AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1310490

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1310490 MtrunA17_Chr8g0337781 98.630 73 1 0 1 73 1 73 1.16e-46 142
Msa1310490 MtrunA17_Chr8g0337711 65.753 73 25 0 1 73 1 73 4.95e-30 100
Msa1310490 MtrunA17_Chr6g0458744 62.162 74 26 2 1 73 37 109 1.80e-22 82.8
Msa1310490 MtrunA17_Chr6g0458644 62.162 74 26 2 1 73 37 109 1.80e-22 82.8
Msa1310490 MtrunA17_Chr8g0337731 56.757 74 31 1 1 73 1 74 2.80e-22 81.3
Msa1310490 MtrunA17_Chr6g0458787 60.811 74 27 2 1 73 1 73 4.18e-22 80.9
Msa1310490 MtrunA17_Chr6g0458701 60.811 74 27 2 1 73 37 109 6.75e-22 81.3
Msa1310490 MtrunA17_Chr8g0337741 57.353 68 29 0 6 73 5 72 5.06e-21 78.2
Msa1310490 MtrunA17_Chr6g0458807 59.459 74 28 2 1 73 1 73 5.93e-21 77.8
Msa1310490 MtrunA17_Chr8g0337061 49.315 73 36 1 1 72 9 81 1.43e-20 77.4
Msa1310490 MtrunA17_Chr8g0337721 55.405 74 32 1 1 73 1 74 2.47e-20 76.3
Msa1310490 MtrunA17_Chr8g0337771 50.000 72 35 1 1 71 1 72 3.61e-20 75.9
Msa1310490 MtrunA17_Chr8g0337761 56.250 48 21 0 1 48 1 48 1.19e-12 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 36 sgRNAs with CRISPR-Local

Find 107 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTTCTGGGATTCTATAAAT+TGG 0.245975 8_4:-7104127 Msa1310490:five_prime_UTR
GTTAAGAACAAAGACATAAA+TGG 0.311592 8_4:-7103030 Msa1310490:three_prime_UTR
AACAATGTGGTTATCTTTGC+AGG 0.321948 8_4:-7103384 Msa1310490:CDS
CGGATAACAATTTAAATTGA+TGG 0.333391 8_4:-7104166 Msa1310490:five_prime_UTR
TCATAGCTAGATTATGTTCA+TGG 0.337702 8_4:-7103238 Msa1310490:three_prime_UTR
ATTAATTCTCTTCTCACTAA+AGG 0.348898 8_4:+7103190 None:intergenic
GCTAGCATGTGCTTCTTTGT+GGG 0.371494 8_4:-7104222 Msa1310490:five_prime_UTR
TGCTAGCATGTGCTTCTTTG+TGG 0.371716 8_4:-7104223 Msa1310490:five_prime_UTR
TTCTTCAGTGGTGCATGTAT+TGG 0.373930 8_4:-7103421 Msa1310490:CDS
TGGTCTTATCACTTTGACTA+AGG 0.375528 8_4:-7104276 Msa1310490:five_prime_UTR
TTAATTCTCTTCTCACTAAA+GGG 0.376554 8_4:+7103191 None:intergenic
TGCAAAGATAACCACATTGT+TGG 0.420533 8_4:+7103386 None:intergenic
GTCTTCTAAAATAATGTAAG+TGG 0.421980 8_4:+7104071 None:intergenic
GAAGAGAATTAATTAATATA+TGG 0.423090 8_4:-7103180 Msa1310490:three_prime_UTR
ATTTATAGAATCCCAGAACT+TGG 0.433246 8_4:+7104130 None:intergenic
AACTCTTACATAAAATTATG+TGG 0.457975 8_4:-7102954 Msa1310490:three_prime_UTR
GGTGCATGTATTGGTTCATC+TGG 0.472404 8_4:-7103412 Msa1310490:CDS
TGACTAAGGAGTAACATTCA+TGG 0.478114 8_4:-7104262 Msa1310490:five_prime_UTR
GCACCACTGAAGAATTTACT+TGG 0.486888 8_4:+7103430 None:intergenic
CAACAGTTAGTGACGTAGTT+CGG 0.487161 8_4:-7104186 Msa1310490:five_prime_UTR
TTCTCTTCTCACTAAAGGGA+AGG 0.492137 8_4:+7103195 None:intergenic
TCATAGTGGAGATGTTCAAC+AGG 0.492350 8_4:+7103309 None:intergenic
CTAGCATGTGCTTCTTTGTG+GGG 0.519231 8_4:-7104221 Msa1310490:five_prime_UTR
GAACAATGAGAAAGAAGCAC+AGG 0.523721 8_4:+7104015 None:intergenic
TATCTTTGCAGGAGAGGAGA+AGG 0.525618 8_4:-7103373 Msa1310490:CDS
TAACAATTTAAATTGATGGT+GGG 0.536329 8_4:-7104162 Msa1310490:five_prime_UTR
TTATTTCTGATACACTATGT+TGG 0.537604 8_4:+7103055 None:intergenic
AGAAGCAGTGGTGCAAATTG+AGG 0.543400 8_4:-7103464 Msa1310490:CDS
TCTCTTCTCACTAAAGGGAA+GGG 0.551142 8_4:+7103196 None:intergenic
ATAACAATTTAAATTGATGG+TGG 0.572344 8_4:-7104163 Msa1310490:five_prime_UTR
GAAAATTGCAGAAGAAGCAG+TGG 0.595907 8_4:-7103476 Msa1310490:intron
TGTGGTTATCTTTGCAGGAG+AGG 0.610983 8_4:-7103379 Msa1310490:CDS
AAACCAAGTAAATTCTTCAG+TGG 0.617297 8_4:-7103433 Msa1310490:CDS
AAATACATCTCATCTCATAG+TGG 0.618646 8_4:+7103295 None:intergenic
AGAGGAGAAGGCTTACTCAG+TGG 0.689859 8_4:-7103361 Msa1310490:CDS
TCATCTGGCAACCAACAATG+TGG 0.701842 8_4:-7103397 Msa1310490:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTTATATTAAAGTAATTT+TGG - chr8_4:7103272-7103291 Msa1310490:three_prime_UTR 10.0%
!!! GTTTATATTAAAGTAATTTT+GGG - chr8_4:7103273-7103292 Msa1310490:three_prime_UTR 10.0%
!!! TTTTATTTTGTCATAAAAAA+TGG + chr8_4:7103341-7103360 None:intergenic 10.0%
!!! ATTTAAGATATATGTTTTTT+AGG + chr8_4:7103566-7103585 None:intergenic 10.0%
!!! AGTTTATATTAAAGTAATTT+TGG - chr8_4:7103272-7103291 Msa1310490:three_prime_UTR 10.0%
!!! GTTTATATTAAAGTAATTTT+GGG - chr8_4:7103273-7103292 Msa1310490:three_prime_UTR 10.0%
!!! TTTTATTTTGTCATAAAAAA+TGG + chr8_4:7103341-7103360 None:intergenic 10.0%
!!! ATTTAAGATATATGTTTTTT+AGG + chr8_4:7103566-7103585 None:intergenic 10.0%
!!! GATTTTTAAAGAATTTTTTC+AGG - chr8_4:7103407-7103426 Msa1310490:CDS 15.0%
!! ATTCCTTAAGAAAAATAATA+TGG - chr8_4:7103743-7103762 Msa1310490:intron 15.0%
!! GAAGAGAATTAATTAATATA+TGG - chr8_4:7104069-7104088 Msa1310490:five_prime_UTR 15.0%
!!! GATTTTTAAAGAATTTTTTC+AGG - chr8_4:7103407-7103426 Msa1310490:CDS 15.0%
!! ATTCCTTAAGAAAAATAATA+TGG - chr8_4:7103743-7103762 Msa1310490:intron 15.0%
!! GAAGAGAATTAATTAATATA+TGG - chr8_4:7104069-7104088 Msa1310490:five_prime_UTR 15.0%
!! ATAACAATTTAAATTGATGG+TGG - chr8_4:7103086-7103105 Msa1310490:three_prime_UTR 20.0%
!!! TAACAATTTAAATTGATGGT+GGG - chr8_4:7103087-7103106 Msa1310490:three_prime_UTR 20.0%
!! TAAGATTATTCATGATTGAT+TGG - chr8_4:7103457-7103476 Msa1310490:CDS 20.0%
!! ATATTTGTATCAAAATCAAG+TGG - chr8_4:7103503-7103522 Msa1310490:intron 20.0%
!!! GAACCATATTATTTTTCTTA+AGG + chr8_4:7103749-7103768 None:intergenic 20.0%
!!! AGTCATATTTTTGTTGTATT+TGG + chr8_4:7104257-7104276 None:intergenic 20.0%
!! AACTCTTACATAAAATTATG+TGG - chr8_4:7104295-7104314 Msa1310490:five_prime_UTR 20.0%
!! ATAACAATTTAAATTGATGG+TGG - chr8_4:7103086-7103105 Msa1310490:three_prime_UTR 20.0%
!!! TAACAATTTAAATTGATGGT+GGG - chr8_4:7103087-7103106 Msa1310490:three_prime_UTR 20.0%
!! TAAGATTATTCATGATTGAT+TGG - chr8_4:7103457-7103476 Msa1310490:CDS 20.0%
!! ATATTTGTATCAAAATCAAG+TGG - chr8_4:7103503-7103522 Msa1310490:intron 20.0%
!!! GAACCATATTATTTTTCTTA+AGG + chr8_4:7103749-7103768 None:intergenic 20.0%
!!! AGTCATATTTTTGTTGTATT+TGG + chr8_4:7104257-7104276 None:intergenic 20.0%
! CGGATAACAATTTAAATTGA+TGG - chr8_4:7103083-7103102 Msa1310490:three_prime_UTR 25.0%
!!! GTCTTCTAAAATAATGTAAG+TGG + chr8_4:7103181-7103200 None:intergenic 25.0%
! TTAGAAGACAAAAAAAGTGA+TGG - chr8_4:7103192-7103211 Msa1310490:three_prime_UTR 25.0%
! GATTGTGGTATTAAATTTGT+TGG - chr8_4:7103608-7103627 Msa1310490:intron 25.0%
! TTAATTCTCTTCTCACTAAA+GGG + chr8_4:7104061-7104080 None:intergenic 25.0%
! ATTAATTCTCTTCTCACTAA+AGG + chr8_4:7104062-7104081 None:intergenic 25.0%
!!! TTATTTCTGATACACTATGT+TGG + chr8_4:7104197-7104216 None:intergenic 25.0%
! GTTAAGAACAAAGACATAAA+TGG - chr8_4:7104219-7104238 Msa1310490:five_prime_UTR 25.0%
! CGGATAACAATTTAAATTGA+TGG - chr8_4:7103083-7103102 Msa1310490:three_prime_UTR 25.0%
!!! GTCTTCTAAAATAATGTAAG+TGG + chr8_4:7103181-7103200 None:intergenic 25.0%
! TTAGAAGACAAAAAAAGTGA+TGG - chr8_4:7103192-7103211 Msa1310490:three_prime_UTR 25.0%
! GATTGTGGTATTAAATTTGT+TGG - chr8_4:7103608-7103627 Msa1310490:intron 25.0%
! TTAATTCTCTTCTCACTAAA+GGG + chr8_4:7104061-7104080 None:intergenic 25.0%
! ATTAATTCTCTTCTCACTAA+AGG + chr8_4:7104062-7104081 None:intergenic 25.0%
!!! TTATTTCTGATACACTATGT+TGG + chr8_4:7104197-7104216 None:intergenic 25.0%
! GTTAAGAACAAAGACATAAA+TGG - chr8_4:7104219-7104238 Msa1310490:five_prime_UTR 25.0%
ATTTATAGAATCCCAGAACT+TGG + chr8_4:7103122-7103141 None:intergenic 30.0%
!! AGTTCTGGGATTCTATAAAT+TGG - chr8_4:7103122-7103141 Msa1310490:three_prime_UTR 30.0%
AATCAATCACGAGAATGAAA+AGG - chr8_4:7103583-7103602 Msa1310490:intron 30.0%
AAACCAAGTAAATTCTTCAG+TGG - chr8_4:7103816-7103835 Msa1310490:intron 30.0%
AAATACATCTCATCTCATAG+TGG + chr8_4:7103957-7103976 None:intergenic 30.0%
TCATAGCTAGATTATGTTCA+TGG - chr8_4:7104011-7104030 Msa1310490:CDS 30.0%
ATTTATAGAATCCCAGAACT+TGG + chr8_4:7103122-7103141 None:intergenic 30.0%
!! AGTTCTGGGATTCTATAAAT+TGG - chr8_4:7103122-7103141 Msa1310490:three_prime_UTR 30.0%
AATCAATCACGAGAATGAAA+AGG - chr8_4:7103583-7103602 Msa1310490:intron 30.0%
AAACCAAGTAAATTCTTCAG+TGG - chr8_4:7103816-7103835 Msa1310490:intron 30.0%
AAATACATCTCATCTCATAG+TGG + chr8_4:7103957-7103976 None:intergenic 30.0%
TCATAGCTAGATTATGTTCA+TGG - chr8_4:7104011-7104030 Msa1310490:CDS 30.0%
!!! ACCACAATCGTTGTCTTTTT+TGG + chr8_4:7102957-7102976 None:intergenic 35.0%
!! TGGTCTTATCACTTTGACTA+AGG - chr8_4:7102973-7102992 Msa1310490:three_prime_UTR 35.0%
TGACTAAGGAGTAACATTCA+TGG - chr8_4:7102987-7103006 Msa1310490:three_prime_UTR 35.0%
! GGAATACTTTTCCAAGTTCT+GGG - chr8_4:7103108-7103127 Msa1310490:three_prime_UTR 35.0%
! AGACAAAAAAAGTGATGGAG+AGG - chr8_4:7103197-7103216 Msa1310490:three_prime_UTR 35.0%
! GAGAATGAAAAGGTTGATTG+TGG - chr8_4:7103593-7103612 Msa1310490:intron 35.0%
TGCAAAGATAACCACATTGT+TGG + chr8_4:7103866-7103885 None:intergenic 35.0%
AACAATGTGGTTATCTTTGC+AGG - chr8_4:7103865-7103884 Msa1310490:intron 35.0%
!!! ACCACAATCGTTGTCTTTTT+TGG + chr8_4:7102957-7102976 None:intergenic 35.0%
!! TGGTCTTATCACTTTGACTA+AGG - chr8_4:7102973-7102992 Msa1310490:three_prime_UTR 35.0%
TGACTAAGGAGTAACATTCA+TGG - chr8_4:7102987-7103006 Msa1310490:three_prime_UTR 35.0%
! GGAATACTTTTCCAAGTTCT+GGG - chr8_4:7103108-7103127 Msa1310490:three_prime_UTR 35.0%
! AGACAAAAAAAGTGATGGAG+AGG - chr8_4:7103197-7103216 Msa1310490:three_prime_UTR 35.0%
! GAGAATGAAAAGGTTGATTG+TGG - chr8_4:7103593-7103612 Msa1310490:intron 35.0%
TGCAAAGATAACCACATTGT+TGG + chr8_4:7103866-7103885 None:intergenic 35.0%
AACAATGTGGTTATCTTTGC+AGG - chr8_4:7103865-7103884 Msa1310490:intron 35.0%
CAACAGTTAGTGACGTAGTT+CGG - chr8_4:7103063-7103082 Msa1310490:three_prime_UTR 40.0%
! GGGAATACTTTTCCAAGTTC+TGG - chr8_4:7103107-7103126 Msa1310490:three_prime_UTR 40.0%
! GAACAATGAGAAAGAAGCAC+AGG + chr8_4:7103237-7103256 None:intergenic 40.0%
GAAAATTGCAGAAGAAGCAG+TGG - chr8_4:7103773-7103792 Msa1310490:intron 40.0%
GCACCACTGAAGAATTTACT+TGG + chr8_4:7103822-7103841 None:intergenic 40.0%
TTCTTCAGTGGTGCATGTAT+TGG - chr8_4:7103828-7103847 Msa1310490:intron 40.0%
! TCATAGTGGAGATGTTCAAC+AGG + chr8_4:7103943-7103962 None:intergenic 40.0%
TCTCTTCTCACTAAAGGGAA+GGG + chr8_4:7104056-7104075 None:intergenic 40.0%
TTCTCTTCTCACTAAAGGGA+AGG + chr8_4:7104057-7104076 None:intergenic 40.0%
CAACAGTTAGTGACGTAGTT+CGG - chr8_4:7103063-7103082 Msa1310490:three_prime_UTR 40.0%
! GGGAATACTTTTCCAAGTTC+TGG - chr8_4:7103107-7103126 Msa1310490:three_prime_UTR 40.0%
! GAACAATGAGAAAGAAGCAC+AGG + chr8_4:7103237-7103256 None:intergenic 40.0%
GAAAATTGCAGAAGAAGCAG+TGG - chr8_4:7103773-7103792 Msa1310490:intron 40.0%
GCACCACTGAAGAATTTACT+TGG + chr8_4:7103822-7103841 None:intergenic 40.0%
TTCTTCAGTGGTGCATGTAT+TGG - chr8_4:7103828-7103847 Msa1310490:intron 40.0%
! TCATAGTGGAGATGTTCAAC+AGG + chr8_4:7103943-7103962 None:intergenic 40.0%
TCTCTTCTCACTAAAGGGAA+GGG + chr8_4:7104056-7104075 None:intergenic 40.0%
TTCTCTTCTCACTAAAGGGA+AGG + chr8_4:7104057-7104076 None:intergenic 40.0%
TGCTAGCATGTGCTTCTTTG+TGG - chr8_4:7103026-7103045 Msa1310490:three_prime_UTR 45.0%
GCTAGCATGTGCTTCTTTGT+GGG - chr8_4:7103027-7103046 Msa1310490:three_prime_UTR 45.0%
CTAGCATGTGCTTCTTTGTG+GGG - chr8_4:7103028-7103047 Msa1310490:three_prime_UTR 45.0%
AGAAGCAGTGGTGCAAATTG+AGG - chr8_4:7103785-7103804 Msa1310490:intron 45.0%
!! GGTGCATGTATTGGTTCATC+TGG - chr8_4:7103837-7103856 Msa1310490:intron 45.0%
TCATCTGGCAACCAACAATG+TGG - chr8_4:7103852-7103871 Msa1310490:intron 45.0%
TGTGGTTATCTTTGCAGGAG+AGG - chr8_4:7103870-7103889 Msa1310490:intron 45.0%
TATCTTTGCAGGAGAGGAGA+AGG - chr8_4:7103876-7103895 Msa1310490:intron 45.0%
TGCTAGCATGTGCTTCTTTG+TGG - chr8_4:7103026-7103045 Msa1310490:three_prime_UTR 45.0%
GCTAGCATGTGCTTCTTTGT+GGG - chr8_4:7103027-7103046 Msa1310490:three_prime_UTR 45.0%
CTAGCATGTGCTTCTTTGTG+GGG - chr8_4:7103028-7103047 Msa1310490:three_prime_UTR 45.0%
AGAAGCAGTGGTGCAAATTG+AGG - chr8_4:7103785-7103804 Msa1310490:intron 45.0%
!! GGTGCATGTATTGGTTCATC+TGG - chr8_4:7103837-7103856 Msa1310490:intron 45.0%
TCATCTGGCAACCAACAATG+TGG - chr8_4:7103852-7103871 Msa1310490:intron 45.0%
TGTGGTTATCTTTGCAGGAG+AGG - chr8_4:7103870-7103889 Msa1310490:intron 45.0%
TATCTTTGCAGGAGAGGAGA+AGG - chr8_4:7103876-7103895 Msa1310490:intron 45.0%
AGAGGAGAAGGCTTACTCAG+TGG - chr8_4:7103888-7103907 Msa1310490:intron 50.0%
AGAGGAGAAGGCTTACTCAG+TGG - chr8_4:7103888-7103907 Msa1310490:intron 50.0%
Chromosome Type Strat End Strand Name
chr8_4 gene 7102954 7104317 7102954 ID=Msa1310490;Name=Msa1310490
chr8_4 mRNA 7102954 7104317 7102954 ID=Msa1310490-mRNA-1;Parent=Msa1310490;Name=Msa1310490-mRNA-1;_AED=0.31;_eAED=0.31;_QI=257|1|1|1|1|1|2|370|73
chr8_4 exon 7102954 7103487 7102954 ID=Msa1310490-mRNA-1:exon:2510;Parent=Msa1310490-mRNA-1
chr8_4 exon 7104003 7104317 7104003 ID=Msa1310490-mRNA-1:exon:2509;Parent=Msa1310490-mRNA-1
chr8_4 five_prime_UTR 7104061 7104317 7104061 ID=Msa1310490-mRNA-1:five_prime_utr;Parent=Msa1310490-mRNA-1
chr8_4 CDS 7104003 7104060 7104003 ID=Msa1310490-mRNA-1:cds;Parent=Msa1310490-mRNA-1
chr8_4 CDS 7103324 7103487 7103324 ID=Msa1310490-mRNA-1:cds;Parent=Msa1310490-mRNA-1
chr8_4 three_prime_UTR 7102954 7103323 7102954 ID=Msa1310490-mRNA-1:three_prime_utr;Parent=Msa1310490-mRNA-1
Gene Sequence

>Msa1310490

ATGGAGAGGAAAACACTTGCTAGCCTGTGCTTCTTTCTCATTGTTCTCTTAGCTGCTCAAGAAGCAGTGGTGCAAATTGAGGCTTGTGAGAAACCAAGTAAATTCTTCAGTGGTGCATGTATTGGTTCATCTGGCAACCAACAATGTGGTTATCTTTGCAGGAGAGGAGAAGGCTTACTCAGTGGTTCTTGCAAAAATCTGAAATGTGTTTGTGCCTGTTGA
Protein sequence

>Msa1310490

MERKTLASLCFFLIVLLAAQEAVVQIEACEKPSKFFSGACIGSSGNQQCGYLCRRGEGLLSGSCKNLKCVCAC*