AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene85901

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85901.t1 AT5G22250 55.839 274 115 3 10 280 7 277 1.39e-103 303
MS.gene85901.t1 AT3G44260 55.019 269 112 5 15 280 17 279 3.17e-97 287
MS.gene85901.t1 AT5G10960 46.182 275 139 6 7 280 1 267 1.08e-79 242
MS.gene85901.t1 AT2G32070 48.315 267 129 6 15 280 10 268 2.85e-79 241
MS.gene85901.t1 AT1G80780 46.241 266 135 5 15 280 10 267 8.34e-75 230
MS.gene85901.t1 AT1G80780 46.241 266 135 5 15 280 10 267 8.34e-75 230
MS.gene85901.t1 AT1G80780 46.241 266 135 5 15 280 10 267 1.38e-74 229
MS.gene85901.t1 AT1G15920 45.324 278 142 6 9 282 8 279 3.27e-71 221
MS.gene85901.t1 AT1G15920 45.324 278 142 6 9 282 8 279 3.27e-71 221
MS.gene85901.t1 AT1G61470 38.618 246 126 8 19 259 4 229 2.64e-40 141
MS.gene85901.t1 AT1G06450 34.545 275 151 11 10 278 3 254 1.55e-37 136
MS.gene85901.t1 AT1G27820 36.220 254 135 9 13 259 2 235 3.58e-34 126
MS.gene85901.t1 AT1G27890 37.247 247 130 9 19 259 3 230 1.17e-32 122
MS.gene85901.t1 AT3G44240 35.193 233 130 8 31 260 3 217 2.47e-31 117

Find 56 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCATGGCGCTTATGATTT+TGG 0.117389 5.3:-30734952 MS.gene85901:CDS
AAATACGCTGGAGTAGTATT+TGG 0.224745 5.3:-30734655 MS.gene85901:CDS
TGAATATGGTGAATATTCTT+TGG 0.278766 5.3:-30735352 MS.gene85901:CDS
CGTGATGTTCTTCCTGAATA+TGG 0.278966 5.3:-30735366 MS.gene85901:CDS
CAATCATTGTCCGAGAAGTT+TGG 0.285300 5.3:-30735422 MS.gene85901:CDS
CTTGGACTCACTTTAATAGA+TGG 0.314324 5.3:-30735204 MS.gene85901:CDS
AAGAAATCTGCCTGATAGTT+TGG 0.321613 5.3:-30734905 MS.gene85901:CDS
CAAACTTCTCGGACAATGAT+TGG 0.324520 5.3:+30735423 None:intergenic
GCTGAACTAATGTTGACTTC+TGG 0.360897 5.3:-30735009 MS.gene85901:CDS
TCGATAGACACCGAGTTTCC+TGG 0.362514 5.3:-30735327 MS.gene85901:CDS
AATCATTGTCCGAGAAGTTT+GGG 0.374317 5.3:-30735421 MS.gene85901:CDS
CGATTATCGGTGTCAAAATC+AGG 0.397384 5.3:+30735168 None:intergenic
AGTTTAAGATCATCAACATT+TGG 0.398324 5.3:+30735234 None:intergenic
ACACCGATAATCGCTACATT+TGG 0.399135 5.3:-30735158 MS.gene85901:CDS
AGGTGGCGATGGTCGACTTT+TGG 0.407532 5.3:+30735291 None:intergenic
CTCAATGTGGATCGGGTTGT+TGG 0.408633 5.3:-30734769 MS.gene85901:CDS
TTGCCAAATGTAGCGATTAT+CGG 0.410093 5.3:+30735155 None:intergenic
AAAGAATATTCACCATATTC+AGG 0.416250 5.3:+30735354 None:intergenic
CATTGTATGGTGGTCTTGAT+CGG 0.438293 5.3:-30734804 MS.gene85901:CDS
AACTATCAGGCAGATTTCTT+CGG 0.444161 5.3:+30734908 None:intergenic
CGCTACAGCAATGCATTGTA+TGG 0.451428 5.3:-30734817 MS.gene85901:CDS
TTGATAATTCTTCACTCAGC+AGG 0.454448 5.3:+30735448 None:intergenic
AGTTGTGTGCCCAAACTTCT+CGG 0.466420 5.3:+30735412 None:intergenic
TATTCAAGAAATCAATGACT+TGG 0.469568 5.3:-30734981 MS.gene85901:CDS
TGTCAACAAGCTATCGGATC+CGG 0.479582 5.3:+30734732 None:intergenic
ATGGCAGACGTTTCATAAGT+TGG 0.479969 5.3:-30734710 MS.gene85901:CDS
TGTAGTAATCAGAGGGTTGA+AGG 0.480186 5.3:+30735271 None:intergenic
ATTGTATGGTGGTCTTGATC+GGG 0.514058 5.3:-30734803 MS.gene85901:CDS
AAGTACACTCAATGTGGATC+GGG 0.524067 5.3:-30734776 MS.gene85901:CDS
TTTGGTGCATGGATAACTCC+AGG 0.535086 5.3:+30735309 None:intergenic
CAATAGAATCCTTGTTGTGA+GGG 0.537270 5.3:+30735100 None:intergenic
TTCAATCGTTGTGTCTCTCA+AGG 0.540052 5.3:-30735051 MS.gene85901:CDS
GTTGGAAGGTCTCATCAATC+CGG 0.540408 5.3:-30734751 MS.gene85901:CDS
ATGTGGATCGGGTTGTTGGA+AGG 0.540595 5.3:-30734765 MS.gene85901:CDS
ATTCAAGAAATCAATGACTT+GGG 0.542864 5.3:-30734980 MS.gene85901:CDS
GATCTTAAACTCATCCAACT+TGG 0.545194 5.3:-30735222 MS.gene85901:CDS
CAAGTACACTCAATGTGGAT+CGG 0.548190 5.3:-30734777 MS.gene85901:CDS
CTGCCATGTCAACAAGCTAT+CGG 0.556385 5.3:+30734726 None:intergenic
CTATTAAAGTGAGTCCAAGT+TGG 0.558411 5.3:+30735208 None:intergenic
CAGAGGGTTGAAGGTGGCGA+TGG 0.559485 5.3:+30735280 None:intergenic
CATACAATGCATTGCTGTAG+CGG 0.560379 5.3:+30734818 None:intergenic
TCAACATTAGTTCAGCAAAA+CGG 0.564358 5.3:+30735016 None:intergenic
GAAGAACATCACGAATGAGA+TGG 0.565749 5.3:+30735376 None:intergenic
ATTGATTTACTTCGTCGACA+AGG 0.582823 5.3:-30735081 MS.gene85901:CDS
GATCCGATAGCTTGTTGACA+TGG 0.582907 5.3:-30734729 MS.gene85901:CDS
TTGATTTACTTCGTCGACAA+GGG 0.585861 5.3:-30735080 MS.gene85901:CDS
ATGGATAACTCCAGGAAACT+CGG 0.585861 5.3:+30735317 None:intergenic
GACGTATCTGTAGTAATCAG+AGG 0.593946 5.3:+30735263 None:intergenic
ACGTATCTGTAGTAATCAGA+GGG 0.599199 5.3:+30735264 None:intergenic
TCAATAGAATCCTTGTTGTG+AGG 0.602182 5.3:+30735099 None:intergenic
CTCACTTTAATAGATGGTTG+CGG 0.607202 5.3:-30735198 MS.gene85901:CDS
TACAGCAATGCATTGTATGG+TGG 0.620242 5.3:-30734814 MS.gene85901:CDS
GGTTGCAAGTACACTCAATG+TGG 0.665808 5.3:-30734782 MS.gene85901:CDS
TGAGCATGACCCTCACAACA+AGG 0.672608 5.3:-30735109 MS.gene85901:CDS
TATCGGTGTCAAAATCAGGA+AGG 0.683593 5.3:+30735172 None:intergenic
AGTAATCAGAGGGTTGAAGG+TGG 0.690515 5.3:+30735274 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AACATTTTGGAAATGTTATT+TGG - chr5.3:30735227-30735246 MS.gene85901:CDS 20.0%
! AAAGAATATTCACCATATTC+AGG + chr5.3:30734747-30734766 None:intergenic 25.0%
! AAAGAATTTGAAAAATACGC+TGG - chr5.3:30735431-30735450 MS.gene85901:CDS 25.0%
! ATTCAAGAAATCAATGACTT+GGG - chr5.3:30735118-30735137 MS.gene85901:CDS 25.0%
! TATTCAAGAAATCAATGACT+TGG - chr5.3:30735117-30735136 MS.gene85901:CDS 25.0%
! TGAATATGGTGAATATTCTT+TGG - chr5.3:30734746-30734765 MS.gene85901:CDS 25.0%
!! AGTTTAAGATCATCAACATT+TGG + chr5.3:30734867-30734886 None:intergenic 25.0%
!!! TTTTGGAAATGTTATTTGGA+AGG - chr5.3:30735231-30735250 MS.gene85901:CDS 25.0%
AAAAACTCTTCCAAACTATC+AGG + chr5.3:30735206-30735225 None:intergenic 30.0%
TCAACATTAGTTCAGCAAAA+CGG + chr5.3:30735085-30735104 None:intergenic 30.0%
! GGAAGAGTTTTTGAACATTT+TGG - chr5.3:30735214-30735233 MS.gene85901:CDS 30.0%
AAATACGCTGGAGTAGTATT+TGG - chr5.3:30735443-30735462 MS.gene85901:CDS 35.0%
AACTATCAGGCAGATTTCTT+CGG + chr5.3:30735193-30735212 None:intergenic 35.0%
AAGAAATCTGCCTGATAGTT+TGG - chr5.3:30735193-30735212 MS.gene85901:CDS 35.0%
AATCATTGTCCGAGAAGTTT+GGG - chr5.3:30734677-30734696 MS.gene85901:CDS 35.0%
ACGTATCTGTAGTAATCAGA+GGG + chr5.3:30734837-30734856 None:intergenic 35.0%
CTATTAAAGTGAGTCCAAGT+TGG + chr5.3:30734893-30734912 None:intergenic 35.0%
CTCACTTTAATAGATGGTTG+CGG - chr5.3:30734900-30734919 MS.gene85901:CDS 35.0%
CTTGGACTCACTTTAATAGA+TGG - chr5.3:30734894-30734913 MS.gene85901:CDS 35.0%
GATCTTAAACTCATCCAACT+TGG - chr5.3:30734876-30734895 MS.gene85901:CDS 35.0%
TTGATTTACTTCGTCGACAA+GGG - chr5.3:30735018-30735037 MS.gene85901:CDS 35.0%
TTGCCAAATGTAGCGATTAT+CGG + chr5.3:30734946-30734965 None:intergenic 35.0%
! ATTGATTTACTTCGTCGACA+AGG - chr5.3:30735017-30735036 MS.gene85901:CDS 35.0%
! CAATAGAATCCTTGTTGTGA+GGG + chr5.3:30735001-30735020 None:intergenic 35.0%
! CGCTTATGATTTTGGATACT+TGG - chr5.3:30735154-30735173 MS.gene85901:CDS 35.0%
! TCAATAGAATCCTTGTTGTG+AGG + chr5.3:30735002-30735021 None:intergenic 35.0%
! TTGATAATTCTTCACTCAGC+AGG + chr5.3:30734653-30734672 None:intergenic 35.0%
! TTTCATGGCGCTTATGATTT+TGG - chr5.3:30735146-30735165 MS.gene85901:CDS 35.0%
AAGTACACTCAATGTGGATC+GGG - chr5.3:30735322-30735341 MS.gene85901:CDS 40.0%
ACACCGATAATCGCTACATT+TGG - chr5.3:30734940-30734959 MS.gene85901:CDS 40.0%
ATGGATAACTCCAGGAAACT+CGG + chr5.3:30734784-30734803 None:intergenic 40.0%
ATGGCAGACGTTTCATAAGT+TGG - chr5.3:30735388-30735407 MS.gene85901:CDS 40.0%
CAAACTTCTCGGACAATGAT+TGG + chr5.3:30734678-30734697 None:intergenic 40.0%
CAAGTACACTCAATGTGGAT+CGG - chr5.3:30735321-30735340 MS.gene85901:CDS 40.0%
CAATCATTGTCCGAGAAGTT+TGG - chr5.3:30734676-30734695 MS.gene85901:CDS 40.0%
CATACAATGCATTGCTGTAG+CGG + chr5.3:30735283-30735302 None:intergenic 40.0%
CGTGATGTTCTTCCTGAATA+TGG - chr5.3:30734732-30734751 MS.gene85901:CDS 40.0%
GAAGAACATCACGAATGAGA+TGG + chr5.3:30734725-30734744 None:intergenic 40.0%
GACGTATCTGTAGTAATCAG+AGG + chr5.3:30734838-30734857 None:intergenic 40.0%
TACAGCAATGCATTGTATGG+TGG - chr5.3:30735284-30735303 MS.gene85901:CDS 40.0%
TGTAGTAATCAGAGGGTTGA+AGG + chr5.3:30734830-30734849 None:intergenic 40.0%
TTCAATCGTTGTGTCTCTCA+AGG - chr5.3:30735047-30735066 MS.gene85901:CDS 40.0%
! ATTGTATGGTGGTCTTGATC+GGG - chr5.3:30735295-30735314 MS.gene85901:CDS 40.0%
! CATTGTATGGTGGTCTTGAT+CGG - chr5.3:30735294-30735313 MS.gene85901:CDS 40.0%
!! ATGACTTGGGTGACTTTTCA+TGG - chr5.3:30735131-30735150 MS.gene85901:CDS 40.0%
!! CGATTATCGGTGTCAAAATC+AGG + chr5.3:30734933-30734952 None:intergenic 40.0%
!! GCTGAACTAATGTTGACTTC+TGG - chr5.3:30735089-30735108 MS.gene85901:CDS 40.0%
!! TATCGGTGTCAAAATCAGGA+AGG + chr5.3:30734929-30734948 None:intergenic 40.0%
AGTAATCAGAGGGTTGAAGG+TGG + chr5.3:30734827-30734846 None:intergenic 45.0%
AGTTGTGTGCCCAAACTTCT+CGG + chr5.3:30734689-30734708 None:intergenic 45.0%
CGCTACAGCAATGCATTGTA+TGG - chr5.3:30735281-30735300 MS.gene85901:CDS 45.0%
CTGCCATGTCAACAAGCTAT+CGG + chr5.3:30735375-30735394 None:intergenic 45.0%
GGTTGCAAGTACACTCAATG+TGG - chr5.3:30735316-30735335 MS.gene85901:CDS 45.0%
GTTGGAAGGTCTCATCAATC+CGG - chr5.3:30735347-30735366 MS.gene85901:CDS 45.0%
TGTCAACAAGCTATCGGATC+CGG + chr5.3:30735369-30735388 None:intergenic 45.0%
! TTTGGTGCATGGATAACTCC+AGG + chr5.3:30734792-30734811 None:intergenic 45.0%
!! GATCCGATAGCTTGTTGACA+TGG - chr5.3:30735369-30735388 MS.gene85901:CDS 45.0%
TCGATAGACACCGAGTTTCC+TGG - chr5.3:30734771-30734790 MS.gene85901:CDS 50.0%
TGAGCATGACCCTCACAACA+AGG - chr5.3:30734989-30735008 MS.gene85901:CDS 50.0%
! ATGTGGATCGGGTTGTTGGA+AGG - chr5.3:30735333-30735352 MS.gene85901:CDS 50.0%
! CTCAATGTGGATCGGGTTGT+TGG - chr5.3:30735329-30735348 MS.gene85901:CDS 50.0%
!! GATGGTCGACTTTTGGTGCA+TGG + chr5.3:30734803-30734822 None:intergenic 50.0%
!! AGGTGGCGATGGTCGACTTT+TGG + chr5.3:30734810-30734829 None:intergenic 55.0%
CAGAGGGTTGAAGGTGGCGA+TGG + chr5.3:30734821-30734840 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 30734636 30735484 30734636 ID=MS.gene85901
chr5.3 mRNA 30734636 30735484 30734636 ID=MS.gene85901.t1;Parent=MS.gene85901
chr5.3 exon 30734636 30735484 30734636 ID=MS.gene85901.t1.exon1;Parent=MS.gene85901.t1
chr5.3 CDS 30734636 30735484 30734636 ID=cds.MS.gene85901.t1;Parent=MS.gene85901.t1
Gene Sequence

>MS.gene85901

ATGACAAAAACGTTCCTGCTGAGTGAAGAATTATCAAAACCAATCATTGTCCGAGAAGTTTGGGCACACAACTTAGAGAATGAATTCCATCTCATTCGTGATGTTCTTCCTGAATATGGTGAATATTCTTTGGTCTCGATAGACACCGAGTTTCCTGGAGTTATCCATGCACCAAAAGTCGACCATCGCCACCTTCAACCCTCTGATTACTACAGATACGTCTTAAAGCCAAATGTTGATGATCTTAAACTCATCCAACTTGGACTCACTTTAATAGATGGTTGCGGTCACCTTCCTGATTTTGACACCGATAATCGCTACATTTGGCAATTCAACTTCTGTGACTTCAACGTTGAGCATGACCCTCACAACAAGGATTCTATTGATTTACTTCGTCGACAAGGGATTGACTTCAATCGTTGTGTCTCTCAAGGTGTCGATTCATTCCGTTTTGCTGAACTAATGTTGACTTCTGGACTTCTATTCAAGAAATCAATGACTTGGGTGACTTTTCATGGCGCTTATGATTTTGGATACTTGGTGAAGATATTGATCCGAAGAAATCTGCCTGATAGTTTGGAAGAGTTTTTGAACATTTTGGAAATGTTATTTGGAAGGAATGTCTATGATTTGAAACATATGATCCGCTACAGCAATGCATTGTATGGTGGTCTTGATCGGGTTGCAAGTACACTCAATGTGGATCGGGTTGTTGGAAGGTCTCATCAATCCGGATCCGATAGCTTGTTGACATGGCAGACGTTTCATAAGTTGGTGCAAACACATTTCAGTCACAAAGAATTTGAAAAATACGCTGGAGTAGTATTTGGATTAGAAGTTGCTCGATAA
Protein sequence

>MS.gene85901.t1

MTKTFLLSEELSKPIIVREVWAHNLENEFHLIRDVLPEYGEYSLVSIDTEFPGVIHAPKVDHRHLQPSDYYRYVLKPNVDDLKLIQLGLTLIDGCGHLPDFDTDNRYIWQFNFCDFNVEHDPHNKDSIDLLRRQGIDFNRCVSQGVDSFRFAELMLTSGLLFKKSMTWVTFHGAYDFGYLVKILIRRNLPDSLEEFLNILEMLFGRNVYDLKHMIRYSNALYGGLDRVASTLNVDRVVGRSHQSGSDSLLTWQTFHKLVQTHFSHKEFEKYAGVVFGLEVAR