATATACT+TGG + chr8_1:84227579-84227598 None:intergenic 40.0%
TCGTTGCTAGTGTGAAAGTA+TGG - chr8_1:84227662-84227681 Msa1220850:intron 40.0%
GTATGTGAAGAACAGAGTAG+AGG - chr8_1:84227722-84227741 Msa1220850:intron 40.0%
TTGTTCTTCCATGATCCAGA+TGG - chr8_1:84227768-84227787 Msa1220850:intron 40.0%
TACGTACCATGCACCATTGA+AGG + chr8_1:84227343-84227362 None:intergenic 45.0%
! GTGTGAAAGTATGGCAGTAG+TGG - chr8_1:84227671-84227690 Msa1220850:intron 45.0%
TCATAGTGCCATCTGGATCA+TGG + chr8_1:84227779-84227798 None:intergenic 45.0%
CCATTGAAGGCTAAGGAGGT+AGG + chr8_1:84227330-84227349 None:intergenic 50.0%
! CCTACCTCCTTAGCCTTCAA+TGG - chr8_1:84227327-84227346 Msa1220850:CDS 50.0%
TGCACCATTGAAGGCTAAGG+AGG + chr8_1:84227334-84227353 None:intergenic 50.0%
CCATGCACCATTGAAGGCTA+AGG + chr8_1:84227337-84227356 None:intergenic 50.0%
! CCTTAGCCTTCAATGGTGCA+TGG - chr8_1:84227334-84227353 Msa1220850:CDS 50.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 84227213 84227926 84227213 ID=Msa1220850;Name=Msa1220850
chr8_1 mRNA 84227213 84227926 84227213 ID=Msa1220850-mRNA-1;Parent=Msa1220850;Name=Msa1220850-mRNA-1;_AED=0.15;_eAED=0.15;_QI=0|0|0|1|1|1|3|0|169
chr8_1 exon 84227784 84227926 84227784 ID=Msa1220850-mRNA-1:exon:30232;Parent=Msa1220850-mRNA-1
chr8_1 exon 84227560 84227671 84227560 ID=Msa1220850-mRNA-1:exon:30231;Parent=Msa1220850-mRNA-1
chr8_1 exon 84227213 84227467 84227213 ID=Msa1220850-mRNA-1:exon:30230;Parent=Msa1220850-mRNA-1
chr8_1 CDS 84227784 84227926 84227784 ID=Msa1220850-mRNA-1:cds;Parent=Msa1220850-mRNA-1
chr8_1 CDS 84227560 84227671 84227560 ID=Msa1220850-mRNA-1:cds;Parent=Msa1220850-mRNA-1
chr8_1 CDS 84227213 84227467 84227213 ID=Msa1220850-mRNA-1:cds;Parent=Msa1220850-mRNA-1
Gene Sequence

>Msa1220850

ATGGGCAATCCCCTACAACTCAAATCATTGAATCACATCTCATTGGTGTGTAGATCATTAGACAAGTCAGTTGATTTTTACGTCAATGTTCTTGGCTTCTTTCCTATTAAGAGACCTACCTCCTTAGCCTTCAATGGTGCATGGTTGTTTAATTATGGCATTGGCATACATCTTCTCCAATCAGATGATGATCCAGAAAGTATGACCAAGAATAATGTGCACATTAATCCAAAGGACAACCATATTTCTTTCCAATGTGAAAGTATGGCAGTAGTGGAGAATAAACTGCAGCAAATGAAGATAGAGTATGTGAAGAACAGAGTAGAGGAAAATGGAATCTACGTTGATCAGTTGTTCTTCCATGATCCAGATGGCACTATGATTGAAATCTGCAATTGTGACAATATTCCAATTGTACCTTTATCAGAGAACACAATTTGGTCATGCTCGCGCTTCAACTGCAATATTCAAAATCAGCAGCAGCAAATTCAACAAATGATCTCAATGTAG

Protein sequence

>Msa1220850

MGNPLQLKSLNHISLVCRSLDKSVDFYVNVLGFFPIKRPTSLAFNGAWLFNYGIGIHLLQSDDDPESMTKNNVHINPKDNHISFQCESMAVVENKLQQMKIEYVKNRVEENGIYVDQLFFHDPDGTMIEICNCDNIPIVPLSENTIWSCSRFNCNIQNQQQQIQQMISM*