AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene39218

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39218.t1 MTR_7g107200 32.164 342 196 7 10 322 43 377 1.47e-53 180
MS.gene39218.t1 MTR_8g011730 33.451 284 147 8 38 295 75 342 1.57e-39 142
MS.gene39218.t1 MTR_1g042160 31.690 284 146 8 37 319 72 308 4.14e-38 137
MS.gene39218.t1 MTR_7g107170 42.657 143 79 2 177 319 124 263 1.72e-31 119
MS.gene39218.t1 MTR_7g107160 30.293 307 172 9 19 321 177 445 5.80e-30 118
MS.gene39218.t1 MTR_2g034780 31.319 182 115 3 125 306 84 255 8.38e-24 99.0
MS.gene39218.t1 MTR_3g079840 41.237 97 55 2 10 104 86 182 1.38e-15 78.2
MS.gene39218.t1 MTR_3g079840 41.237 97 55 2 10 104 85 181 1.44e-15 78.2
MS.gene39218.t1 MTR_5g086700 37.736 106 64 2 1 104 81 186 2.12e-15 77.4
MS.gene39218.t1 MTR_5g086700 37.736 106 64 2 1 104 81 186 2.14e-15 77.4
MS.gene39218.t1 MTR_1g041240 38.144 97 58 2 10 104 86 182 3.37e-14 73.9
MS.gene39218.t1 MTR_1g041240 38.144 97 58 2 10 104 87 183 3.37e-14 73.9
MS.gene39218.t1 MTR_1g041240 38.144 97 58 2 10 104 85 181 3.46e-14 73.9
MS.gene39218.t1 MTR_5g091450 33.333 99 63 3 10 105 62 160 2.70e-11 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39218.t1 AT3G11910 42.268 97 54 2 10 104 83 179 1.26e-16 81.3
MS.gene39218.t1 AT3G11910 42.268 97 54 2 10 104 83 179 1.26e-16 81.3
MS.gene39218.t1 AT3G11910 42.268 97 54 2 10 104 84 180 1.26e-16 81.3
MS.gene39218.t1 AT3G11910 42.268 97 54 2 10 104 84 180 1.26e-16 81.3
MS.gene39218.t1 AT5G06600 40.206 97 56 2 10 104 85 181 3.42e-16 80.1
MS.gene39218.t1 AT5G06600 40.206 97 56 2 10 104 85 181 3.47e-16 80.1
MS.gene39218.t1 AT5G06600 40.206 97 56 2 10 104 84 180 3.53e-16 80.1

Find 58 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATGAATTTATTGAAATTT+AGG 0.097481 1.2:-43175530 None:intergenic
TTTAGGTGTGAAACCTTATT+TGG 0.176545 1.2:+43176061 MS.gene39218:CDS
TAGCATTAACATTCATTTCT+TGG 0.196289 1.2:-43176226 None:intergenic
TCACAAGATACCCTTGTTTA+TGG 0.211988 1.2:-43175554 None:intergenic
TTGCTTGCTCTTTCCAAATA+AGG 0.215332 1.2:-43176074 None:intergenic
CCTTATGTTCAATCTGCTTT+AGG 0.228849 1.2:+43176044 MS.gene39218:CDS
GATCTGTTAGAGATGAATTT+TGG 0.232734 1.2:-43175653 None:intergenic
ATTAAGACAATTTATAGATT+TGG 0.265024 1.2:+43175767 MS.gene39218:CDS
CAATGGGCGTTTATTTCATT+AGG 0.313100 1.2:+43175897 MS.gene39218:CDS
GATGTTGAACCTGATGTTCT+TGG 0.313287 1.2:-43175705 None:intergenic
AAGAACAAGAACATTGTAAA+AGG 0.329093 1.2:+43175069 MS.gene39218:CDS
CCATTAAATACAACGTAAAA+TGG 0.335460 1.2:-43174972 None:intergenic
ATCCCGTTTGTTTCGACAAT+GGG 0.347875 1.2:+43175881 MS.gene39218:CDS
GAAGAGGCTTAGAGATGAAT+TGG 0.381597 1.2:+43176142 MS.gene39218:CDS
GCTGATTCTTTACCACCATA+TGG 0.384239 1.2:+43174997 MS.gene39218:CDS
AAGCAAATTGAAGAAATTAC+AGG 0.385891 1.2:+43176091 MS.gene39218:CDS
ATGAATGTTAATGCTACAAT+AGG 0.395264 1.2:+43176233 MS.gene39218:CDS
ACAGGACAAAGTTGTTGCTT+TGG 0.396787 1.2:+43176109 MS.gene39218:CDS
CCTTGAATCTCTCCTTCATC+TGG 0.397555 1.2:-43175732 None:intergenic
CGCCCATTGTCGAAACAAAC+GGG 0.404272 1.2:-43175883 None:intergenic
CCTAAAGCAGATTGAACATA+AGG 0.421896 1.2:-43176044 None:intergenic
TAAATAATCTTAAGAGTTTG+TGG 0.433992 1.2:+43175976 MS.gene39218:CDS
TGGTCAACATCCCTCCTTAG+TGG 0.451823 1.2:-43174952 None:intergenic
CTTCGGAATTCGACTTGAGT+TGG 0.454885 1.2:+43176015 MS.gene39218:CDS
AGATCAATCTTCAGATGAAA+GGG 0.455070 1.2:+43175671 MS.gene39218:CDS
ACGCCCATTGTCGAAACAAA+CGG 0.462214 1.2:-43175884 None:intergenic
GTTAGTTCTCGTTAATCAGC+TGG 0.462338 1.2:+43175044 MS.gene39218:CDS
GAGACTCAGCAAAAGTTCAA+TGG 0.462872 1.2:+43175480 MS.gene39218:intron
ATATGTCTTCATCATGTGAT+AGG 0.463059 1.2:+43174914 MS.gene39218:CDS
AGCTTGTCAGAAATCAGAAA+TGG 0.467999 1.2:+43176200 MS.gene39218:CDS
ACAATTAGTCCAAGAACATC+AGG 0.475342 1.2:+43175696 MS.gene39218:CDS
CAGATCAATCTTCAGATGAA+AGG 0.479808 1.2:+43175670 MS.gene39218:CDS
TGCTTCACAAGCAGAGTTTG+AGG 0.482699 1.2:+43176166 MS.gene39218:CDS
TCAATGGAGGATATAGAAGC+TGG 0.483484 1.2:+43175496 MS.gene39218:CDS
CCAGATGAAGGAGAGATTCA+AGG 0.494194 1.2:+43175732 MS.gene39218:CDS
AGACAATTTATAGATTTGGA+TGG 0.504986 1.2:+43175771 MS.gene39218:CDS
ATTCTTTACCACCATATGGA+TGG 0.506704 1.2:+43175001 MS.gene39218:CDS
GGAGGAACTAGCAAAATCTT+CGG 0.515920 1.2:+43175998 MS.gene39218:CDS
AAATAATCTTAAGAGTTTGT+GGG 0.516642 1.2:+43175977 MS.gene39218:CDS
TTCTTTACCACCATATGGAT+GGG 0.526863 1.2:+43175002 MS.gene39218:CDS
GTGTTTCTATCCCATCCATA+TGG 0.542297 1.2:-43175012 None:intergenic
AATCCCGTTTGTTTCGACAA+TGG 0.547890 1.2:+43175880 MS.gene39218:CDS
AAGCAGAGTTTGAGGTTGCA+AGG 0.553922 1.2:+43176174 MS.gene39218:CDS
CTTTGGATATTAAAATGAAG+AGG 0.557203 1.2:+43176126 MS.gene39218:CDS
ATTTGACTTTGTATCAAAGA+CGG 0.558711 1.2:-43175852 None:intergenic
CAATGGAGGATATAGAAGCT+GGG 0.563913 1.2:+43175497 MS.gene39218:CDS
AGATCCTTGTGCATCCACTA+AGG 0.569109 1.2:+43174938 MS.gene39218:CDS
AACGAGAACTAACTTGAAGA+AGG 0.575362 1.2:-43175034 None:intergenic
TCAACATCTAGTCCAGATGA+AGG 0.586033 1.2:+43175720 MS.gene39218:CDS
AAATTCATTGACCATAAACA+AGG 0.592420 1.2:+43175543 MS.gene39218:CDS
TCCTTGTGCATCCACTAAGG+AGG 0.614099 1.2:+43174941 MS.gene39218:CDS
CCTTGTGCATCCACTAAGGA+GGG 0.618988 1.2:+43174942 MS.gene39218:CDS
CCCTCCTTAGTGGATGCACA+AGG 0.633723 1.2:-43174942 None:intergenic
TAATCTTAAGAGTTTGTGGG+AGG 0.635857 1.2:+43175980 MS.gene39218:CDS
TTTCTATCCCATCCATATGG+TGG 0.636196 1.2:-43175009 None:intergenic
ACTCAGCAAAAGTTCAATGG+AGG 0.650485 1.2:+43175483 MS.gene39218:CDS
AATGGAGGATATAGAAGCTG+GGG 0.652315 1.2:+43175498 MS.gene39218:CDS
AATTCATTGACCATAAACAA+GGG 0.668373 1.2:+43175544 MS.gene39218:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAAAAAATATTATCATTAG+AGG - chr1.2:43175416-43175435 None:intergenic 15.0%
!! ATTAAGACAATTTATAGATT+TGG + chr1.2:43175767-43175786 MS.gene39218:CDS 15.0%
!! CAATGAATTTATTGAAATTT+AGG - chr1.2:43175533-43175552 None:intergenic 15.0%
!! AAATAATCTTAAGAGTTTGT+GGG + chr1.2:43175977-43175996 MS.gene39218:CDS 20.0%
!! TAAATAATCTTAAGAGTTTG+TGG + chr1.2:43175976-43175995 MS.gene39218:CDS 20.0%
! AAATTCATTGACCATAAACA+AGG + chr1.2:43175543-43175562 MS.gene39218:CDS 25.0%
! AAGAACAAGAACATTGTAAA+AGG + chr1.2:43175069-43175088 MS.gene39218:CDS 25.0%
! AAGCAAATTGAAGAAATTAC+AGG + chr1.2:43176091-43176110 MS.gene39218:CDS 25.0%
! AATTCATTGACCATAAACAA+GGG + chr1.2:43175544-43175563 MS.gene39218:CDS 25.0%
! AGACAATTTATAGATTTGGA+TGG + chr1.2:43175771-43175790 MS.gene39218:CDS 25.0%
! ATAAATGACAAAACTAGCAA+AGG - chr1.2:43175119-43175138 None:intergenic 25.0%
! ATGAACAGTTTGATCTTAAT+AGG + chr1.2:43175242-43175261 MS.gene39218:intron 25.0%
! ATGAATGTTAATGCTACAAT+AGG + chr1.2:43176233-43176252 MS.gene39218:CDS 25.0%
! CCATTAAATACAACGTAAAA+TGG - chr1.2:43174975-43174994 None:intergenic 25.0%
! CTTTGGATATTAAAATGAAG+AGG + chr1.2:43176126-43176145 MS.gene39218:CDS 25.0%
! TAAATGACAAAACTAGCAAA+GGG - chr1.2:43175118-43175137 None:intergenic 25.0%
! TAGCATTAACATTCATTTCT+TGG - chr1.2:43176229-43176248 None:intergenic 25.0%
!! ATTTGACTTTGTATCAAAGA+CGG - chr1.2:43175855-43175874 None:intergenic 25.0%
!! ATTTTAGACTTCTAGATGAA+AGG + chr1.2:43175333-43175352 MS.gene39218:intron 25.0%
!! CCATTTTACGTTGTATTTAA+TGG + chr1.2:43174972-43174991 MS.gene39218:CDS 25.0%
!! GAATTGATGTCATGAATTTT+TGG - chr1.2:43175627-43175646 None:intergenic 25.0%
!! TTTTAGACTTCTAGATGAAA+GGG + chr1.2:43175334-43175353 MS.gene39218:intron 25.0%
AAATGACAAAACTAGCAAAG+GGG - chr1.2:43175117-43175136 None:intergenic 30.0%
AAGATCTAAAGGCTCATATT+TGG + chr1.2:43175208-43175227 MS.gene39218:intron 30.0%
AGATCAATCTTCAGATGAAA+GGG + chr1.2:43175671-43175690 MS.gene39218:CDS 30.0%
ATATGTCTTCATCATGTGAT+AGG + chr1.2:43174914-43174933 MS.gene39218:CDS 30.0%
TTTAGGTGTGAAACCTTATT+TGG + chr1.2:43176061-43176080 MS.gene39218:CDS 30.0%
! GATCTGTTAGAGATGAATTT+TGG - chr1.2:43175656-43175675 None:intergenic 30.0%
!!! TAGAGATGAATTTTGGTTCA+AGG - chr1.2:43175649-43175668 None:intergenic 30.0%
AAAGGGGAGAATGAAGATAA+GGG - chr1.2:43175101-43175120 None:intergenic 35.0%
AACGAGAACTAACTTGAAGA+AGG - chr1.2:43175037-43175056 None:intergenic 35.0%
ACAATTAGTCCAAGAACATC+AGG + chr1.2:43175696-43175715 MS.gene39218:CDS 35.0%
AGCTTGTCAGAAATCAGAAA+TGG + chr1.2:43176200-43176219 MS.gene39218:CDS 35.0%
ATTCCCTACCGAATAAGTTA+GGG + chr1.2:43175175-43175194 MS.gene39218:intron 35.0%
ATTCTTTACCACCATATGGA+TGG + chr1.2:43175001-43175020 MS.gene39218:CDS 35.0%
CAATGGGCGTTTATTTCATT+AGG + chr1.2:43175897-43175916 MS.gene39218:CDS 35.0%
CAGATCAATCTTCAGATGAA+AGG + chr1.2:43175670-43175689 MS.gene39218:CDS 35.0%
CCTAAAGCAGATTGAACATA+AGG - chr1.2:43176047-43176066 None:intergenic 35.0%
CCTTATGTTCAATCTGCTTT+AGG + chr1.2:43176044-43176063 MS.gene39218:CDS 35.0%
TAATCTTAAGAGTTTGTGGG+AGG + chr1.2:43175980-43175999 MS.gene39218:CDS 35.0%
TGAGCCTTTAGATCTTGATT+AGG - chr1.2:43175204-43175223 None:intergenic 35.0%
TTCTTTACCACCATATGGAT+GGG + chr1.2:43175002-43175021 MS.gene39218:CDS 35.0%
TTGCTTGCTCTTTCCAAATA+AGG - chr1.2:43176077-43176096 None:intergenic 35.0%
! CGGAACAAAATGCTTTTCTT+CGG - chr1.2:43175805-43175824 None:intergenic 35.0%
! GGAACAAAATGCTTTTCTTC+GGG - chr1.2:43175804-43175823 None:intergenic 35.0%
! GTGCAAACTTCCTCTAAAAA+CGG - chr1.2:43175825-43175844 None:intergenic 35.0%
! TCACAAGATACCCTTGTTTA+TGG - chr1.2:43175557-43175576 None:intergenic 35.0%
!! GCATTTTGTTCCGTTTTTAG+AGG + chr1.2:43175812-43175831 MS.gene39218:CDS 35.0%
AATCCCGTTTGTTTCGACAA+TGG + chr1.2:43175880-43175899 MS.gene39218:CDS 40.0%
AATGGAGGATATAGAAGCTG+GGG + chr1.2:43175498-43175517 MS.gene39218:CDS 40.0%
ACTCAGCAAAAGTTCAATGG+AGG + chr1.2:43175483-43175502 MS.gene39218:CDS 40.0%
ATCCCGTTTGTTTCGACAAT+GGG + chr1.2:43175881-43175900 MS.gene39218:CDS 40.0%
CAAAGGGGAGAATGAAGATA+AGG - chr1.2:43175102-43175121 None:intergenic 40.0%
CAATGGAGGATATAGAAGCT+GGG + chr1.2:43175497-43175516 MS.gene39218:CDS 40.0%
GAAGAGGCTTAGAGATGAAT+TGG + chr1.2:43176142-43176161 MS.gene39218:CDS 40.0%
GAGACTCAGCAAAAGTTCAA+TGG + chr1.2:43175480-43175499 MS.gene39218:intron 40.0%
GATGTTGAACCTGATGTTCT+TGG - chr1.2:43175708-43175727 None:intergenic 40.0%
GATTCCCTACCGAATAAGTT+AGG + chr1.2:43175174-43175193 MS.gene39218:intron 40.0%
GCGTCCTAATCAAGATCTAA+AGG + chr1.2:43175197-43175216 MS.gene39218:intron 40.0%
GGAGGAACTAGCAAAATCTT+CGG + chr1.2:43175998-43176017 MS.gene39218:CDS 40.0%
TCAACATCTAGTCCAGATGA+AGG + chr1.2:43175720-43175739 MS.gene39218:CDS 40.0%
TCAATGGAGGATATAGAAGC+TGG + chr1.2:43175496-43175515 MS.gene39218:CDS 40.0%
TTAGGACGCCCTAACTTATT+CGG - chr1.2:43175186-43175205 None:intergenic 40.0%
TTTCTATCCCATCCATATGG+TGG - chr1.2:43175012-43175031 None:intergenic 40.0%
! ACAGGACAAAGTTGTTGCTT+TGG + chr1.2:43176109-43176128 MS.gene39218:CDS 40.0%
! GCTGATTCTTTACCACCATA+TGG + chr1.2:43174997-43175016 MS.gene39218:CDS 40.0%
! GTGTTTCTATCCCATCCATA+TGG - chr1.2:43175015-43175034 None:intergenic 40.0%
! GTTAGTTCTCGTTAATCAGC+TGG + chr1.2:43175044-43175063 MS.gene39218:CDS 40.0%
!! TTTTAGAGGAAGTTTGCACG+TGG + chr1.2:43175826-43175845 MS.gene39218:CDS 40.0%
ACGCCCATTGTCGAAACAAA+CGG - chr1.2:43175887-43175906 None:intergenic 45.0%
ACGCCCTAACTTATTCGGTA+GGG - chr1.2:43175181-43175200 None:intergenic 45.0%
AGATCCTTGTGCATCCACTA+AGG + chr1.2:43174938-43174957 MS.gene39218:CDS 45.0%
CCAGATGAAGGAGAGATTCA+AGG + chr1.2:43175732-43175751 MS.gene39218:CDS 45.0%
CCTTGAATCTCTCCTTCATC+TGG - chr1.2:43175735-43175754 None:intergenic 45.0%
TGCTTCACAAGCAGAGTTTG+AGG + chr1.2:43176166-43176185 MS.gene39218:CDS 45.0%
! AAGCAGAGTTTGAGGTTGCA+AGG + chr1.2:43176174-43176193 MS.gene39218:CDS 45.0%
! CTTCGGAATTCGACTTGAGT+TGG + chr1.2:43176015-43176034 MS.gene39218:CDS 45.0%
CCTTGTGCATCCACTAAGGA+GGG + chr1.2:43174942-43174961 MS.gene39218:CDS 50.0%
CGCCCATTGTCGAAACAAAC+GGG - chr1.2:43175886-43175905 None:intergenic 50.0%
GACGCCCTAACTTATTCGGT+AGG - chr1.2:43175182-43175201 None:intergenic 50.0%
TCCTTGTGCATCCACTAAGG+AGG + chr1.2:43174941-43174960 MS.gene39218:CDS 50.0%
TGGTCAACATCCCTCCTTAG+TGG - chr1.2:43174955-43174974 None:intergenic 50.0%
! CCCTCCTTAGTGGATGCACA+AGG - chr1.2:43174945-43174964 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 43174910 43176271 43174910 ID=MS.gene39218
chr1.2 mRNA 43174910 43176271 43174910 ID=MS.gene39218.t1;Parent=MS.gene39218
chr1.2 exon 43174910 43175090 43174910 ID=MS.gene39218.t1.exon1;Parent=MS.gene39218.t1
chr1.2 CDS 43174910 43175090 43174910 ID=cds.MS.gene39218.t1;Parent=MS.gene39218.t1
chr1.2 exon 43175481 43176271 43175481 ID=MS.gene39218.t1.exon2;Parent=MS.gene39218.t1
chr1.2 CDS 43175481 43176271 43175481 ID=cds.MS.gene39218.t1;Parent=MS.gene39218.t1
Gene Sequence

>MS.gene39218

ATGTATATGTCTTCATCATGTGATAGGAAGATCCTTGTGCATCCACTAAGGAGGGATGTTGACCATTTTACGTTGTATTTAATGGTTGCTGATTCTTTACCACCATATGGATGGGATAGAAACACCTTCTTCAAGTTAGTTCTCGTTAATCAGCTGGATAAGAACAAGAACATTGTAAAAGGTTCTAACCCTTATCTTCATTCTCCCCTTTGCTAGTTTTGTCATTTATAATAACAAATTTTAAACTAATTCAGTAATTTAGTAGATTCCCTACCGAATAAGTTAGGGCGTCCTAATCAAGATCTAAAGGCTCATATTTGGTTTTCTCAAATATGAACAGTTTGATCTTAATAGGACGATACTGACTTGTTGATTGTGTTAATACGTAAATTACATAGAGAATTGAGACTATTTTGAGAGTTAATTTTAGACTTCTAGATGAAAGGGAATTGAGACTTCTAGATCTAAAATTTAGATTTCTAGATTCTATTTTGAGATATTTTCCTCTAATGATAATATTTTTTGTTAAATATGAAAGCTAATTCTTCTTATGCGTACTTATTATTTTTAGAGACTCAGCAAAAGTTCAATGGAGGATATAGAAGCTGGGGTGCATTTTTCCTAAATTTCAATAAATTCATTGACCATAAACAAGGGTATCTTGTGAGAGACACATGCATAATTGAAGCTCATATTTGTGTGTCTAACTTTGCACCAAAAATTCATGACATCAATTCCTTGAACCAAAATTCATCTCTAACAGATCAATCTTCAGATGAAAGGGAAACAATTAGTCCAAGAACATCAGGTTCAACATCTAGTCCAGATGAAGGAGAGATTCAAGGTACAGATTTAACATTAAGACAATTTATAGATTTGGATGGATTAAAACCCGAAGAAAAGCATTTTGTTCCGTTTTTAGAGGAAGTTTGCACGTGGCGTCCGTCTTTGATACAAAGTCAAATGAAAAAATCCCGTTTGTTTCGACAATGGGCGTTTATTTCATTAGGAAAAGTTCTGTATTTTCTTAAGACGAAGAAAGTGAAAGATATGAGTGAAGATGACATAAATAATCTTAAGAGTTTGTGGGAGGAACTAGCAAAATCTTCGGAATTCGACTTGAGTTGGTTAGAGCCTTATGTTCAATCTGCTTTAGGTGTGAAACCTTATTTGGAAAGAGCAAGCAAATTGAAGAAATTACAGGACAAAGTTGTTGCTTTGGATATTAAAATGAAGAGGCTTAGAGATGAATTGGCTGCTTCACAAGCAGAGTTTGAGGTTGCAAGGAAAAGCTTGTCAGAAATCAGAAATGGTTTCCAAGAAATGAATGTTAATGCTACAATAGGTTATGCTATGTTTTAA
Protein sequence

>MS.gene39218.t1

MYMSSSCDRKILVHPLRRDVDHFTLYLMVADSLPPYGWDRNTFFKLVLVNQLDKNKNIVKETQQKFNGGYRSWGAFFLNFNKFIDHKQGYLVRDTCIIEAHICVSNFAPKIHDINSLNQNSSLTDQSSDERETISPRTSGSTSSPDEGEIQGTDLTLRQFIDLDGLKPEEKHFVPFLEEVCTWRPSLIQSQMKKSRLFRQWAFISLGKVLYFLKTKKVKDMSEDDINNLKSLWEELAKSSEFDLSWLEPYVQSALGVKPYLERASKLKKLQDKVVALDIKMKRLRDELAASQAEFEVARKSLSEIRNGFQEMNVNATIGYAMF