AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene67544

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene67544.t1 MTR_7g063520 66.798 253 50 3 1 219 1 253 3.29e-102 296
MS.gene67544.t1 MTR_5g080880 38.168 262 113 10 1 220 1 255 1.11e-39 139
MS.gene67544.t1 MTR_5g080870 31.188 202 97 7 47 219 31 219 2.67e-16 76.6
MS.gene67544.t1 MTR_4g006560 29.577 142 85 2 85 219 102 235 1.35e-12 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.gene67544.t1 AT5G02050 36.364 275 110 9 1 219 1 266 2.15e-41 142
MS.gene67544.t1 AT2G39795 36.328 256 119 10 1 219 1 249 2.67e-34 123
MS.gene67544.t1 AT3G55605 49.057 106 53 1 115 219 152 257 4.38e-30 112
MS.gene67544.t1 AT5G05990 47.170 106 55 1 115 219 153 258 5.44e-28 107
MS.gene67544.t1 AT2G39790 33.005 203 95 8 50 219 45 239 4.75e-20 85.5
MS.gene67544.t1 AT1G15870 33.010 103 66 2 118 219 140 240 4.67e-15 72.0
MS.gene67544.t1 AT1G80720 32.692 104 66 3 118 219 139 240 5.16e-11 60.8
MS.gene67544.t1 AT1G80720 32.692 104 66 3 118 219 87 188 7.97e-11 59.7

Find 46 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGAGTGTGTCTGGAGTTT+GGG 0.192697 5.4:-15128957 MS.gene67544:CDS
TTGATAAGGTTAGGATTAAT+TGG 0.252499 5.4:-15128921 MS.gene67544:CDS
AATGGAGTGTGTCTGGAGTT+TGG 0.285363 5.4:-15128958 MS.gene67544:CDS
TAGCAAATCTTTAATTCCTT+TGG 0.316098 5.4:-15129001 MS.gene67544:CDS
ACTTGTGAAAAGCCTCTTGC+AGG 0.359866 5.4:+15128751 None:intergenic
ATATCTCAATGAAGCTCTTC+AGG 0.390493 5.4:+15128631 None:intergenic
TAGACGAGGAATGTCGATTC+AGG 0.392577 5.4:-15128858 MS.gene67544:intron
CAAAGGAAATGGAGTGTGTC+TGG 0.417993 5.4:-15128965 MS.gene67544:CDS
AGCTGGTCTTCAGATTCATC+AGG 0.457345 5.4:+15128883 None:intergenic
GAGAGGGACTGCGGCAGCAG+TGG 0.463811 5.4:+15129660 None:intergenic
TTAGGTTGGGTGTTATCCCT+CGG 0.486971 5.4:+15128718 None:intergenic
CAAAGACAACAAGGAACACT+TGG 0.495891 5.4:-15128667 MS.gene67544:CDS
TGCGCTGTGGAAGGTTCTGT+TGG 0.520863 5.4:+15129612 None:intergenic
AATTAATCCTAACCTTATCA+AGG 0.522305 5.4:+15128923 None:intergenic
GACATTCCTCGTCTACCAGC+TGG 0.533874 5.4:+15128866 None:intergenic
TGATGAATCTGAAGACCAGC+TGG 0.536120 5.4:-15128881 MS.gene67544:CDS
CACAGTTGATTTCAGTGTCA+AGG 0.537097 5.4:+15129494 None:intergenic
AACGGCGGTTGCGCTGTGGA+AGG 0.541938 5.4:+15129603 None:intergenic
TGAAATCAACTGTGCTCTTG+AGG 0.545251 5.4:-15129485 MS.gene67544:CDS
TTGCTGACGCACGGTGAGAG+AGG 0.549631 5.4:+15129638 None:intergenic
TCTGTGGCGAAGGAGGTTAA+CGG 0.551979 5.4:+15129585 None:intergenic
CGAAGGAGAGTATCATCTGC+GGG 0.556549 5.4:+15129520 None:intergenic
TGGTTTCTCTGTGGCGAAGG+AGG 0.561688 5.4:+15129578 None:intergenic
CTGCGGCAGCAGTGGCGCGA+CGG 0.566342 5.4:+15129668 None:intergenic
GAGTGGTTTCTCTGTGGCGA+AGG 0.568348 5.4:+15129575 None:intergenic
TCCTCAACTGAGTGAGGACG+AGG 0.570977 5.4:-15129055 MS.gene67544:CDS
TGTTGGAAGTTGCTGACGCA+CGG 0.582391 5.4:+15129629 None:intergenic
GTGAGAGAGGAGAGGGACTG+CGG 0.586728 5.4:+15129651 None:intergenic
CACAAGTATCTCGAGATCCG+AGG 0.586948 5.4:-15128735 MS.gene67544:CDS
GGTTAACGGCGGTTGCGCTG+TGG 0.599839 5.4:+15129599 None:intergenic
ACGCACGGTGAGAGAGGAGA+GGG 0.615081 5.4:+15129644 None:intergenic
ACAAGTATCTCGAGATCCGA+GGG 0.616212 5.4:-15128734 MS.gene67544:CDS
TCCTCGTCCTCACTCAGTTG+AGG 0.617239 5.4:+15129054 None:intergenic
TGAAGACCAGCTGGTAGACG+AGG 0.628324 5.4:-15128872 MS.gene67544:CDS
AGTGTATCCTCAACTGAGTG+AGG 0.633940 5.4:-15129061 MS.gene67544:CDS
TGGAGTGTGTCTGGAGTTTG+GGG 0.633955 5.4:-15128956 MS.gene67544:CDS
TTTCAGTGTCAAGGACTCGA+AGG 0.640274 5.4:+15129503 None:intergenic
TTTGGATGATAACCTGCAAG+AGG 0.640299 5.4:-15128763 MS.gene67544:CDS
GACGCACGGTGAGAGAGGAG+AGG 0.646844 5.4:+15129643 None:intergenic
CATGTTAAACAAAGACAACA+AGG 0.647062 5.4:-15128676 MS.gene67544:CDS
ACAACAAGGAACACTTGGTG+TGG 0.651165 5.4:-15128662 MS.gene67544:CDS
TTGAAAACAGACACAACCAA+AGG 0.667458 5.4:+15128985 None:intergenic
ACGAGAGGGTACAAAATGAG+TGG 0.672739 5.4:+15129558 None:intergenic
CAAAATGAGTGGTTTCTCTG+TGG 0.680224 5.4:+15129569 None:intergenic
TCGAAGGAGAGTATCATCTG+CGG 0.691462 5.4:+15129519 None:intergenic
GTGGCGAAGGAGGTTAACGG+CGG 0.745353 5.4:+15129588 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAGGTCATTTAAAAATA+CGG + chr5.4:15128961-15128980 None:intergenic 15.0%
!! AAATATAAACAAAAATGGAG+TGG + chr5.4:15128934-15128953 None:intergenic 20.0%
!! ACTAAAAGATCAATAACTTA+GGG + chr5.4:15128896-15128915 None:intergenic 20.0%
!! GAGTGAAATATAAACAAAAA+TGG + chr5.4:15128939-15128958 None:intergenic 20.0%
!! TAAATCCAGACTTATAAAAT+AGG + chr5.4:15128977-15128996 None:intergenic 20.0%
! AATTAATCCTAACCTTATCA+AGG + chr5.4:15129397-15129416 None:intergenic 25.0%
! CACTAAAAGATCAATAACTT+AGG + chr5.4:15128897-15128916 None:intergenic 25.0%
! TAGCAAATCTTTAATTCCTT+TGG - chr5.4:15129316-15129335 MS.gene67544:intron 25.0%
! TTGATAAGGTTAGGATTAAT+TGG - chr5.4:15129396-15129415 MS.gene67544:intron 25.0%
!! AATGACCTATTTTATAAGTC+TGG - chr5.4:15128969-15128988 MS.gene67544:CDS 25.0%
!! CTAAGTTATTGATCTTTTAG+TGG - chr5.4:15128895-15128914 MS.gene67544:CDS 25.0%
!! TTTTGCAATTATTTACGTGT+AGG - chr5.4:15129028-15129047 MS.gene67544:CDS 25.0%
!!! TGTTATTTTTTGCAGTGATT+TGG - chr5.4:15129536-15129555 MS.gene67544:CDS 25.0%
AGTTGAAAAAATCTTTCTCC+AGG + chr5.4:15129194-15129213 None:intergenic 30.0%
ATCTCAAAAGGAAAATCACA+AGG + chr5.4:15129161-15129180 None:intergenic 30.0%
ATTCCTGCAAAAATTTGGTT+AGG + chr5.4:15129620-15129639 None:intergenic 30.0%
CATGTATTCCTGCAAAAATT+TGG + chr5.4:15129625-15129644 None:intergenic 30.0%
CATGTTAAACAAAGACAACA+AGG - chr5.4:15129641-15129660 MS.gene67544:CDS 30.0%
GTTGAAAAAATCTTTCTCCA+GGG + chr5.4:15129193-15129212 None:intergenic 30.0%
TGCAAAAATTTGGTTAGGTT+GGG + chr5.4:15129615-15129634 None:intergenic 30.0%
!! GGATTTATTTTTCTCTGTCT+TGG - chr5.4:15128990-15129009 MS.gene67544:CDS 30.0%
!!! TGATTTTCCTTTTGAGATTG+TGG - chr5.4:15129163-15129182 MS.gene67544:intron 30.0%
AATCACAAGGAAATTCAAGC+TGG + chr5.4:15129148-15129167 None:intergenic 35.0%
ATATCTCAATGAAGCTCTTC+AGG + chr5.4:15129689-15129708 None:intergenic 35.0%
CTGCAAAAATTTGGTTAGGT+TGG + chr5.4:15129616-15129635 None:intergenic 35.0%
TTGAAAACAGACACAACCAA+AGG + chr5.4:15129335-15129354 None:intergenic 35.0%
! CAACCTAACCAAATTTTTGC+AGG - chr5.4:15129614-15129633 MS.gene67544:CDS 35.0%
! CTGTTTTCCTTGATAAGGTT+AGG - chr5.4:15129387-15129406 MS.gene67544:intron 35.0%
! GTGTCTGTTTTCAAAGGAAA+TGG - chr5.4:15129341-15129360 MS.gene67544:intron 35.0%
! TTGGTTGTGTCTGTTTTCAA+AGG - chr5.4:15129335-15129354 MS.gene67544:intron 35.0%
CAAAATGAGTGGTTTCTCTG+TGG + chr5.4:15128751-15128770 None:intergenic 40.0%
CAAAGACAACAAGGAACACT+TGG - chr5.4:15129650-15129669 MS.gene67544:CDS 40.0%
TGAAATCAACTGTGCTCTTG+AGG - chr5.4:15128832-15128851 MS.gene67544:intron 40.0%
TTTGGATGATAACCTGCAAG+AGG - chr5.4:15129554-15129573 MS.gene67544:CDS 40.0%
! CACAGTTGATTTCAGTGTCA+AGG + chr5.4:15128826-15128845 None:intergenic 40.0%
! GGTGACTGTTTTCCTTGATA+AGG - chr5.4:15129382-15129401 MS.gene67544:intron 40.0%
ACAAGTATCTCGAGATCCGA+GGG - chr5.4:15129583-15129602 MS.gene67544:CDS 45.0%
ACTTGTGAAAAGCCTCTTGC+AGG + chr5.4:15129569-15129588 None:intergenic 45.0%
AGTGTATCCTCAACTGAGTG+AGG - chr5.4:15129256-15129275 MS.gene67544:intron 45.0%
CAAAGGAAATGGAGTGTGTC+TGG - chr5.4:15129352-15129371 MS.gene67544:intron 45.0%
GGGTTGTCCACAATCTCAAA+AGG + chr5.4:15129173-15129192 None:intergenic 45.0%
TGATGAATCTGAAGACCAGC+TGG - chr5.4:15129436-15129455 MS.gene67544:intron 45.0%
TTTCAGTGTCAAGGACTCGA+AGG + chr5.4:15128817-15128836 None:intergenic 45.0%
! AATGGAGTGTGTCTGGAGTT+TGG - chr5.4:15129359-15129378 MS.gene67544:intron 45.0%
! ACAACAAGGAACACTTGGTG+TGG - chr5.4:15129655-15129674 MS.gene67544:CDS 45.0%
! ACGAGAGGGTACAAAATGAG+TGG + chr5.4:15128762-15128781 None:intergenic 45.0%
! ATGGAGTGTGTCTGGAGTTT+GGG - chr5.4:15129360-15129379 MS.gene67544:intron 45.0%
! TTTGAGATTGTGGACAACCC+TGG - chr5.4:15129173-15129192 MS.gene67544:intron 45.0%
!! AGCTGGTCTTCAGATTCATC+AGG + chr5.4:15129437-15129456 None:intergenic 45.0%
!! TAGACGAGGAATGTCGATTC+AGG - chr5.4:15129459-15129478 MS.gene67544:CDS 45.0%
!! TCGAAGGAGAGTATCATCTG+CGG + chr5.4:15128801-15128820 None:intergenic 45.0%
!! TTAGGTTGGGTGTTATCCCT+CGG + chr5.4:15129602-15129621 None:intergenic 45.0%
CACAAGTATCTCGAGATCCG+AGG - chr5.4:15129582-15129601 MS.gene67544:CDS 50.0%
TCTGTGGCGAAGGAGGTTAA+CGG + chr5.4:15128735-15128754 None:intergenic 50.0%
TGTTGGAAGTTGCTGACGCA+CGG + chr5.4:15128691-15128710 None:intergenic 50.0%
! AGTTTTCGCGAAGCTACGAG+AGG + chr5.4:15128777-15128796 None:intergenic 50.0%
! GTTTTCGCGAAGCTACGAGA+GGG + chr5.4:15128776-15128795 None:intergenic 50.0%
! TGGAGTGTGTCTGGAGTTTG+GGG - chr5.4:15129361-15129380 MS.gene67544:intron 50.0%
!! CGAAGGAGAGTATCATCTGC+GGG + chr5.4:15128800-15128819 None:intergenic 50.0%
GACATTCCTCGTCTACCAGC+TGG + chr5.4:15129454-15129473 None:intergenic 55.0%
GAGTGGTTTCTCTGTGGCGA+AGG + chr5.4:15128745-15128764 None:intergenic 55.0%
TCCTCAACTGAGTGAGGACG+AGG - chr5.4:15129262-15129281 MS.gene67544:intron 55.0%
TCCTCGTCCTCACTCAGTTG+AGG + chr5.4:15129266-15129285 None:intergenic 55.0%
TGAAGACCAGCTGGTAGACG+AGG - chr5.4:15129445-15129464 MS.gene67544:intron 55.0%
TGCGCTGTGGAAGGTTCTGT+TGG + chr5.4:15128708-15128727 None:intergenic 55.0%
TGGTTTCTCTGTGGCGAAGG+AGG + chr5.4:15128742-15128761 None:intergenic 55.0%
ACGCACGGTGAGAGAGGAGA+GGG + chr5.4:15128676-15128695 None:intergenic 60.0%
GTGAGAGAGGAGAGGGACTG+CGG + chr5.4:15128669-15128688 None:intergenic 60.0%
GTGGCGAAGGAGGTTAACGG+CGG + chr5.4:15128732-15128751 None:intergenic 60.0%
TTGCTGACGCACGGTGAGAG+AGG + chr5.4:15128682-15128701 None:intergenic 60.0%
AACGGCGGTTGCGCTGTGGA+AGG + chr5.4:15128717-15128736 None:intergenic 65.0%
GACGCACGGTGAGAGAGGAG+AGG + chr5.4:15128677-15128696 None:intergenic 65.0%
GGTTAACGGCGGTTGCGCTG+TGG + chr5.4:15128721-15128740 None:intergenic 65.0%
GAGAGGGACTGCGGCAGCAG+TGG + chr5.4:15128660-15128679 None:intergenic 70.0%
CTGCGGCAGCAGTGGCGCGA+CGG + chr5.4:15128652-15128671 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 15128629 15129710 15128629 ID=MS.gene67544
chr5.4 mRNA 15128629 15129710 15128629 ID=MS.gene67544.t1;Parent=MS.gene67544
chr5.4 exon 15129458 15129710 15129458 ID=MS.gene67544.t1.exon1;Parent=MS.gene67544.t1
chr5.4 CDS 15129458 15129710 15129458 ID=cds.MS.gene67544.t1;Parent=MS.gene67544.t1
chr5.4 exon 15128859 15129108 15128859 ID=MS.gene67544.t1.exon2;Parent=MS.gene67544.t1
chr5.4 CDS 15128859 15129108 15128859 ID=cds.MS.gene67544.t1;Parent=MS.gene67544.t1
chr5.4 exon 15128629 15128788 15128629 ID=MS.gene67544.t1.exon3;Parent=MS.gene67544.t1
chr5.4 CDS 15128629 15128788 15128629 ID=cds.MS.gene67544.t1;Parent=MS.gene67544.t1
Gene Sequence

>MS.gene67544

ATGGCTATGTACACTGCTCTCCGTCGCGCCACTGCTGCCGCAGTCCCTCTCCTCTCTCACCGTGCGTCAGCAACTTCCAACAGAACCTTCCACAGCGCAACCGCCGTTAACCTCCTTCGCCACAGAGAAACCACTCATTTTGTACCCTCTCGTAGCTTCGCGAAAACTCCCGCAGATGATACTCTCCTTCGAGTCCTTGACACTGAAATCAACTGTGCTCTTGAGGATAATCAAAACGTTGCAGCGAACATAAGTTTTTTCTTACCCTAAGTTATTGATCTTTTAGTGGTTAAAAATACATACCACTCCATTTTTGTTTATATTTCACTCCGTATTTTTAAATGACCTATTTTATAAGTCTGGATTTATTTTTCTCTGTCTTGGATTCTTGCGTTTGTATTTTGCAATTATTTACGTGTAGGATTTAATAAAATTTACATATGAATATTTTATGTCAACACATTTGCTTTTGATATTAACTGTCATTAAGTTCTCTGTCACTTTTGTGTAATTTTTCCAGCTTGAATTTCCTTGTGATTTTCCTTTTGAGATTGTGGACAACCCTGGAGAAAGATTTTTTCAACTAAAAAGACAATTTGAAGATGAAACTATCACAGTTCAAGTTAAAGTGTATCCTCAACTGAGTGAGGACGAGGATGACATCGAGAAGATTGAGAATAAGAATTATAGCAAATCTTTAATTCCTTTGGTTGTGTCTGTTTTCAAAGGAAATGGAGTGTGTCTGGAGTTTGGGGTGACTGTTTTCCTTGATAAGGTTAGGATTAATTGGTTGTCATTAAAGAAGCCTGATGAATCTGAAGACCAGCTGGTAGACGAGGAATGTCGATTCAGGTAAGCATTTTAATTTTATCAAATGATAATGTCTCTATTACAGTTTCTGAATGTTTGTTATTTTTTGCAGTGATTTGGATGATAACCTGCAAGAGGCTTTTCACAAGTATCTCGAGATCCGAGGGATAACACCCAACCTAACCAAATTTTTGCAGGAATACATGTTAAACAAAGACAACAAGGAACACTTGGTGTGGCTGAAGAACCTGAAGAGCTTCATTGAGATATGA
Protein sequence

>MS.gene67544.t1

MAMYTALRRATAAAVPLLSHRASATSNRTFHSATAVNLLRHRETTHFVPSRSFAKTPADDTLLRVLDTEINCALEDNQNVAANINETITVQVKVYPQLSEDEDDIEKIENKNYSKSLIPLVVSVFKGNGVCLEFGVTVFLDKVRINWLSLKKPDESEDQLVDEECRFSDLDDNLQEAFHKYLEIRGITPNLTKFLQEYMLNKDNKEHLVWLKNLKSFIEI