AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene045474

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene045474.t1 MTR_4g080200 62.745 204 68 5 1 201 55 253 6.40e-80 243
MS.gene045474.t1 MTR_1g009110 49.533 214 81 10 1 201 82 281 4.88e-47 159
MS.gene045474.t1 MTR_1g023400 46.729 214 84 11 1 201 63 259 2.12e-42 146
MS.gene045474.t1 MTR_1g022200 44.762 210 96 8 3 202 77 276 1.00e-38 137
MS.gene045474.t1 MTR_1g037540 43.137 204 89 9 13 201 108 299 1.18e-33 124
MS.gene045474.t1 MTR_1g022105 32.057 209 81 9 1 201 88 243 2.46e-18 81.6
MS.gene045474.t1 MTR_8g093280 79.070 43 9 0 2 44 65 107 2.06e-17 75.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 52 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACATTAATAATTCCTTCTA+TGG 0.170109 4.2:+29809428 MS.gene045474:CDS
GGGGTTGCATCACGTAAATT+TGG 0.213603 4.2:-29809740 None:intergenic
ATGACATCATCACGGAAATA+TGG 0.240051 4.2:-29809770 None:intergenic
CTCGATTCTTGCTACGCCTT+TGG 0.250093 4.2:-29809264 None:intergenic
TCGATTCTTGCTACGCCTTT+GGG 0.294864 4.2:-29809263 None:intergenic
GGGTTGCATCACGTAAATTT+GGG 0.309278 4.2:-29809739 None:intergenic
GTTCCATGCAATCAATTGAT+AGG 0.324579 4.2:-29809348 None:intergenic
AATAATTCCTTCTATGGGTT+TGG 0.329443 4.2:+29809434 MS.gene045474:CDS
TGATGATGTCATTGAGATAA+AGG 0.339225 4.2:+29809781 MS.gene045474:CDS
AGGGAGCATGGGGAATAATA+AGG 0.352582 4.2:-29809391 None:intergenic
GGGCTTCAAGTTGCCGAAAC+TGG 0.353162 4.2:-29809718 None:intergenic
CACGGAAATATGGGATAAAC+GGG 0.358789 4.2:-29809760 None:intergenic
ATAATCTAAGCACTAAATCT+TGG 0.371440 4.2:+29809549 MS.gene045474:CDS
TTGGTTATGTTGTGGAATAT+AGG 0.372818 4.2:+29809811 MS.gene045474:CDS
TTGTTAACGGTGTTTATCAT+TGG 0.381352 4.2:+29809642 MS.gene045474:CDS
TATGGGTTTGGTGCTATTAA+CGG 0.396830 4.2:+29809446 MS.gene045474:CDS
AACAAAGATTTGACGAGGAT+TGG 0.404402 4.2:-29809239 None:intergenic
TCACGGAAATATGGGATAAA+CGG 0.406577 4.2:-29809761 None:intergenic
AGATACAACACTCTTGTTAA+CGG 0.411459 4.2:+29809629 MS.gene045474:CDS
ACTTTCACAATAACCAGTTT+CGG 0.425983 4.2:+29809705 MS.gene045474:CDS
GGTGAACCTCATTAGTTGTT+GGG 0.430302 4.2:-29809370 None:intergenic
TTGAGATAAAGGGGCTCTCT+TGG 0.433826 4.2:+29809792 MS.gene045474:CDS
AATAGCACCAAACCCATAGA+AGG 0.434037 4.2:-29809441 None:intergenic
ACAAGAGTGTTGTATCTTGA+AGG 0.436670 4.2:-29809623 None:intergenic
GATGATGTCATTGAGATAAA+GGG 0.447892 4.2:+29809782 MS.gene045474:CDS
TGACATCATCACGGAAATAT+GGG 0.450897 4.2:-29809769 None:intergenic
CGATTAGTGACAACAGTTTG+AGG 0.452474 4.2:-29809596 None:intergenic
ACATTAATAATTCCTTCTAT+GGG 0.491595 4.2:+29809429 MS.gene045474:CDS
AGTTACCGAGTGAGGGAGCA+TGG 0.508885 4.2:-29809403 None:intergenic
GGAGAAGGACTATTGAGGAT+AGG 0.512834 4.2:-29809575 None:intergenic
AGGTGAACCTCATTAGTTGT+TGG 0.516554 4.2:-29809371 None:intergenic
GTGACAACAGTTTGAGGAGA+AGG 0.525103 4.2:-29809590 None:intergenic
GTCCCTATCAATTGATTGCA+TGG 0.535833 4.2:+29809345 MS.gene045474:CDS
GGGCTCTCTTGGTTATGTTG+TGG 0.537926 4.2:+29809803 MS.gene045474:CDS
TTCCATGCAATCAATTGATA+GGG 0.546535 4.2:-29809347 None:intergenic
GTCAAATCTTTGTTTCCCAA+AGG 0.549086 4.2:+29809248 MS.gene045474:CDS
ATTCCCCATGCTCCCTCACT+CGG 0.556846 4.2:+29809398 MS.gene045474:CDS
GTTACCGAGTGAGGGAGCAT+GGG 0.557104 4.2:-29809402 None:intergenic
GTAGCAAGAATCGAGACATA+TGG 0.563186 4.2:+29809272 MS.gene045474:CDS
TTTGAGGAGAAGGACTATTG+AGG 0.563775 4.2:-29809580 None:intergenic
GAGACATATGGTAGTTGCAA+TGG 0.585733 4.2:+29809284 MS.gene045474:CDS
TGTCTCAAAGGTATTTACCC+AGG 0.588520 4.2:+29809314 MS.gene045474:CDS
AATGTAATAGTTACCGAGTG+AGG 0.590634 4.2:-29809411 None:intergenic
ATGTAATAGTTACCGAGTGA+GGG 0.597182 4.2:-29809410 None:intergenic
GGTTGCATCACGTAAATTTG+GGG 0.600619 4.2:-29809738 None:intergenic
ATGAAGCTTCTCTCATGTGA+CGG 0.614422 4.2:+29809203 MS.gene045474:CDS
ATGGAACCCAACAACTAATG+AGG 0.623538 4.2:+29809364 MS.gene045474:CDS
ATGATGTCATTGAGATAAAG+GGG 0.642734 4.2:+29809783 MS.gene045474:CDS
TGGGAAACAAAGATTTGACG+AGG 0.648151 4.2:-29809244 None:intergenic
TTACCGAGTGAGGGAGCATG+GGG 0.648669 4.2:-29809401 None:intergenic
TTATCTCAATGACATCATCA+CGG 0.687959 4.2:-29809778 None:intergenic
ACGGAAATATGGGATAAACG+GGG 0.809322 4.2:-29809759 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAAATGCTTTATCTTTTAT+CGG + chr4.2:29809517-29809536 MS.gene045474:CDS 15.0%
!! ACATTAATAATTCCTTCTAT+GGG + chr4.2:29809429-29809448 MS.gene045474:CDS 20.0%
!! TACATTAATAATTCCTTCTA+TGG + chr4.2:29809428-29809447 MS.gene045474:CDS 20.0%
! ATAATCTAAGCACTAAATCT+TGG + chr4.2:29809549-29809568 MS.gene045474:CDS 25.0%
AATAATTCCTTCTATGGGTT+TGG + chr4.2:29809434-29809453 MS.gene045474:CDS 30.0%
ACTTTCACAATAACCAGTTT+CGG + chr4.2:29809705-29809724 MS.gene045474:CDS 30.0%
AGATACAACACTCTTGTTAA+CGG + chr4.2:29809629-29809648 MS.gene045474:CDS 30.0%
ATGATGTCATTGAGATAAAG+GGG + chr4.2:29809783-29809802 MS.gene045474:CDS 30.0%
GATGATGTCATTGAGATAAA+GGG + chr4.2:29809782-29809801 MS.gene045474:CDS 30.0%
TTATCTCAATGACATCATCA+CGG - chr4.2:29809781-29809800 None:intergenic 30.0%
TTCCATGCAATCAATTGATA+GGG - chr4.2:29809350-29809369 None:intergenic 30.0%
TTGTTAACGGTGTTTATCAT+TGG + chr4.2:29809642-29809661 MS.gene045474:CDS 30.0%
! TGATGATGTCATTGAGATAA+AGG + chr4.2:29809781-29809800 MS.gene045474:CDS 30.0%
!!! AATGGTGTTTTTTGTCTCAA+AGG + chr4.2:29809302-29809321 MS.gene045474:CDS 30.0%
AACAAAGATTTGACGAGGAT+TGG - chr4.2:29809242-29809261 None:intergenic 35.0%
AATGTAATAGTTACCGAGTG+AGG - chr4.2:29809414-29809433 None:intergenic 35.0%
ATGACATCATCACGGAAATA+TGG - chr4.2:29809773-29809792 None:intergenic 35.0%
ATGTAATAGTTACCGAGTGA+GGG - chr4.2:29809413-29809432 None:intergenic 35.0%
GTTCCATGCAATCAATTGAT+AGG - chr4.2:29809351-29809370 None:intergenic 35.0%
TCACGGAAATATGGGATAAA+CGG - chr4.2:29809764-29809783 None:intergenic 35.0%
TGACATCATCACGGAAATAT+GGG - chr4.2:29809772-29809791 None:intergenic 35.0%
! GTCAAATCTTTGTTTCCCAA+AGG + chr4.2:29809248-29809267 MS.gene045474:CDS 35.0%
!! ACAAGAGTGTTGTATCTTGA+AGG - chr4.2:29809626-29809645 None:intergenic 35.0%
!! TATGGGTTTGGTGCTATTAA+CGG + chr4.2:29809446-29809465 MS.gene045474:CDS 35.0%
AATAGCACCAAACCCATAGA+AGG - chr4.2:29809444-29809463 None:intergenic 40.0%
ACGGAAATATGGGATAAACG+GGG - chr4.2:29809762-29809781 None:intergenic 40.0%
AGGTGAACCTCATTAGTTGT+TGG - chr4.2:29809374-29809393 None:intergenic 40.0%
ATGAAGCTTCTCTCATGTGA+CGG + chr4.2:29809203-29809222 MS.gene045474:CDS 40.0%
ATGGAACCCAACAACTAATG+AGG + chr4.2:29809364-29809383 MS.gene045474:CDS 40.0%
CACGGAAATATGGGATAAAC+GGG - chr4.2:29809763-29809782 None:intergenic 40.0%
CGATTAGTGACAACAGTTTG+AGG - chr4.2:29809599-29809618 None:intergenic 40.0%
GAGACATATGGTAGTTGCAA+TGG + chr4.2:29809284-29809303 MS.gene045474:CDS 40.0%
GGGTTGCATCACGTAAATTT+GGG - chr4.2:29809742-29809761 None:intergenic 40.0%
GGTGAACCTCATTAGTTGTT+GGG - chr4.2:29809373-29809392 None:intergenic 40.0%
GGTTGCATCACGTAAATTTG+GGG - chr4.2:29809741-29809760 None:intergenic 40.0%
GTAGCAAGAATCGAGACATA+TGG + chr4.2:29809272-29809291 MS.gene045474:CDS 40.0%
GTCCCTATCAATTGATTGCA+TGG + chr4.2:29809345-29809364 MS.gene045474:CDS 40.0%
TGGGAAACAAAGATTTGACG+AGG - chr4.2:29809247-29809266 None:intergenic 40.0%
TTTGAGGAGAAGGACTATTG+AGG - chr4.2:29809583-29809602 None:intergenic 40.0%
!! TGTCTCAAAGGTATTTACCC+AGG + chr4.2:29809314-29809333 MS.gene045474:CDS 40.0%
GGAGAAGGACTATTGAGGAT+AGG - chr4.2:29809578-29809597 None:intergenic 45.0%
GGGGTTGCATCACGTAAATT+TGG - chr4.2:29809743-29809762 None:intergenic 45.0%
GTGACAACAGTTTGAGGAGA+AGG - chr4.2:29809593-29809612 None:intergenic 45.0%
TCGATTCTTGCTACGCCTTT+GGG - chr4.2:29809266-29809285 None:intergenic 45.0%
TTGAGATAAAGGGGCTCTCT+TGG + chr4.2:29809792-29809811 MS.gene045474:CDS 45.0%
! AGGGAGCATGGGGAATAATA+AGG - chr4.2:29809394-29809413 None:intergenic 45.0%
CTCGATTCTTGCTACGCCTT+TGG - chr4.2:29809267-29809286 None:intergenic 50.0%
GGGCTCTCTTGGTTATGTTG+TGG + chr4.2:29809803-29809822 MS.gene045474:CDS 50.0%
! GATAGGGACGAGTTTTGCCT+GGG - chr4.2:29809334-29809353 None:intergenic 50.0%
! TGATAGGGACGAGTTTTGCC+TGG - chr4.2:29809335-29809354 None:intergenic 50.0%
AGTTACCGAGTGAGGGAGCA+TGG - chr4.2:29809406-29809425 None:intergenic 55.0%
ATTCCCCATGCTCCCTCACT+CGG + chr4.2:29809398-29809417 MS.gene045474:CDS 55.0%
! GTTACCGAGTGAGGGAGCAT+GGG - chr4.2:29809405-29809424 None:intergenic 55.0%
! TTACCGAGTGAGGGAGCATG+GGG - chr4.2:29809404-29809423 None:intergenic 55.0%
!! GGGCTTCAAGTTGCCGAAAC+TGG - chr4.2:29809721-29809740 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 29809203 29809832 29809203 ID=MS.gene045474
chr4.2 mRNA 29809203 29809832 29809203 ID=MS.gene045474.t1;Parent=MS.gene045474
chr4.2 exon 29809203 29809832 29809203 ID=MS.gene045474.t1.exon1;Parent=MS.gene045474.t1
chr4.2 CDS 29809203 29809832 29809203 ID=cds.MS.gene045474.t1;Parent=MS.gene045474.t1
Gene Sequence

>MS.gene045474

ATGAAGCTTCTCTCATGTGACGGTGACAACGAGAAACCAATCCTCGTCAAATCTTTGTTTCCCAAAGGCGTAGCAAGAATCGAGACATATGGTAGTTGCAATGGTGTTTTTTGTCTCAAAGGTATTTACCCAGGCAAAACTCGTCCCTATCAATTGATTGCATGGAACCCAACAACTAATGAGGTTCACCTTATTATTCCCCATGCTCCCTCACTCGGTAACTATTACATTAATAATTCCTTCTATGGGTTTGGTGCTATTAACGGCGACTTCAAAGTTGTCAAATTCAATCTCTCTAATTACAATGAAACTACAAAAATGCTTTATCTTTTATCGGCAGAAGTTTATAATCTAAGCACTAAATCTTGGACACCTATCCTCAATAGTCCTTCTCCTCAAACTGTTGTCACTAATCGACTACCTTCAAGATACAACACTCTTGTTAACGGTGTTTATCATTGGATTACGAGTGATTACTTTACTTCAAAAATTATTTGCTTTGACTTTCACAATAACCAGTTTCGGCAACTTGAAGCCCCAAATTTACGTGATGCAACCCCGTTTATCCCATATTTCCGTGATGATGTCATTGAGATAAAGGGGCTCTCTTGGTTATGTTGTGGAATATAG
Protein sequence

>MS.gene045474.t1

MKLLSCDGDNEKPILVKSLFPKGVARIETYGSCNGVFCLKGIYPGKTRPYQLIAWNPTTNEVHLIIPHAPSLGNYYINNSFYGFGAINGDFKVVKFNLSNYNETTKMLYLLSAEVYNLSTKSWTPILNSPSPQTVVTNRLPSRYNTLVNGVYHWITSDYFTSKIICFDFHNNQFRQLEAPNLRDATPFIPYFRDDVIEIKGLSWLCCGI