AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene85903

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.gene85903.t1 AT5G22250 56.569 274 113 3 10 280 7 277 6.55e-105 306
MS.gene85903.t1 AT3G44260 55.762 269 110 5 15 280 17 279 1.16e-98 291
MS.gene85903.t1 AT5G10960 45.818 275 140 6 7 280 1 267 1.06e-79 242
MS.gene85903.t1 AT2G32070 47.940 267 130 6 15 280 10 268 2.40e-79 241
MS.gene85903.t1 AT1G80780 45.865 266 136 5 15 280 10 267 5.77e-75 230
MS.gene85903.t1 AT1G80780 45.865 266 136 5 15 280 10 267 5.77e-75 230
MS.gene85903.t1 AT1G80780 45.865 266 136 5 15 280 10 267 1.12e-74 230
MS.gene85903.t1 AT1G15920 44.964 278 143 6 9 282 8 279 2.44e-71 221
MS.gene85903.t1 AT1G15920 44.964 278 143 6 9 282 8 279 2.44e-71 221
MS.gene85903.t1 AT1G61470 38.618 246 126 8 19 259 4 229 6.90e-41 143
MS.gene85903.t1 AT1G06450 34.307 274 153 11 10 278 3 254 4.55e-37 135
MS.gene85903.t1 AT1G27820 35.878 262 141 9 13 267 2 243 1.16e-34 127
MS.gene85903.t1 AT1G27890 36.863 255 136 9 19 267 3 238 2.13e-33 124
MS.gene85903.t1 AT3G44240 35.193 233 130 8 31 260 3 217 2.15e-31 117

Find 59 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCATGGCGCTTATGATTT+TGG 0.117389 5.3:-30762740 MS.gene85903:CDS
AAATACGCTGGAGTAGTATT+TGG 0.224745 5.3:-30762443 MS.gene85903:CDS
TGAATATGGTGAATATTCTT+TGG 0.278766 5.3:-30763140 MS.gene85903:CDS
CGTGATGTTCTTCCTGAATA+TGG 0.278966 5.3:-30763154 MS.gene85903:CDS
CAAACTTCTCTGACAATGAT+TGG 0.307379 5.3:+30763211 None:intergenic
CTTGGACTCACTTTAATAGA+TGG 0.314324 5.3:-30762992 MS.gene85903:CDS
CAATCATTGTCAGAGAAGTT+TGG 0.315172 5.3:-30763210 MS.gene85903:CDS
AAGAAATCTGCCTGATAGTT+TGG 0.321613 5.3:-30762693 MS.gene85903:CDS
AACATCTTGGAAATGTTATT+CGG 0.335246 5.3:-30762659 MS.gene85903:CDS
TCGATAGACACCGAGTTTCC+TGG 0.362514 5.3:-30763115 MS.gene85903:CDS
AATCATTGTCAGAGAAGTTT+GGG 0.392755 5.3:-30763209 MS.gene85903:CDS
CGATTATCGGTGTCAAAATC+AGG 0.397384 5.3:+30762956 None:intergenic
AGTTTAAGATCATCAACATT+TGG 0.398324 5.3:+30763022 None:intergenic
ACACCGATAATCGCTACATT+TGG 0.399135 5.3:-30762946 MS.gene85903:CDS
AGGTGGCGATGGTCGACTTT+TGG 0.407532 5.3:+30763079 None:intergenic
TTGCCAAATGTAGCGATTAT+CGG 0.410093 5.3:+30762943 None:intergenic
AAAGAATATTCACCATATTC+AGG 0.416250 5.3:+30763142 None:intergenic
CATTGTATGGTGGTCTTGAT+CGG 0.438293 5.3:-30762592 MS.gene85903:CDS
AACTATCAGGCAGATTTCTT+CGG 0.444161 5.3:+30762696 None:intergenic
CTCAATGTGGATCGGGCTGT+TGG 0.449645 5.3:-30762557 MS.gene85903:CDS
CGCTACAGCAATGCATTGTA+TGG 0.451428 5.3:-30762605 MS.gene85903:CDS
TGTCAACAAGCTGTCGGATC+CGG 0.457649 5.3:+30762520 None:intergenic
TATTCAAGAAATCAATGACT+TGG 0.469568 5.3:-30762769 MS.gene85903:CDS
ATGGCAGACGTTTCATAAGT+TGG 0.479969 5.3:-30762498 MS.gene85903:CDS
TGTAGTAATCAGAGGGTTGA+AGG 0.480186 5.3:+30763059 None:intergenic
GCTGAACTAATGTTGACGTC+TGG 0.481099 5.3:-30762797 MS.gene85903:CDS
ATTGTATGGTGGTCTTGATC+GGG 0.514058 5.3:-30762591 MS.gene85903:CDS
AAGTACACTCAATGTGGATC+GGG 0.516852 5.3:-30762564 MS.gene85903:CDS
TTGTCGACGAAGCAAATCAA+TGG 0.516920 5.3:+30762871 None:intergenic
ATGTGGATCGGGCTGTTGGA+AGG 0.522206 5.3:-30762553 MS.gene85903:CDS
TTTGGTGCATGGATAACTCC+AGG 0.535086 5.3:+30763097 None:intergenic
GTTGGAAGGTCTCATCAATC+CGG 0.537925 5.3:-30762539 MS.gene85903:CDS
TTCAATCGTTGTGTCTCTCA+AGG 0.540052 5.3:-30762839 MS.gene85903:CDS
ATTCAAGAAATCAATGACTT+GGG 0.542864 5.3:-30762768 MS.gene85903:CDS
GATCTTAAACTCATCCAACT+TGG 0.545194 5.3:-30763010 MS.gene85903:CDS
TCTTGGAAATGTTATTCGGA+AGG 0.546839 5.3:-30762655 MS.gene85903:CDS
CACGCTCAACGTTGAAGTCA+CGG 0.550608 5.3:+30762912 None:intergenic
CAAGTACACTCAATGTGGAT+CGG 0.550934 5.3:-30762565 MS.gene85903:CDS
CAATGGAATCCTTGTTGTGA+GGG 0.555858 5.3:+30762888 None:intergenic
CTATTAAAGTGAGTCCAAGT+TGG 0.558411 5.3:+30762996 None:intergenic
CAGAGGGTTGAAGGTGGCGA+TGG 0.559485 5.3:+30763068 None:intergenic
ATTGATTTGCTTCGTCGACA+AGG 0.559543 5.3:-30762869 MS.gene85903:CDS
CATACAATGCATTGCTGTAG+CGG 0.560379 5.3:+30762606 None:intergenic
TTCGGATCAATATCTTCACC+AGG 0.564436 5.3:+30762714 None:intergenic
GAAGAACATCACGAATGAGA+TGG 0.565749 5.3:+30763164 None:intergenic
TCAACATTAGTTCAGCAAAA+CGG 0.571611 5.3:+30762804 None:intergenic
GATCCGACAGCTTGTTGACA+TGG 0.577163 5.3:-30762517 MS.gene85903:CDS
TTGATTTGCTTCGTCGACAA+GGG 0.585778 5.3:-30762868 MS.gene85903:CDS
ATGGATAACTCCAGGAAACT+CGG 0.585861 5.3:+30763105 None:intergenic
GACGTATCTGTAGTAATCAG+AGG 0.593946 5.3:+30763051 None:intergenic
ACGTATCTGTAGTAATCAGA+GGG 0.599199 5.3:+30763052 None:intergenic
CTCACTTTAATAGATGGTTG+CGG 0.607202 5.3:-30762986 MS.gene85903:CDS
CTGCCATGTCAACAAGCTGT+CGG 0.613501 5.3:+30762514 None:intergenic
TCAATGGAATCCTTGTTGTG+AGG 0.615657 5.3:+30762887 None:intergenic
TACAGCAATGCATTGTATGG+TGG 0.620242 5.3:-30762602 MS.gene85903:CDS
GGTTGCAAGTACACTCAATG+TGG 0.665808 5.3:-30762570 MS.gene85903:CDS
TGAGCGTGACCCTCACAACA+AGG 0.672608 5.3:-30762897 MS.gene85903:CDS
TATCGGTGTCAAAATCAGGA+AGG 0.683593 5.3:+30762960 None:intergenic
AGTAATCAGAGGGTTGAAGG+TGG 0.690515 5.3:+30763062 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGAATATTCACCATATTC+AGG + chr5.3:30762535-30762554 None:intergenic 25.0%
! AACATCTTGGAAATGTTATT+CGG - chr5.3:30763015-30763034 MS.gene85903:CDS 25.0%
! ATTCAAGAAATCAATGACTT+GGG - chr5.3:30762906-30762925 MS.gene85903:CDS 25.0%
! TATTCAAGAAATCAATGACT+TGG - chr5.3:30762905-30762924 MS.gene85903:CDS 25.0%
! TGAATATGGTGAATATTCTT+TGG - chr5.3:30762534-30762553 MS.gene85903:CDS 25.0%
!! AGTTTAAGATCATCAACATT+TGG + chr5.3:30762655-30762674 None:intergenic 25.0%
AAAAACTCTTCCAAACTATC+AGG + chr5.3:30762994-30763013 None:intergenic 30.0%
AATCATTGTCAGAGAAGTTT+GGG - chr5.3:30762465-30762484 MS.gene85903:CDS 30.0%
AGAGAATTTGAAAAATACGC+TGG - chr5.3:30763219-30763238 MS.gene85903:CDS 30.0%
TCAACATTAGTTCAGCAAAA+CGG + chr5.3:30762873-30762892 None:intergenic 30.0%
AAATACGCTGGAGTAGTATT+TGG - chr5.3:30763231-30763250 MS.gene85903:CDS 35.0%
AACTATCAGGCAGATTTCTT+CGG + chr5.3:30762981-30763000 None:intergenic 35.0%
AAGAAATCTGCCTGATAGTT+TGG - chr5.3:30762981-30763000 MS.gene85903:CDS 35.0%
ACGTATCTGTAGTAATCAGA+GGG + chr5.3:30762625-30762644 None:intergenic 35.0%
CAAACTTCTCTGACAATGAT+TGG + chr5.3:30762466-30762485 None:intergenic 35.0%
CAATCATTGTCAGAGAAGTT+TGG - chr5.3:30762464-30762483 MS.gene85903:CDS 35.0%
CTATTAAAGTGAGTCCAAGT+TGG + chr5.3:30762681-30762700 None:intergenic 35.0%
CTCACTTTAATAGATGGTTG+CGG - chr5.3:30762688-30762707 MS.gene85903:CDS 35.0%
CTTGGACTCACTTTAATAGA+TGG - chr5.3:30762682-30762701 MS.gene85903:CDS 35.0%
GATCTTAAACTCATCCAACT+TGG - chr5.3:30762664-30762683 MS.gene85903:CDS 35.0%
TCTTGGAAATGTTATTCGGA+AGG - chr5.3:30763019-30763038 MS.gene85903:CDS 35.0%
TTGCCAAATGTAGCGATTAT+CGG + chr5.3:30762734-30762753 None:intergenic 35.0%
! GGAAGAGTTTTTGAACATCT+TGG - chr5.3:30763002-30763021 MS.gene85903:CDS 35.0%
! TTTCATGGCGCTTATGATTT+TGG - chr5.3:30762934-30762953 MS.gene85903:CDS 35.0%
AAGTACACTCAATGTGGATC+GGG - chr5.3:30763110-30763129 MS.gene85903:CDS 40.0%
ACACCGATAATCGCTACATT+TGG - chr5.3:30762728-30762747 MS.gene85903:CDS 40.0%
ATGGATAACTCCAGGAAACT+CGG + chr5.3:30762572-30762591 None:intergenic 40.0%
ATGGCAGACGTTTCATAAGT+TGG - chr5.3:30763176-30763195 MS.gene85903:CDS 40.0%
CAAGTACACTCAATGTGGAT+CGG - chr5.3:30763109-30763128 MS.gene85903:CDS 40.0%
CATACAATGCATTGCTGTAG+CGG + chr5.3:30763071-30763090 None:intergenic 40.0%
CGTGATGTTCTTCCTGAATA+TGG - chr5.3:30762520-30762539 MS.gene85903:CDS 40.0%
GAAGAACATCACGAATGAGA+TGG + chr5.3:30762513-30762532 None:intergenic 40.0%
GACGTATCTGTAGTAATCAG+AGG + chr5.3:30762626-30762645 None:intergenic 40.0%
TACAGCAATGCATTGTATGG+TGG - chr5.3:30763072-30763091 MS.gene85903:CDS 40.0%
TGTAGTAATCAGAGGGTTGA+AGG + chr5.3:30762618-30762637 None:intergenic 40.0%
TTCAATCGTTGTGTCTCTCA+AGG - chr5.3:30762835-30762854 MS.gene85903:CDS 40.0%
TTCGGATCAATATCTTCACC+AGG + chr5.3:30762963-30762982 None:intergenic 40.0%
TTGTCGACGAAGCAAATCAA+TGG + chr5.3:30762806-30762825 None:intergenic 40.0%
! ATTGTATGGTGGTCTTGATC+GGG - chr5.3:30763083-30763102 MS.gene85903:CDS 40.0%
! CAATGGAATCCTTGTTGTGA+GGG + chr5.3:30762789-30762808 None:intergenic 40.0%
! CATTGTATGGTGGTCTTGAT+CGG - chr5.3:30763082-30763101 MS.gene85903:CDS 40.0%
! CGCTTATGATTTTGGATACC+TGG - chr5.3:30762942-30762961 MS.gene85903:CDS 40.0%
! TCAATGGAATCCTTGTTGTG+AGG + chr5.3:30762790-30762809 None:intergenic 40.0%
!! ATGACTTGGGTGACTTTTCA+TGG - chr5.3:30762919-30762938 MS.gene85903:CDS 40.0%
!! ATTGATTTGCTTCGTCGACA+AGG - chr5.3:30762805-30762824 MS.gene85903:CDS 40.0%
!! CGATTATCGGTGTCAAAATC+AGG + chr5.3:30762721-30762740 None:intergenic 40.0%
!! TATCGGTGTCAAAATCAGGA+AGG + chr5.3:30762717-30762736 None:intergenic 40.0%
!! TTGATTTGCTTCGTCGACAA+GGG - chr5.3:30762806-30762825 MS.gene85903:CDS 40.0%
AGTAATCAGAGGGTTGAAGG+TGG + chr5.3:30762615-30762634 None:intergenic 45.0%
CGCTACAGCAATGCATTGTA+TGG - chr5.3:30763069-30763088 MS.gene85903:CDS 45.0%
GCTGAACTAATGTTGACGTC+TGG - chr5.3:30762877-30762896 MS.gene85903:CDS 45.0%
GGTTGCAAGTACACTCAATG+TGG - chr5.3:30763104-30763123 MS.gene85903:CDS 45.0%
GTTGGAAGGTCTCATCAATC+CGG - chr5.3:30763135-30763154 MS.gene85903:CDS 45.0%
! TTTGGTGCATGGATAACTCC+AGG + chr5.3:30762580-30762599 None:intergenic 45.0%
CACGCTCAACGTTGAAGTCA+CGG + chr5.3:30762765-30762784 None:intergenic 50.0%
CTGCCATGTCAACAAGCTGT+CGG + chr5.3:30763163-30763182 None:intergenic 50.0%
TCGATAGACACCGAGTTTCC+TGG - chr5.3:30762559-30762578 MS.gene85903:CDS 50.0%
TGTCAACAAGCTGTCGGATC+CGG + chr5.3:30763157-30763176 None:intergenic 50.0%
!! GATCCGACAGCTTGTTGACA+TGG - chr5.3:30763157-30763176 MS.gene85903:CDS 50.0%
!! GATGGTCGACTTTTGGTGCA+TGG + chr5.3:30762591-30762610 None:intergenic 50.0%
ATGTGGATCGGGCTGTTGGA+AGG - chr5.3:30763121-30763140 MS.gene85903:CDS 55.0%
CTCAATGTGGATCGGGCTGT+TGG - chr5.3:30763117-30763136 MS.gene85903:CDS 55.0%
TGAGCGTGACCCTCACAACA+AGG - chr5.3:30762777-30762796 MS.gene85903:CDS 55.0%
!! AGGTGGCGATGGTCGACTTT+TGG + chr5.3:30762598-30762617 None:intergenic 55.0%
CAGAGGGTTGAAGGTGGCGA+TGG + chr5.3:30762609-30762628 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 30762424 30763272 30762424 ID=MS.gene85903
chr5.3 mRNA 30762424 30763272 30762424 ID=MS.gene85903.t1;Parent=MS.gene85903
chr5.3 exon 30762424 30763272 30762424 ID=MS.gene85903.t1.exon1;Parent=MS.gene85903.t1
chr5.3 CDS 30762424 30763272 30762424 ID=cds.MS.gene85903.t1;Parent=MS.gene85903.t1
Gene Sequence

>MS.gene85903

ATGACAAAAACGTGCATGCTGAGTGAAGAGTTATCGAAACCAATCATTGTCAGAGAAGTTTGGGCACACAACTTAGAGAATGAATTCCATCTCATTCGTGATGTTCTTCCTGAATATGGTGAATATTCTTTGGTCTCGATAGACACCGAGTTTCCTGGAGTTATCCATGCACCAAAAGTCGACCATCGCCACCTTCAACCCTCTGATTACTACAGATACGTCTTAAAGCCAAATGTTGATGATCTTAAACTCATCCAACTTGGACTCACTTTAATAGATGGTTGCGGTCACCTTCCTGATTTTGACACCGATAATCGCTACATTTGGCAATTCAACTTCCGTGACTTCAACGTTGAGCGTGACCCTCACAACAAGGATTCCATTGATTTGCTTCGTCGACAAGGGATTGACTTCAATCGTTGTGTCTCTCAAGGTGTCAATTCATTCCGTTTTGCTGAACTAATGTTGACGTCTGGACTTCTATTCAAGAAATCAATGACTTGGGTGACTTTTCATGGCGCTTATGATTTTGGATACCTGGTGAAGATATTGATCCGAAGAAATCTGCCTGATAGTTTGGAAGAGTTTTTGAACATCTTGGAAATGTTATTCGGAAGGAATGTCTATGATTTGAAACATATGATCCGCTACAGCAATGCATTGTATGGTGGTCTTGATCGGGTTGCAAGTACACTCAATGTGGATCGGGCTGTTGGAAGGTCTCATCAATCCGGATCCGACAGCTTGTTGACATGGCAGACGTTTCATAAGTTGGTGCAAACACATCTCAGTCACAGAGAATTTGAAAAATACGCTGGAGTAGTATTTGGATTAGAAGTTGCTCGATAA
Protein sequence

>MS.gene85903.t1

MTKTCMLSEELSKPIIVREVWAHNLENEFHLIRDVLPEYGEYSLVSIDTEFPGVIHAPKVDHRHLQPSDYYRYVLKPNVDDLKLIQLGLTLIDGCGHLPDFDTDNRYIWQFNFRDFNVERDPHNKDSIDLLRRQGIDFNRCVSQGVNSFRFAELMLTSGLLFKKSMTWVTFHGAYDFGYLVKILIRRNLPDSLEEFLNILEMLFGRNVYDLKHMIRYSNALYGGLDRVASTLNVDRAVGRSHQSGSDSLLTWQTFHKLVQTHLSHREFEKYAGVVFGLEVAR