AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene30465

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene30465.t1 MTR_5g026960 90.323 93 3 2 40 131 1 88 6.56e-50 166
MS.gene30465.t1 MTR_8g071230 81.720 93 11 2 40 131 1 88 6.88e-45 152
MS.gene30465.t1 MTR_8g012450 52.688 93 38 2 40 131 1 88 1.85e-25 100
MS.gene30465.t1 MTR_8g012450 52.688 93 38 2 40 131 1 88 2.31e-25 100
MS.gene30465.t1 MTR_3g054080 40.625 96 48 3 37 128 7 97 4.02e-13 65.9
MS.gene30465.t1 MTR_2g072840 37.143 105 55 3 34 132 16 115 5.77e-11 59.7
MS.gene30465.t1 MTR_4g094430 34.091 88 52 2 40 126 1 83 6.41e-11 59.3
MS.gene30465.t1 MTR_2g072840 37.624 101 52 3 38 132 20 115 9.42e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene30465.t1 AT4G19110 82.796 93 10 2 40 131 1 88 2.09e-47 159
MS.gene30465.t1 AT4G19110 82.796 93 10 2 40 131 1 88 2.24e-47 159
MS.gene30465.t1 AT5G45430 77.419 93 15 2 40 131 1 88 2.51e-43 149
MS.gene30465.t1 AT5G45430 77.419 93 15 2 40 131 1 88 2.66e-43 149
MS.gene30465.t1 AT4G13020 62.069 87 28 1 40 126 1 82 3.99e-32 117
MS.gene30465.t1 AT4G13020 62.069 87 28 1 40 126 1 82 4.48e-32 118
MS.gene30465.t1 AT4G13020 62.069 87 28 1 40 126 1 82 4.54e-32 118
MS.gene30465.t1 AT4G13020 62.069 87 28 1 40 126 1 82 5.97e-32 118
MS.gene30465.t1 AT4G13020 61.176 85 28 1 42 126 11 90 1.95e-30 114
MS.gene30465.t1 AT4G13020 61.176 85 28 1 42 126 11 90 1.97e-30 114
MS.gene30465.t1 AT4G13020 56.250 96 28 2 40 126 1 91 3.71e-29 110
MS.gene30465.t1 AT4G13020 56.250 96 28 2 40 126 1 91 5.28e-29 110
MS.gene30465.t1 AT5G39420 39.560 91 47 3 39 126 101 186 5.85e-12 62.8
MS.gene30465.t1 AT3G14720 37.143 105 55 3 34 132 16 115 1.22e-11 62.0
MS.gene30465.t1 AT3G01085 36.264 91 50 3 39 126 111 196 1.37e-11 61.6
MS.gene30465.t1 AT3G14720 37.624 101 52 3 38 132 20 115 1.42e-11 61.6
MS.gene30465.t1 AT3G14720 37.624 101 52 3 38 132 20 115 1.42e-11 61.6
MS.gene30465.t1 AT3G01085 36.264 91 50 3 39 126 111 196 1.45e-11 61.6
MS.gene30465.t1 AT3G01085 36.264 91 50 3 39 126 111 196 1.45e-11 61.6
MS.gene30465.t1 AT1G53510 36.634 101 53 3 38 132 20 115 4.37e-11 60.5
MS.gene30465.t1 AT3G48750 35.227 88 51 2 40 126 1 83 6.02e-11 59.3

Find 34 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCTTCAGTTTCACAATATT+TGG 0.029934 6.4:+40455434 None:intergenic
GTAATACCTTGACTTCTCTT+AGG 0.281840 6.4:+40455571 None:intergenic
GAAGTTGGTGATGGAACATT+TGG 0.311288 6.4:-40455767 MS.gene30465:CDS
CCTTCAGTTTCACAATATTT+GGG 0.336199 6.4:+40455435 None:intergenic
TAATCAGTTACAAAATTTGC+AGG 0.375942 6.4:-40455646 MS.gene30465:intron
TCATTCACCTTCGCACGATT+AGG 0.394102 6.4:-40456272 MS.gene30465:CDS
TGAAGAAGAAATATTACTCC+TGG 0.433782 6.4:-40455608 MS.gene30465:CDS
ATGGAACATTTGGGAGTGTC+TGG 0.443342 6.4:-40455757 MS.gene30465:CDS
TGTCCGACACAAACATGGTT+GGG 0.452336 6.4:+40455210 None:intergenic
AAGTTGGTGATGGAACATTT+GGG 0.510987 6.4:-40455766 MS.gene30465:CDS
AATCATACTTACAACTTCAC+CGG 0.516771 6.4:+40455715 None:intergenic
TACAAAATAATCAAGGAAGT+TGG 0.517126 6.4:-40455782 MS.gene30465:CDS
AATGAGATGGCGGCGTTCGA+CGG 0.536025 6.4:+40456290 None:intergenic
TTACGAAGCAGAAGGTTCAA+TGG 0.544196 6.4:+40456244 None:intergenic
TAGGTTTACACACTCCTCCC+AGG 0.552266 6.4:+40455590 None:intergenic
TTGTCCGACACAAACATGGT+TGG 0.556533 6.4:+40455209 None:intergenic
AACATTGTCCGACACAAACA+TGG 0.557828 6.4:+40455205 None:intergenic
ACAAAAGACAGAATATCTAC+AGG 0.563192 6.4:-40455351 MS.gene30465:intron
TCAGTTTCACAATATTTGGG+TGG 0.564489 6.4:+40455438 None:intergenic
CTACAGGTACAAAATAATCA+AGG 0.564500 6.4:-40455789 MS.gene30465:intron
GGACGAACTGCGAAAGTGAA+GGG 0.568045 6.4:+40456311 None:intergenic
GAAGAAGAAATATTACTCCT+GGG 0.573081 6.4:-40455607 MS.gene30465:CDS
TGTAAACCTAAGAGAAGTCA+AGG 0.578485 6.4:-40455577 MS.gene30465:intron
ATAATCAAGGAAGTTGGTGA+TGG 0.578661 6.4:-40455776 MS.gene30465:CDS
AGAGCTATTAGTAAGCAAAC+CGG 0.583714 6.4:-40455734 MS.gene30465:CDS
TCGTGCGAAGGTGAATGAGA+TGG 0.590939 6.4:+40456277 None:intergenic
CCCAAATATTGTGAAACTGA+AGG 0.592543 6.4:-40455435 MS.gene30465:CDS
AAAAGGAATTACGAAGCAGA+AGG 0.610324 6.4:+40456236 None:intergenic
CGGACGAACTGCGAAAGTGA+AGG 0.613022 6.4:+40456310 None:intergenic
TGTTTGTGTCAGATATGTTG+TGG 0.613443 6.4:-40455246 MS.gene30465:intron
GGACAAACCTAATCGTGCGA+AGG 0.641400 6.4:+40456265 None:intergenic
AATCCCAACCATGTTTGTGT+CGG 0.642986 6.4:-40455213 MS.gene30465:CDS
TGCGAAGGTGAATGAGATGG+CGG 0.668306 6.4:+40456280 None:intergenic
GAAGAAATATTACTCCTGGG+AGG 0.712706 6.4:-40455604 MS.gene30465:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAACAATAATAAGTTAAAA+AGG + chr6.4:40455583-40455602 None:intergenic 10.0%
!! ATCAATAATTTAGAAGAATG+AGG + chr6.4:40455388-40455407 None:intergenic 20.0%
!! TATATAACTCTTTATTAGGA+AGG - chr6.4:40456199-40456218 MS.gene30465:intron 20.0%
!! TGTGTATATAACTCTTTATT+AGG - chr6.4:40456195-40456214 MS.gene30465:intron 20.0%
! AAGTTGTAAGTATGATTTAC+TGG - chr6.4:40455808-40455827 MS.gene30465:intron 25.0%
! AGACAAAAGCAATATATGAA+TGG + chr6.4:40455336-40455355 None:intergenic 25.0%
! ATAACACATAACAACAACAA+AGG + chr6.4:40455993-40456012 None:intergenic 25.0%
! TAATCAGTTACAAAATTTGC+AGG - chr6.4:40455871-40455890 MS.gene30465:intron 25.0%
! TACAAAATAATCAAGGAAGT+TGG - chr6.4:40455735-40455754 MS.gene30465:CDS 25.0%
! TATGAATGGAAGAAGAAATA+AGG + chr6.4:40455322-40455341 None:intergenic 25.0%
! TGTTTACATCTGTTGAATAA+AGG - chr6.4:40455597-40455616 MS.gene30465:CDS 25.0%
! TTACTTCATACTTATCTTTC+TGG - chr6.4:40455965-40455984 MS.gene30465:intron 25.0%
!! TAATTTTCTCATTTACTGTG+TGG - chr6.4:40455680-40455699 MS.gene30465:intron 25.0%
!! TGCAAATTTTGTAACTGATT+AGG + chr6.4:40455872-40455891 None:intergenic 25.0%
AATCATACTTACAACTTCAC+CGG + chr6.4:40455805-40455824 None:intergenic 30.0%
ACAAAAGACAGAATATCTAC+AGG - chr6.4:40456166-40456185 MS.gene30465:intron 30.0%
CCTTCAGTTTCACAATATTT+GGG + chr6.4:40456085-40456104 None:intergenic 30.0%
CTACAGGTACAAAATAATCA+AGG - chr6.4:40455728-40455747 MS.gene30465:CDS 30.0%
GAAGAAGAAATATTACTCCT+GGG - chr6.4:40455910-40455929 MS.gene30465:intron 30.0%
TCCTTCAGTTTCACAATATT+TGG + chr6.4:40456086-40456105 None:intergenic 30.0%
TGAAGAAGAAATATTACTCC+TGG - chr6.4:40455909-40455928 MS.gene30465:intron 30.0%
! ACATTTTTCCTTAACACTAC+AGG - chr6.4:40455712-40455731 MS.gene30465:intron 30.0%
! ATTTTGTACCTGTAGTGTTA+AGG + chr6.4:40455723-40455742 None:intergenic 30.0%
! GTAGATATTCTGTCTTTTGT+TGG + chr6.4:40456166-40456185 None:intergenic 30.0%
!!! GTACTTTGTTTTTGAGTACA+TGG - chr6.4:40456130-40456149 MS.gene30465:intron 30.0%
AAAAGGAATTACGAAGCAGA+AGG + chr6.4:40455284-40455303 None:intergenic 35.0%
AGAGCTATTAGTAAGCAAAC+CGG - chr6.4:40455783-40455802 MS.gene30465:CDS 35.0%
CCCAAATATTGTGAAACTGA+AGG - chr6.4:40456082-40456101 MS.gene30465:intron 35.0%
GAAGAAATAAGGTTCTGCAA+AGG + chr6.4:40455311-40455330 None:intergenic 35.0%
GTAATACCTTGACTTCTCTT+AGG + chr6.4:40455949-40455968 None:intergenic 35.0%
TCAGTTTCACAATATTTGGG+TGG + chr6.4:40456082-40456101 None:intergenic 35.0%
TGTAAACCTAAGAGAAGTCA+AGG - chr6.4:40455940-40455959 MS.gene30465:intron 35.0%
TGTTTGTGTCAGATATGTTG+TGG - chr6.4:40456271-40456290 MS.gene30465:CDS 35.0%
! TTATCTCTTGTTTCCCTTGT+TGG - chr6.4:40456036-40456055 MS.gene30465:intron 35.0%
!! AAGTTGGTGATGGAACATTT+GGG - chr6.4:40455751-40455770 MS.gene30465:CDS 35.0%
!! ATAATCAAGGAAGTTGGTGA+TGG - chr6.4:40455741-40455760 MS.gene30465:CDS 35.0%
AACATTGTCCGACACAAACA+TGG + chr6.4:40456315-40456334 None:intergenic 40.0%
AATCCCAACCATGTTTGTGT+CGG - chr6.4:40456304-40456323 MS.gene30465:CDS 40.0%
ACAGTGTCAATTATACGCGT+AGG + chr6.4:40455518-40455537 None:intergenic 40.0%
ATCGAGAAGCAGAAGAATGA+TGG + chr6.4:40455360-40455379 None:intergenic 40.0%
GAAGAAATATTACTCCTGGG+AGG - chr6.4:40455913-40455932 MS.gene30465:intron 40.0%
TTACGAAGCAGAAGGTTCAA+TGG + chr6.4:40455276-40455295 None:intergenic 40.0%
TTCGTAAAGACTGCCAACAA+GGG + chr6.4:40456052-40456071 None:intergenic 40.0%
TTTCGTAAAGACTGCCAACA+AGG + chr6.4:40456053-40456072 None:intergenic 40.0%
! CGTAGGAATCAGAAAGCATA+AGG + chr6.4:40455501-40455520 None:intergenic 40.0%
!! AAGCGTTGCTTTGAGTTTTG+CGG - chr6.4:40455620-40455639 MS.gene30465:CDS 40.0%
!! CTTTGAGTTTTGCGGGAAAA+TGG - chr6.4:40455628-40455647 MS.gene30465:CDS 40.0%
!! GAAGTTGGTGATGGAACATT+TGG - chr6.4:40455750-40455769 MS.gene30465:CDS 40.0%
GGTTCTGCAAAGGAGTGAAA+AGG + chr6.4:40455301-40455320 None:intergenic 45.0%
TCATTCACCTTCGCACGATT+AGG - chr6.4:40455245-40455264 MS.gene30465:intron 45.0%
TGTCCGACACAAACATGGTT+GGG + chr6.4:40456310-40456329 None:intergenic 45.0%
TTGTCCGACACAAACATGGT+TGG + chr6.4:40456311-40456330 None:intergenic 45.0%
! AGTTTTGCGGGAAAATGGAG+AGG - chr6.4:40455633-40455652 MS.gene30465:CDS 45.0%
!! AGCGTTGCTTTGAGTTTTGC+GGG - chr6.4:40455621-40455640 MS.gene30465:CDS 45.0%
!! ATGGAACATTTGGGAGTGTC+TGG - chr6.4:40455760-40455779 MS.gene30465:CDS 45.0%
GGACAAACCTAATCGTGCGA+AGG + chr6.4:40455255-40455274 None:intergenic 50.0%
GGACGAACTGCGAAAGTGAA+GGG + chr6.4:40455209-40455228 None:intergenic 50.0%
TAGGTTTACACACTCCTCCC+AGG + chr6.4:40455930-40455949 None:intergenic 50.0%
TCGTGCGAAGGTGAATGAGA+TGG + chr6.4:40455243-40455262 None:intergenic 50.0%
TGCGAAGGTGAATGAGATGG+CGG + chr6.4:40455240-40455259 None:intergenic 50.0%
CGGACGAACTGCGAAAGTGA+AGG + chr6.4:40455210-40455229 None:intergenic 55.0%
! AATGAGATGGCGGCGTTCGA+CGG + chr6.4:40455230-40455249 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.4 gene 40455203 40456336 40455203 ID=MS.gene30465
chr6.4 mRNA 40455203 40456336 40455203 ID=MS.gene30465.t1;Parent=MS.gene30465
chr6.4 exon 40456248 40456336 40456248 ID=MS.gene30465.t1.exon1;Parent=MS.gene30465.t1
chr6.4 CDS 40456248 40456336 40456248 ID=cds.MS.gene30465.t1;Parent=MS.gene30465.t1
chr6.4 exon 40455885 40455920 40455885 ID=MS.gene30465.t1.exon2;Parent=MS.gene30465.t1
chr6.4 CDS 40455885 40455920 40455885 ID=cds.MS.gene30465.t1;Parent=MS.gene30465.t1
chr6.4 exon 40455727 40455805 40455727 ID=MS.gene30465.t1.exon3;Parent=MS.gene30465.t1
chr6.4 CDS 40455727 40455805 40455727 ID=cds.MS.gene30465.t1;Parent=MS.gene30465.t1
chr6.4 exon 40455578 40455661 40455578 ID=MS.gene30465.t1.exon4;Parent=MS.gene30465.t1
chr6.4 CDS 40455578 40455661 40455578 ID=cds.MS.gene30465.t1;Parent=MS.gene30465.t1
chr6.4 exon 40455352 40455477 40455352 ID=MS.gene30465.t1.exon5;Parent=MS.gene30465.t1
chr6.4 CDS 40455352 40455477 40455352 ID=cds.MS.gene30465.t1;Parent=MS.gene30465.t1
chr6.4 exon 40455203 40455256 40455203 ID=MS.gene30465.t1.exon6;Parent=MS.gene30465.t1
chr6.4 CDS 40455203 40455256 40455203 ID=cds.MS.gene30465.t1;Parent=MS.gene30465.t1
Gene Sequence

>MS.gene30465

ATGCCCTTCACTTTCGCAGTTCGTCCGTCGAACGCCGCCATCTCATTCACCTTCGCACGATTAGGTTTGTCCATTGAACCTTCTGCTTCGTAATTCCTTTTCACTCCTTTGCAGAACCTTATTTCTTCTTCCATTCATATATTGCTTTTGTCTTCCATCATTCTTCTGCTTCTCGATTGACTCCTCATTCTTCTAAATTATTGATTTGATATATTTCTATGTAGTAAATTTAATTGTTCATTTTCTTTGTTTGTTAATTCACTCAATTGTTAATTTTTTTTTTGTTATTTTTGTTCCTTATGCTTTCTGATTCCTACGCGTATAATTGACACTGTTAATATTTTTATACATAGAGCATCATCTACAAGAGATAAATGCCTTTTTAACTTATTATTGTTTACATCTGTTGAATAAAGGAAGCGTTGCTTTGAGTTTTGCGGGAAAATGGAGAGGTGATTCATTTTCTGAAGAAATTACTAATTTTCTCATTTACTGTGTGGACTATTTTAACATTTTTCCTTAACACTACAGGTACAAAATAATCAAGGAAGTTGGTGATGGAACATTTGGGAGTGTCTGGAGAGCTATTAGTAAGCAAACCGGTGAAGTTGTAAGTATGATTTACTGGTATGTTGAAGTTTTCTCTATTTGAAGTGACATTTTTCTCCTAATCAGTTACAAAATTTGCAGGCTGCGATCAAGAAAATGAAGAAGAAATATTACTCCTGGGAGGAGTGTGTAAACCTAAGAGAAGTCAAGGTATTACTTCATACTTATCTTTCTGGAGCCTTTGTTGTTGTTATGTGTTATTATATTCTTTTGTATTTAGTCTCTTATCTCTTGTTTCCCTTGTTGGCAGTCTTTACGAAAAATGAACCACCCAAATATTGTGAAACTGAAGGAAGTTATTCGAGAAAGTGACATTTTGTACTTTGTTTTTGAGTACATGGTGACATTGTACCAACAAAAGACAGAATATCTACAGGTGTGTATGTGTATATAACTCTTTATTAGGAAGGTGACATTGTATTTCATGATTCAAGTCGAGTCACTCATGTTATTTCATTTTGTTTGTGTCAGATATGTTGTGGAATGCTGCTGAATCCCAACCATGTTTGTGTCGGACAATGTTAA
Protein sequence

>MS.gene30465.t1

MPFTFAVRPSNAAISFTFARLGLSIEPSASKRCFEFCGKMERYKIIKEVGDGTFGSVWRAISKQTGEVLQNLQAAIKKMKKKYYSWEECVNLREVKSLRKMNHPNIVKLKEVIRESDILYFVFEYMVTLYQQKTEYLQICCGMLLNPNHVCVGQC